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keiono/Lesson_2_reproducible_workflow.ipynb

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Lesson_2_reproducible_workflow.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Introduction to _py2cytoscape_\n",
"#### Pythonista-friendly wrapper for cyREST\n",
"\n",
"![](http://cl.ly/XohP/logo300.png)\n",
"\n",
"<h1 align=\"center\">For</h1> \n",
"\n",
"![](https://www.python.org/static/community_logos/python-logo-master-v3-TM.png)\n",
"\n",
"by [Keiichiro Ono](http://keiono.github.io/) - University of California, San Diego [Trey Ideker Lab](http://healthsciences.ucsd.edu/som/medicine/research/labs/ideker/Pages/default.aspx)\n",
"\n",
"* TSRI Lecture: Applied Bioinformatics\n",
"* 5/12/2016 (Lecture 2)\n",
"\n",
"## What is _py2cytoscape_?\n",
"\n",
"py2cytoscape is a Python package to wrap Cytoscape REST API. You can easily access basic Cytoscape functions through simple Python API.\n",
"\n",
"\n",
"## System Requirments\n",
"* Java 8\n",
"* Cytoscape 3.3.0+\n",
"* py2cytoscape 0.5.0+"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Quick Overview of py2cytoscape\n",
"\n",
"**To run this script, you need to start Cytoscape before executing the following cells!** "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"application/javascript": [
"if (window['cytoscape'] === undefined) {\n",
" var paths = {\n",
" cytoscape: 'http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/cytoscape.min'\n",
" };\n",
"\n",
" require.config({\n",
" paths: paths\n",
" });\n",
"\n",
" require(['cytoscape'], function (cytoscape) {\n",
" console.log('Loading Cytoscape.js Module...');\n",
" window['cytoscape'] = cytoscape;\n",
"\n",
" var event = document.createEvent(\"HTMLEvents\");\n",
" event.initEvent(\"load_cytoscape\", true, false);\n",
" window.dispatchEvent(event);\n",
" });\n",
"}"
],
"text/plain": [
"<IPython.core.display.Javascript object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# Loading dependencies\n",
"from py2cytoscape.data.cynetwork import CyNetwork\n",
"from py2cytoscape.data.cyrest_client import CyRestClient\n",
"from py2cytoscape.data.style import StyleUtil\n",
"import py2cytoscape.util.cytoscapejs as cyjs\n",
"import py2cytoscape.cytoscapejs as renderer\n",
"\n",
"import networkx as nx\n",
"import pandas as pd\n",
"import json"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Creating Cytoscape network from file"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# Step 1: Create py2cytoscape client\n",
"cy = CyRestClient()\n",
"\n",
"# Reset (delete all existing networks)\n",
"cy.session.delete()\n",
"\n",
"# Step 2: Load network from somewhere\n",
"yeast_net = cy.network.create_from('https://raw.githubusercontent.com/idekerlab/tsri-lecture/master/lecture2/data/galFiltered.json')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# Step 3: Apply layout\n",
"cy.layout.apply(name='force-directed', network=yeast_net)\n",
"\n",
"# Step 4: Create Visual Style as code (or by hand if you prefer)\n",
"my_yeast_style = cy.style.create('GAL Style')\n",
"\n",
"\n",
"basic_settings = {\n",
" \n",
" # You can set default values as key-value pairs.\n",
" \n",
" 'NODE_FILL_COLOR': '#6AACB8',\n",
" 'NODE_SIZE': 55,\n",
" 'NODE_BORDER_WIDTH': 0,\n",
" 'NODE_LABEL_COLOR': '#555555',\n",
" \n",
" 'EDGE_WIDTH': 2,\n",
" 'EDGE_TRANSPARENCY': 100,\n",
" 'EDGE_STROKE_UNSELECTED_PAINT': '#333333'\n",
"}\n",
"\n",
"my_yeast_style.update_defaults(basic_settings)\n",
"\n",
"# Create some mappings\n",
"my_yeast_style.create_passthrough_mapping(column='COMMON', vp='NODE_LABEL', col_type='String')\n",
"\n",
"degrees = yeast_net.get_node_column('Degree') \n",
"color_gradient = StyleUtil.create_2_color_gradient(min=degrees.min(), max=degrees.max(), colors=('white', '#6AACB8'))\n",
"degree_to_size = StyleUtil.create_slope(min=degrees.min(), max=degrees.max(), values=(10, 100))\n",
"my_yeast_style.create_continuous_mapping(column='Degree', vp='NODE_FILL_COLOR', col_type='Integer', points=color_gradient)\n",
"my_yeast_style.create_continuous_mapping(column='Degree', vp='NODE_HEIGHT', col_type='Integer', points=degree_to_size)\n",
"my_yeast_style.create_continuous_mapping(column='Degree', vp='NODE_WIDTH', col_type='Integer', points=degree_to_size)\n",
"\n",
"my_yeast_style.create_continuous_mapping(column='Degree', vp='NODE_LABEL_FONT_SIZE', col_type='Integer', points=degree_to_size)\n",
"\n",
"cy.style.apply(my_yeast_style, yeast_net)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<!DOCTYPE html>\n",
"<html>\n",
"<head>\n",
" <meta charset=utf-8 />\n",
" <style type=\"text/css\">\n",
" body {\n",
" font: 14px helvetica neue, helvetica, arial, sans-serif;\n",
" }\n",
"\n",
" #cya6312872-861b-4b6a-82a2-b83352c19254 {\n",
" height: 700px;\n",
" width: 1098px;\n",
" position: absolute;\n",
" left: 4px;\n",
" top: 5px;\n",
" background: radial-gradient(#FFFFFF 15%, #DDDDDD 105%);\n",
" }\n",
" </style>\n",
"\n",
" <script>\n",
" (function() {\n",
" function render() {\n",
" $('#cya6312872-861b-4b6a-82a2-b83352c19254').cytoscape({\n",
" elements: {\n",
" nodes: [{\"position\": {\"y\": 2119.3565077825447, \"x\": 1375.117362815161}, \"selected\": false, \"data\": {\"id_original\": \"1869\", \"name\": \"YDL194W\", \"Eccentricity\": 26, \"IsSingleNode\": false, \"COMMON\": \"SNF3\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.018043, \"annotation_GO_CELLULAR_COMPONENT\": [\"plasma membrane\"], \"alias\": [\"S000002353\", \"SNF3\", \"glucose sensor\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"glucose binding\", \"glucose transporter activity\", \"receptor activity\"], \"gal4RGsig\": 0.033961, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YDL194W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.07623732, \"AverageShortestPathLength\": 13.11693548, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.449, \"gal1RGexp\": 0.139, \"gal80Rsig\": 0.011348, \"Stress\": 0.0, \"id\": \"1806\", \"gal4RGexp\": 0.333, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"response to glucose stimulus\", \"signal transduction\"], \"Radiality\": 0.55122461, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1806}}, {\"position\": {\"y\": 1990.1930556341072, \"x\": 1408.8522871315672}, \"selected\": false, \"data\": {\"id_original\": \"1870\", \"name\": \"YDR277C\", \"Eccentricity\": 25, \"IsSingleNode\": false, \"COMMON\": \"MTH1\", \"selected\": false, \"BetweennessCentrality\": 0.00806452, \"gal1RGsig\": 2.186e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cellular_component\"], \"alias\": [\"BPC1\", \"DGT1\", \"HTR1\", \"MTH1\", \"S000002685\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"molecular_function\"], \"gal4RGsig\": 0.028044, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YDR277C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.08250166, \"AverageShortestPathLength\": 12.12096774, \"NeighborhoodConnectivity\": 4.0, \"gal80Rexp\": 0.448, \"gal1RGexp\": 0.243, \"gal80Rsig\": 0.0005727, \"Stress\": 2722.0, \"id\": \"1805\", \"gal4RGexp\": 0.192, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"glucose transport\", \"signal transduction\"], \"Radiality\": 0.58811231, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1805}}, {\"position\": {\"y\": 4368.24196386775, \"x\": 1382.2365797341063}, \"selected\": false, \"data\": {\"id_original\": \"1871\", \"name\": \"YBR043C\", \"Eccentricity\": 2, \"IsSingleNode\": false, \"COMMON\": \"YBR043C\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 5.373e-08, \"annotation_GO_CELLULAR_COMPONENT\": [\"integral to plasma membrane\", \"plasma membrane\"], \"alias\": [\"AQR2\", \"QDR3\", \"S000000247\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"multidrug efflux pump activity\"], \"gal4RGsig\": 0.94178, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YBR043C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.66666667, \"AverageShortestPathLength\": 1.5, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.0, \"gal1RGexp\": 0.454, \"gal80Rsig\": 0.999999, \"Stress\": 0.0, \"id\": \"1804\", \"gal4RGexp\": 0.023, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"multidrug transport\"], \"Radiality\": 0.75, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1804}}, {\"position\": {\"y\": 1540.499210362043, \"x\": 3369.569755393286}, \"selected\": false, \"data\": {\"id_original\": \"1872\", \"name\": \"YPR145W\", \"Eccentricity\": 18, \"IsSingleNode\": false, \"COMMON\": \"ASN1\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 3.174e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\"], \"alias\": [\"ASN1\", \"S000006349\", \"asparagine synthetase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"asparagine synthase (glutamine-hydrolyzing) activity\"], \"gal4RGsig\": 1.1525e-07, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YPR145W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10205761, \"AverageShortestPathLength\": 9.7983871, \"NeighborhoodConnectivity\": 3.0, \"gal80Rexp\": -0.232, \"gal1RGexp\": -0.195, \"gal80Rsig\": 0.0011873, \"Stress\": 0.0, \"id\": \"1803\", \"gal4RGexp\": -0.614, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"asparagine biosynthetic process\"], \"Radiality\": 0.67413381, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1803}}, {\"position\": {\"y\": 2682.230348114576, \"x\": 2301.087852317114}, \"selected\": false, \"data\": {\"id_original\": \"1873\", \"name\": \"YER054C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"GIP2\", \"selected\": false, \"BetweennessCentrality\": 0.04427321, \"gal1RGsig\": 0.16958, \"annotation_GO_CELLULAR_COMPONENT\": [\"protein phosphatase type 1 complex\"], \"alias\": [\"GIP2\", \"S000000856\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"protein phosphatase regulator activity\"], \"gal4RGsig\": 0.00062032, \"TopologicalCoefficient\": 0.58333333, \"shared_name\": \"YER054C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11339735, \"AverageShortestPathLength\": 8.81854839, \"NeighborhoodConnectivity\": 4.5, \"gal80Rexp\": 0.247, \"gal1RGexp\": 0.057, \"gal80Rsig\": 0.0043603, \"Stress\": 11544.0, \"id\": \"1802\", \"gal4RGexp\": 0.206, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"glycogen metabolic process\", \"protein amino acid dephosphorylation\"], \"Radiality\": 0.71042413, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1802}}, {\"position\": {\"y\": 2738.890016083326, \"x\": 2445.081230002661}, \"selected\": false, \"data\": {\"id_original\": \"1874\", \"name\": \"YBR045C\", \"Eccentricity\": 20, \"IsSingleNode\": false, \"COMMON\": \"GIP1\", \"selected\": false, \"BetweennessCentrality\": 0.08528144, \"gal1RGsig\": 5.5911e-06, \"annotation_GO_CELLULAR_COMPONENT\": [\"prospore membrane\", \"protein phosphatase type 1 complex\"], \"alias\": [\"GIP1\", \"Glc7p regulatory subunit\", \"S000000249\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"protein phosphatase 1 binding\", \"protein phosphatase type 1 regulator activity\"], \"gal4RGsig\": 1.2945e-05, \"TopologicalCoefficient\": 0.44444444, \"shared_name\": \"YBR045C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10367893, \"AverageShortestPathLength\": 9.64516129, \"NeighborhoodConnectivity\": 2.33333333, \"gal80Rexp\": 0.94, \"gal1RGexp\": 0.786, \"gal80Rsig\": 0.016389, \"Stress\": 21474.0, \"id\": \"1801\", \"gal4RGexp\": 1.022, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"regulation of phosphoprotein phosphatase activity\", \"spore wall assembly (sensu the Fungi research community)\"], \"Radiality\": 0.67980884, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 3.0, \"Degree\": 3, \"SUID\": 1801}}, {\"position\": {\"y\": 3777.1561293645764, \"x\": 1059.283508139868}, \"selected\": false, \"data\": {\"id_original\": \"1875\", \"name\": \"YBL079W\", \"Eccentricity\": 3, \"IsSingleNode\": false, \"COMMON\": \"NUP170\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.00025668, \"annotation_GO_CELLULAR_COMPONENT\": [\"nuclear pore\"], \"alias\": [\"NLE3\", \"NUP170\", \"S000000175\", \"nuclear pore complex subunit\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"structural molecule activity\"], \"gal4RGsig\": 0.45723, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YBL079W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.5, \"AverageShortestPathLength\": 2.0, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": -0.42, \"gal1RGexp\": -0.186, \"gal80Rsig\": 2.9469e-09, \"Stress\": 0.0, \"id\": \"1800\", \"gal4RGexp\": -0.032, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"NLS-bearing substrate import into nucleus\", \"chromosome segregation\", \"mRNA export from nucleus\", \"mRNA-binding (hnRNP) protein import into nucleus\", \"nuclear pore organization and biogenesis\", \"protein export from nucleus\", \"protein import into nucleus\", \"docking\", \"rRNA export from nucleus\", \"ribosomal protein import into nucleus\", \"snRNA export from nucleus\", \"snRNP protein import into nucleus\", \"tRNA export from nucleus\"], \"Radiality\": 0.66666667, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1800}}, {\"position\": {\"y\": 2567.582154755201, \"x\": 1710.5166242897703}, \"selected\": false, \"data\": {\"id_original\": \"1876\", \"name\": \"YLR345W\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"YLR345W\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.012373, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\"], \"alias\": [\"S000004337\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"6-phosphofructo-2-kinase activity\"], \"gal4RGsig\": 7.892e-05, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YLR345W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10968598, \"AverageShortestPathLength\": 9.11693548, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.116, \"gal1RGexp\": 0.108, \"gal80Rsig\": 0.073789, \"Stress\": 0.0, \"id\": \"1799\", \"gal4RGexp\": 0.234, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"fructose 2\", \"6-bisphosphate metabolic process\", \"regulation of glycolysis\"], \"Radiality\": 0.69937276, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1799}}, {\"position\": {\"y\": 528.2944960637947, \"x\": 1935.7426679909422}, \"selected\": false, \"data\": {\"id_original\": \"1877\", \"name\": \"YIL052C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"RPL34B\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 3.7855e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosolic large ribosomal subunit (sensu the Eukaryota research community)\"], \"alias\": [\"RPL34B\", \"S000001314\", \"ribosomal protein L34B\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"structural constituent of ribosome\"], \"gal4RGsig\": 3.4652e-07, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YIL052C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10929925, \"AverageShortestPathLength\": 9.14919355, \"NeighborhoodConnectivity\": 8.0, \"gal80Rexp\": -0.025, \"gal1RGexp\": -0.258, \"gal80Rsig\": 0.66627, \"Stress\": 0.0, \"id\": \"1798\", \"gal4RGexp\": -0.451, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"telomere maintenance\"], \"Radiality\": 0.69817802, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1798}}, {\"position\": {\"y\": 572.2568984075447, \"x\": 1888.4369123757078}, \"selected\": false, \"data\": {\"id_original\": \"1878\", \"name\": \"YER056CA\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"shared_name\": \"YER056CA\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10929925, \"AverageShortestPathLength\": 9.14919355, \"NeighborhoodConnectivity\": 8.0, \"Stress\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"Radiality\": 0.69817802, \"ClusteringCoefficient\": 0.0, \"id\": \"1797\", \"TopologicalCoefficient\": 0.0, \"Degree\": 1, \"SUID\": 1797}}, {\"position\": {\"y\": 533.0689711614509, \"x\": 2005.1980055153563}, \"selected\": false, \"data\": {\"id_original\": \"1879\", \"name\": \"YNL069C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"RPL16B\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 2.6481e-07, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosolic large ribosomal subunit (sensu the Eukaryota research community)\"], \"alias\": [\"RP23\", \"RPL16B\", \"S000005013\", \"ribosomal protein L16B (L21B) (rp23) (YL15)\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"RNA binding\", \"structural constituent of ribosome\"], \"gal4RGsig\": 5.1994e-05, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YNL069C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10929925, \"AverageShortestPathLength\": 9.14919355, \"NeighborhoodConnectivity\": 8.0, \"gal80Rexp\": -0.124, \"gal1RGexp\": -0.346, \"gal80Rsig\": 0.026888, \"Stress\": 0.0, \"id\": \"1796\", \"gal4RGexp\": -0.284, \"Radiality\": 0.69817802, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1796}}, {\"position\": {\"y\": 569.6334242864509, \"x\": 2074.058513480444}, \"selected\": false, \"data\": {\"id_original\": \"1880\", \"name\": \"YDL075W\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"RPL31A\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.0041386, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosolic large ribosomal subunit (sensu the Eukaryota research community)\"], \"alias\": [\"RPL31A\", \"RPL34\", \"S000002233\", \"ribosomal protein L31A (L34A) (YL28)\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"structural constituent of ribosome\"], \"gal4RGsig\": 1.5697e-06, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YDL075W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10929925, \"AverageShortestPathLength\": 9.14919355, \"NeighborhoodConnectivity\": 8.0, \"gal80Rexp\": 0.056, \"gal1RGexp\": -0.218, \"gal80Rsig\": 0.38208, \"Stress\": 0.0, \"id\": \"1795\", \"gal4RGexp\": -0.451, \"Radiality\": 0.69817802, \"ClusteringCoefficient\": 0.0, 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false, \"data\": {\"id_original\": \"1933\", \"name\": \"YPR102C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"RPL11A\", \"selected\": false, \"BetweennessCentrality\": 0.00401593, \"gal1RGsig\": 0.00037183, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosolic large ribosomal subunit (sensu the Eukaryota research community)\"], \"alias\": [\"RPL11A\", \"S000006306\", \"ribosomal protein L11A (L16A) (rp39A) (YL22)\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"structural constituent of ribosome\"], \"gal4RGsig\": 1.7424e-06, \"TopologicalCoefficient\": 0.57142857, \"shared_name\": \"YPR102C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10939568, \"AverageShortestPathLength\": 9.14112903, \"NeighborhoodConnectivity\": 5.0, \"gal80Rexp\": -0.058, \"gal1RGexp\": -0.177, \"gal80Rsig\": 0.26052, \"Stress\": 2038.0, \"id\": \"1742\", \"gal4RGexp\": -0.38, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"ribosomal large subunit assembly and 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\"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": -0.002, \"gal1RGexp\": -0.169, \"gal80Rsig\": 0.9794, \"Stress\": 2.0, \"id\": \"1741\", \"gal4RGexp\": -0.2, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"ribosomal large subunit assembly and maintenance\"], \"Radiality\": 0.66188769, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1741}}, {\"position\": {\"y\": 1879.2874465032478, \"x\": 2774.140067893286}, \"selected\": false, \"data\": {\"id_original\": \"1935\", \"name\": \"YKL161C\", \"Eccentricity\": 16, \"IsSingleNode\": false, \"COMMON\": \"YKL161C\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.00075801, \"annotation_GO_CELLULAR_COMPONENT\": [\"cellular_component\"], \"alias\": [\"MLP1\", \"S000001644\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"protein kinase activity\"], \"gal4RGsig\": 0.022048, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YKL161C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11106135, \"AverageShortestPathLength\": 9.00403226, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.202, \"gal1RGexp\": -0.198, \"gal80Rsig\": 0.18731, \"Stress\": 0.0, \"id\": \"1740\", \"gal4RGexp\": -0.319, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"biological_process\"], \"Radiality\": 0.70355436, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1740}}, {\"position\": {\"y\": 1036.7802748723884, \"x\": 1487.8471601784422}, \"selected\": false, \"data\": {\"id_original\": \"1936\", \"name\": \"YAR007C\", \"Eccentricity\": 18, \"IsSingleNode\": false, \"COMMON\": \"RFA1\", \"selected\": false, \"BetweennessCentrality\": 0.00401593, \"gal1RGsig\": 0.0081844, \"annotation_GO_CELLULAR_COMPONENT\": [\"DNA replication factor A complex\", \"chromosome\", \"telomeric region\", \"cytoplasm\", \"nucleus\"], \"alias\": [\"heterotrimeric RPA (RF-A) single-stranded DNA binding protein 69 kDa subunit\", \"BUF2\", \"FUN3\", \"RF-A\", \"RFA1\", \"RPA1\", \"S000000065\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"damaged DNA binding\", \"single-stranded DNA binding\"], \"gal4RGsig\": 0.91522, \"TopologicalCoefficient\": 0.75, \"shared_name\": \"YAR007C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10222589, \"AverageShortestPathLength\": 9.78225806, \"NeighborhoodConnectivity\": 2.5, \"gal80Rexp\": -0.302, \"gal1RGexp\": 0.2, \"gal80Rsig\": 0.0060792, \"Stress\": 1030.0, \"id\": \"1739\", \"gal4RGexp\": -0.007, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"DNA recombination\", \"DNA replication\", \"synthesis of RNA primer\", \"DNA strand elongation during DNA replication\", \"DNA unwinding during replication\", \"double-strand break repair via homologous recombination\", \"nucleotide-excision repair\", \"postreplication repair\"], \"Radiality\": 0.67473118, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1739}}, {\"position\": {\"y\": 3584.6231474920173, \"x\": 943.4944380104735}, \"selected\": false, \"data\": {\"id_original\": \"1937\", \"name\": \"YIL160C\", \"Eccentricity\": 3, \"IsSingleNode\": false, \"COMMON\": \"POT1\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 1.071e-06, \"annotation_GO_CELLULAR_COMPONENT\": [\"peroxisomal matrix\"], \"alias\": [\"3-oxoacyl CoA thiolase\", \"FOX3\", \"POT1\", \"POX3\", \"S000001422\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"acetyl-CoA C-acyltransferase activity\"], \"gal4RGsig\": 3.103e-08, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YIL160C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.42857143, \"AverageShortestPathLength\": 2.33333333, \"NeighborhoodConnectivity\": 3.0, \"gal80Rexp\": 0.92, \"gal1RGexp\": 1.044, \"gal80Rsig\": 6.0801e-07, \"Stress\": 0.0, \"id\": \"1738\", \"gal4RGexp\": 0.674, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"fatty acid beta-oxidation\"], \"Radiality\": 0.55555556, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1738}}, {\"position\": {\"y\": 3396.6752944036384, \"x\": 1172.8320844948485}, \"selected\": false, \"data\": {\"id_original\": \"1938\", \"name\": \"YDL078C\", \"Eccentricity\": 3, \"IsSingleNode\": false, \"COMMON\": \"MDH3\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 4.0255e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"peroxisomal matrix\", \"peroxisome\"], \"alias\": [\"MDH3\", \"S000002236\", \"malate dehydrogenase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"L-malate dehydrogenase activity\"], \"gal4RGsig\": 0.038943, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YDL078C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.5, \"AverageShortestPathLength\": 2.0, \"NeighborhoodConnectivity\": 5.0, \"gal80Rexp\": -0.08, \"gal1RGexp\": 0.217, \"gal80Rsig\": 0.16505, \"Stress\": 0.0, \"id\": \"1737\", \"gal4RGexp\": 0.102, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"NADH regeneration\", \"fatty acid beta-oxidation\", \"glyoxylate cycle\", \"malate metabolic process\"], \"Radiality\": 0.66666667, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1737}}, {\"position\": {\"y\": 3557.027284149732, \"x\": 1053.246024924536}, \"selected\": false, \"data\": {\"id_original\": \"1939\", \"name\": \"YDR142C\", \"Eccentricity\": 2, \"IsSingleNode\": false, \"COMMON\": \"PEX7\", \"selected\": false, \"BetweennessCentrality\": 0.33333333, \"gal1RGsig\": 0.016464, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosol\", \"peroxisomal matrix\"], \"alias\": [\"PAS7\", \"PEB1\", \"PEX7\", \"S000002549\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"peroxisome 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\"BetweennessCentrality\": 0.5, \"gal1RGsig\": 2.7503e-06, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosol\", \"peroxisome\"], \"alias\": [\"PAS10\", \"PEX5\", \"S000002652\", \"peroxin\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"peroxisome targeting sequence binding\", \"peroxisome targeting signal-1 binding\"], \"gal4RGsig\": 0.73489, \"TopologicalCoefficient\": 0.44, \"shared_name\": \"YDR244W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.85714286, \"AverageShortestPathLength\": 1.16666667, \"NeighborhoodConnectivity\": 2.4, \"gal80Rexp\": 0.483, \"gal1RGexp\": 0.369, \"gal80Rsig\": 0.00043149, \"Stress\": 20.0, \"id\": \"1735\", \"gal4RGexp\": -0.021, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"peroxisome organization and biogenesis\", \"protein targeting to peroxisome\"], \"Radiality\": 0.94444444, \"ClusteringCoefficient\": 0.3, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 5.0, \"Degree\": 5, \"SUID\": 1735}}, {\"position\": {\"y\": 304.0595717473884, \"x\": 2033.2780988991453}, \"selected\": false, \"data\": {\"id_original\": \"1941\", \"name\": \"YLR432W\", \"Eccentricity\": 22, \"IsSingleNode\": false, \"COMMON\": \"YLR432W\", \"selected\": false, \"BetweennessCentrality\": 0.01606373, \"gal1RGsig\": 6.6826e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\"], \"alias\": [\"IMD3\", \"S000004424\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"IMP dehydrogenase activity\"], \"gal4RGsig\": 0.36112, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YLR432W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.09668616, \"AverageShortestPathLength\": 10.34274194, \"NeighborhoodConnectivity\": 2.5, \"gal80Rexp\": -0.301, \"gal1RGexp\": -0.197, \"gal80Rsig\": 4.8207e-05, \"Stress\": 5116.0, \"id\": \"1734\", \"gal4RGexp\": -0.054, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"GTP biosynthetic process\"], \"Radiality\": 0.65397252, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1734}}, {\"position\": {\"y\": 187.48681784113842, \"x\": 1962.123481589575}, \"selected\": false, \"data\": {\"id_original\": \"1942\", \"name\": \"YDR167W\", \"Eccentricity\": 23, \"IsSingleNode\": false, \"COMMON\": \"TAF25\", \"selected\": false, \"BetweennessCentrality\": 0.00806452, \"gal1RGsig\": 0.00021837, \"annotation_GO_CELLULAR_COMPONENT\": [\"SAGA complex\", \"SLIK (SAGA-like) complex\", \"transcription factor TFIID complex\"], \"alias\": [\"TafII25\", \"S000002574\", \"TAF10\", \"TAF23\", \"TAF25\", \"TFIID subunit\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"general RNA polymerase II transcription factor activity\"], \"gal4RGsig\": 0.0039024, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YDR167W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.08825623, \"AverageShortestPathLength\": 11.33064516, \"NeighborhoodConnectivity\": 1.5, \"gal80Rexp\": 0.355, \"gal1RGexp\": 0.246, \"gal80Rsig\": 0.01484, \"Stress\": 2560.0, \"id\": \"1733\", \"gal4RGexp\": -0.219, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"G1-specific transcription in mitotic cell cycle\", \"chromatin modification\", \"establishment and/or maintenance of chromatin architecture\", \"histone acetylation\", \"protein amino acid acetylation\", \"transcription initiation from RNA polymerase II promoter\"], \"Radiality\": 0.61738351, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1733}}, {\"position\": {\"y\": 749.2350478216072, \"x\": 2669.630058127661}, \"selected\": false, \"data\": {\"id_original\": \"1943\", \"name\": \"YLR175W\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"CBF5\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.47804, \"annotation_GO_CELLULAR_COMPONENT\": [\"box H/ACA snoRNP complex\", \"nucleolus\"], \"alias\": [\"CBF5\", \"S000004165\", \"pseudouridine synthase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"pseudouridylate synthase activity\"], \"gal4RGsig\": 5.549e-05, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YLR175W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11221719, \"AverageShortestPathLength\": 8.91129032, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.498, \"gal1RGexp\": 0.038, \"gal80Rsig\": 1.4113e-07, \"Stress\": 0.0, \"id\": \"1732\", \"gal4RGexp\": -0.597, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"35S primary transcript processing\", \"rRNA pseudouridine synthesis\"], \"Radiality\": 0.70698925, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1732}}, {\"position\": {\"y\": 1500.0232787176033, \"x\": 2116.9473703682615}, \"selected\": false, \"data\": {\"id_original\": \"1944\", \"name\": \"YNL117W\", \"Eccentricity\": 16, \"IsSingleNode\": false, \"COMMON\": \"MLS1\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 1.92e-11, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"peroxisomal matrix\"], \"alias\": [\"MLS1\", \"S000005061\", \"carbon-catabolite sensitive malate synthase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"malate synthase activity\"], \"gal4RGsig\": 9.0335e-05, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YNL117W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.1302521, \"AverageShortestPathLength\": 7.67741935, \"NeighborhoodConnectivity\": 4.0, \"gal80Rexp\": 0.941, \"gal1RGexp\": 0.973, \"gal80Rsig\": 1.2597e-05, \"Stress\": 0.0, \"id\": \"1731\", \"gal4RGexp\": 0.452, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"glyoxylate cycle\"], \"Radiality\": 0.75268817, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1731}}, {\"position\": {\"y\": 2193.0361952825447, \"x\": 3121.664054709692}, \"selected\": false, \"data\": {\"id_original\": \"1945\", \"name\": \"YOR089C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"VPS21\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.00011748, \"annotation_GO_CELLULAR_COMPONENT\": [\"late endosome\", \"mitochondrial outer membrane\", \"mitochondrion\"], \"alias\": [\"S000005615\", \"VPS12\", \"VPS21\", \"VPT12\", \"YPT21\", \"YPT51\", \"small GTP-binding protein\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"GTPase activity\"], \"gal4RGsig\": 0.32501, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YOR089C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.0977918, \"AverageShortestPathLength\": 10.22580645, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.378, \"gal1RGexp\": 0.193, \"gal80Rsig\": 8.2229e-06, \"Stress\": 0.0, \"id\": \"1730\", \"gal4RGexp\": -0.042, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"endocytosis\", \"protein 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\"Degree\": 1, \"SUID\": 1720}}, {\"position\": {\"y\": 1853.1281752630134, \"x\": 1274.4085005104735}, \"selected\": false, \"data\": {\"id_original\": \"1956\", \"name\": \"YER102W\", \"Eccentricity\": 18, \"IsSingleNode\": false, \"COMMON\": \"RPS8B\", \"selected\": false, \"BetweennessCentrality\": 0.04463374, \"gal1RGsig\": 3.2712e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosolic small ribosomal subunit (sensu the Eukaryota research community)\"], \"alias\": [\"RPS8B\", \"S000000904\", \"ribosomal protein S8B (S14B) (rp19) (YS9)\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"structural constituent of ribosome\"], \"gal4RGsig\": 3.6609e-06, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YER102W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11687088, \"AverageShortestPathLength\": 8.55645161, \"NeighborhoodConnectivity\": 3.5, \"gal80Rexp\": -0.135, \"gal1RGexp\": -0.249, \"gal80Rsig\": 0.017595, \"Stress\": 5590.0, \"id\": 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\"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1714}}, {\"position\": {\"y\": 1119.4570632024665, \"x\": 2227.694595176001}, \"selected\": false, \"data\": {\"id_original\": \"1962\", \"name\": \"YDR354W\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"TRP4\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.0090277, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"nucleus\"], \"alias\": [\"S000002762\", \"TRP4\", \"anthranilate phosphoribosyl transferase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"anthranilate phosphoribosyltransferase activity\"], \"gal4RGsig\": 0.0028196, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YDR354W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11605054, \"AverageShortestPathLength\": 8.61693548, \"NeighborhoodConnectivity\": 7.0, \"gal80Rexp\": -0.253, \"gal1RGexp\": -0.122, \"gal80Rsig\": 0.0012089, \"Stress\": 0.0, \"id\": \"1713\", \"gal4RGexp\": 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\"COMMON\": \"SWI4\", \"selected\": false, \"BetweennessCentrality\": 0.0323843, \"gal1RGsig\": 0.00056134, \"annotation_GO_CELLULAR_COMPONENT\": [\"nucleus\"], \"alias\": [\"ART1\", \"S000000913\", \"SWI4\", \"transcription factor\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"DNA binding\", \"transcription factor activity\"], \"gal4RGsig\": 0.33211, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YER111C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.15158924, \"AverageShortestPathLength\": 6.59677419, \"NeighborhoodConnectivity\": 11.0, \"gal80Rexp\": 0.16, \"gal1RGexp\": 0.195, \"gal80Rsig\": 0.15558, \"Stress\": 3188.0, \"id\": \"1709\", \"gal4RGexp\": -0.105, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"G1/S transition of mitotic cell cycle\", \"transcription\"], \"Radiality\": 0.79271207, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1709}}, {\"position\": {\"y\": 3908.0143752141857, \"x\": 2025.1792372048094}, \"selected\": false, \"data\": {\"id_original\": \"1967\", \"name\": \"YOR039W\", \"Eccentricity\": 2, \"IsSingleNode\": false, \"COMMON\": \"CKB2\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.87354, \"annotation_GO_CELLULAR_COMPONENT\": [\"protein kinase CK2 complex\"], \"alias\": [\"beta' subunit\", \"CKB2\", \"S000005565\", \"protein kinase CK2\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"protein kinase CK2 regulator activity\"], \"gal4RGsig\": 0.20402, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YOR039W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.66666667, \"AverageShortestPathLength\": 1.5, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": -0.006, \"gal1RGexp\": -0.006, \"gal80Rsig\": 0.92034, \"Stress\": 0.0, \"id\": \"1708\", \"gal4RGexp\": -0.058, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"G1/S transition of mitotic cell cycle\", \"G2/M transition of 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15, \"IsSingleNode\": false, \"COMMON\": \"YIL113W\", \"selected\": false, \"BetweennessCentrality\": 0.00806452, \"gal1RGsig\": 0.002113, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"nucleus\"], \"alias\": [\"S000001375\", \"SDP1\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"MAP kinase phosphatase activity\"], \"gal4RGsig\": 0.002831, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YIL113W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.12487412, \"AverageShortestPathLength\": 8.00806452, \"NeighborhoodConnectivity\": 2.5, \"gal80Rexp\": -0.137, \"gal1RGexp\": -0.236, \"gal80Rsig\": 0.23739, \"Stress\": 746.0, \"id\": \"1706\", \"gal4RGexp\": 0.211, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"MAPKKK cascade during cell wall biogenesis\"], \"Radiality\": 0.74044205, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1706}}, {\"position\": {\"y\": 2004.7683424993415, \"x\": 2717.0452802956297}, \"selected\": false, \"data\": {\"id_original\": \"1970\", \"name\": \"YLL019C\", \"Eccentricity\": 16, \"IsSingleNode\": false, \"COMMON\": \"KNS1\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 1.3809e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cellular_component\"], \"alias\": [\"KNS1\", \"L124\", \"S000003942\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"protein serine/threonine kinase activity\", \"protein-tyrosine kinase activity\"], \"gal4RGsig\": 6.085e-05, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YLL019C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11106135, \"AverageShortestPathLength\": 9.00403226, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.295, \"gal1RGexp\": 0.258, \"gal80Rsig\": 9.3514e-05, \"Stress\": 0.0, \"id\": \"1705\", \"gal4RGexp\": 0.215, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"protein amino acid phosphorylation\"], 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0.0, \"ClosenessCentrality\": 0.13121693, \"AverageShortestPathLength\": 7.62096774, \"NeighborhoodConnectivity\": 5.33333333, \"gal80Rexp\": -1.167, \"gal1RGexp\": -0.07, \"gal80Rsig\": 8.1952e-17, \"Stress\": 26.0, \"id\": \"1703\", \"gal4RGexp\": -0.606, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"galactose metabolic process\", \"positive regulation of transcription by galactose\"], \"Radiality\": 0.75477897, \"ClusteringCoefficient\": 0.33333333, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 4.0, \"Degree\": 4, \"SUID\": 1703}}, {\"position\": {\"y\": 2539.9719862981697, \"x\": 3169.713554221411}, \"selected\": false, \"data\": {\"id_original\": \"1973\", \"name\": \"YHR071W\", \"Eccentricity\": 25, \"IsSingleNode\": false, \"COMMON\": \"PCL5\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 5.0065e-11, \"annotation_GO_CELLULAR_COMPONENT\": [\"cyclin-dependent protein kinase holoenzyme complex\"], \"alias\": [\"PCL5\", \"S000001113\"], 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0.012838, \"annotation_GO_CELLULAR_COMPONENT\": [\"nucleus\"], \"alias\": [\"LDB15\", \"PHO85\", \"S000005952\", \"cyclin-dependent protein kinase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"cyclin-dependent protein kinase activity\"], \"gal4RGsig\": 0.0056375, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YPL031C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.07434053, \"AverageShortestPathLength\": 13.4516129, \"NeighborhoodConnectivity\": 1.5, \"gal80Rexp\": -0.139, \"gal1RGexp\": -0.106, \"gal80Rsig\": 0.019984, \"Stress\": 1970.0, \"id\": \"1701\", \"gal4RGexp\": 0.125, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"cell cycle\", \"glycogen metabolic process\", \"phosphate metabolic process\", \"protein amino acid phosphorylation\", \"telomere maintenance\"], \"Radiality\": 0.53882915, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1701}}, {\"position\": {\"y\": 600.5227065130134, \"x\": 2628.748924094458}, \"selected\": false, \"data\": {\"id_original\": \"1975\", \"name\": \"YML123C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"PHO84\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.0015163, \"annotation_GO_CELLULAR_COMPONENT\": [\"integral to plasma membrane\"], \"alias\": [\"PHO84\", \"S000004592\", \"inorganic phosphate transporter\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"inorganic phosphate transporter activity\", \"manganese ion transporter activity\"], \"gal4RGsig\": 0.019412, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YML123C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.108061, \"AverageShortestPathLength\": 9.25403226, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": 0.692, \"gal1RGexp\": 0.283, \"gal80Rsig\": 6.9606e-07, \"Stress\": 0.0, \"id\": \"1700\", \"gal4RGexp\": -0.114, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"manganese ion 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5.9656e-07, \"Stress\": 0.0, \"id\": \"1699\", \"gal4RGexp\": -0.78, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"high affinity iron ion transport\"], \"Radiality\": 1.0, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1699}}, {\"position\": {\"y\": 4315.51573706111, \"x\": 2100.3412931740477}, \"selected\": false, \"data\": {\"id_original\": \"1977\", \"name\": \"YMR058W\", \"Eccentricity\": 1, \"IsSingleNode\": false, \"COMMON\": \"FET3\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 3.6962e-08, \"annotation_GO_CELLULAR_COMPONENT\": [\"plasma membrane\"], \"alias\": [\"FET3\", \"S000004662\", \"multicopper oxidase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"ferroxidase activity\", \"iron ion transporter activity\"], \"gal4RGsig\": 0.00047738, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YMR058W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 1.0, \"AverageShortestPathLength\": 1.0, \"NeighborhoodConnectivity\": 1.0, \"gal80Rexp\": 0.64, \"gal1RGexp\": 0.449, \"gal80Rsig\": 1.6005e-08, \"Stress\": 0.0, \"id\": \"1698\", \"gal4RGexp\": -0.293, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"high affinity iron ion transport\", \"response to copper ion\"], \"Radiality\": 1.0, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1698}}, {\"position\": {\"y\": 4207.79356909236, \"x\": 2000.3412931740477}, \"selected\": false, \"data\": {\"id_original\": \"1978\", \"name\": \"YJL190C\", \"Eccentricity\": 1, \"IsSingleNode\": false, \"COMMON\": \"RPS22A\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 1.0479e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytosolic small ribosomal subunit (sensu the Eukaryota research community)\"], \"alias\": [\"RPS22A\", \"RPS24\", \"S000003726\", \"ribosomal protein S22A (S24A) (rp50) (YS22)\"], 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\"annotation_GO_CELLULAR_COMPONENT\": [\"nucleolus\"], \"alias\": [\"FPR3\", \"NPI46\", \"S000004539\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"peptidyl-prolyl cis-trans isomerase activity\"], \"gal4RGsig\": 5.2953e-05, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YML074C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 1.0, \"AverageShortestPathLength\": 1.0, \"NeighborhoodConnectivity\": 1.0, \"gal80Rexp\": 0.389, \"gal1RGexp\": 0.118, \"gal80Rsig\": 3.3233e-05, \"Stress\": 0.0, \"id\": \"1696\", \"gal4RGexp\": -0.38, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"meiotic recombination checkpoint\"], \"Radiality\": 1.0, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1696}}, {\"position\": {\"y\": 731.2512221380134, \"x\": 2379.830253440161}, \"selected\": false, \"data\": {\"id_original\": \"1980\", \"name\": \"YOR355W\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"GDS1\", \"selected\": false, \"BetweennessCentrality\": 0.03283069, \"gal1RGsig\": 0.00016613, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"mitochondrion\", \"nucleus\"], \"alias\": [\"GDS1\", \"S000005882\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"molecular_function\"], \"gal4RGsig\": 0.45777, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YOR355W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.12393803, \"AverageShortestPathLength\": 8.06854839, \"NeighborhoodConnectivity\": 3.0, \"gal80Rexp\": 0.43, \"gal1RGexp\": -0.176, \"gal80Rsig\": 0.0062666, \"Stress\": 4248.0, \"id\": \"1695\", \"gal4RGexp\": -0.044, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"aerobic respiration\"], \"Radiality\": 0.73820191, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1695}}, {\"position\": {\"y\": 2037.171052460279, \"x\": 3003.6543501198485}, \"selected\": false, \"data\": {\"id_original\": \"1981\", \"name\": \"YFL038C\", \"Eccentricity\": 18, \"IsSingleNode\": false, \"COMMON\": \"YPT1\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.056883, \"annotation_GO_CELLULAR_COMPONENT\": [\"Golgi membrane\", \"endoplasmic reticulum membrane\", \"mitochondrion\"], \"alias\": [\"GTP-binding protein\", \"S000001856\", \"YP2\", \"YPT1\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"GTPase activity\"], \"gal4RGsig\": 0.44841, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YFL038C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10824967, \"AverageShortestPathLength\": 9.23790323, \"NeighborhoodConnectivity\": 6.0, \"gal80Rexp\": 0.12, \"gal1RGexp\": 0.075, \"gal80Rsig\": 0.073548, \"Stress\": 0.0, \"id\": \"1694\", \"gal4RGexp\": -0.033, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"ER to Golgi vesicle-mediated transport\", \"protein complex assembly\"], \"Radiality\": 0.69489247, 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1316.7989058538337, \"x\": 2878.4678877175047}, \"selected\": false, \"data\": {\"id_original\": \"2088\", \"name\": \"YLR256W\", \"Eccentricity\": 17, \"IsSingleNode\": false, \"COMMON\": \"HAP1\", \"selected\": false, \"BetweennessCentrality\": 0.03202952, \"gal1RGsig\": 0.79725, \"annotation_GO_CELLULAR_COMPONENT\": [\"nucleus\"], \"alias\": [\"CYP1\", \"HAP1\", \"S000004246\", \"zinc finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"specific RNA polymerase II transcription factor activity\"], \"gal4RGsig\": 0.063023, \"TopologicalCoefficient\": 0.25, \"shared_name\": \"YLR256W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11720227, \"AverageShortestPathLength\": 8.53225806, \"NeighborhoodConnectivity\": 2.25, \"gal80Rexp\": 0.104, \"gal1RGexp\": 0.011, \"gal80Rsig\": 0.2243, \"Stress\": 7130.0, \"id\": \"1587\", \"gal4RGexp\": -0.087, 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2043.9910292669197, \"x\": 2344.253852683325}, \"selected\": false, \"data\": {\"id_original\": \"2099\", \"name\": \"YNL236W\", \"Eccentricity\": 17, \"IsSingleNode\": false, \"COMMON\": \"SIN4\", \"selected\": false, \"BetweennessCentrality\": 0.00806452, \"gal1RGsig\": 0.018347, \"annotation_GO_CELLULAR_COMPONENT\": [\"mediator complex\"], \"alias\": [\"BEL2\", \"GAL22\", \"MED16\", \"RNA polymerase II holoenzyme/mediator subunit\", \"RYE1\", \"S000005180\", \"SDI3\", \"SIN4\", \"SSF5\", \"SSN4\", \"TSF3\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"RNA polymerase II transcription mediator activity\"], \"gal4RGsig\": 0.053936, \"TopologicalCoefficient\": 0.5, \"shared_name\": \"YNL236W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.11412793, \"AverageShortestPathLength\": 8.76209677, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": -0.141, \"gal1RGexp\": -0.146, \"gal80Rsig\": 0.39009, \"Stress\": 1044.0, \"id\": \"1576\", \"gal4RGexp\": 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\"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1515}}, {\"position\": {\"y\": 746.0173354192634, \"x\": 2305.530204612036}, \"selected\": false, \"data\": {\"id_original\": \"2161\", \"name\": \"YCR012W\", \"Eccentricity\": 17, \"IsSingleNode\": false, \"COMMON\": \"PGK1\", \"selected\": false, \"BetweennessCentrality\": 0.04462853, \"gal1RGsig\": 7.3129e-10, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"mitochondrion\"], \"alias\": [\"3-phosphoglycerate kinase\", \"PGK1\", \"S000000605\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"phosphoglycerate kinase activity\"], \"gal4RGsig\": 2.4163e-05, \"TopologicalCoefficient\": 0.42592593, \"shared_name\": \"YCR012W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.1443539, \"AverageShortestPathLength\": 6.92741935, \"NeighborhoodConnectivity\": 8.66666667, \"gal80Rexp\": -0.746, \"gal1RGexp\": -0.668, \"gal80Rsig\": 4.2315e-13, \"Stress\": 16638.0, \"id\": \"1514\", \"gal4RGexp\": 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\"gal80Rsig\": 0.22451, \"Stress\": 0.0, \"id\": \"1496\", \"gal4RGexp\": -0.085, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"biological_process\"], \"Radiality\": 0.68264636, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1496}}, {\"position\": {\"y\": 3598.6790480657482, \"x\": 2806.1638754189207}, \"selected\": false, \"data\": {\"id_original\": \"2180\", \"name\": \"YJL013C\", \"Eccentricity\": 2, \"IsSingleNode\": false, \"COMMON\": \"MAD3\", \"selected\": false, \"BetweennessCentrality\": 0.16666667, \"gal1RGsig\": 0.14469, \"annotation_GO_CELLULAR_COMPONENT\": [\"nucleus\"], \"alias\": [\"MAD3\", \"S000003550\", \"spindle checkpoint complex subunit\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"molecular_function\"], \"gal4RGsig\": 0.046575, \"TopologicalCoefficient\": 0.75, \"shared_name\": \"YJL013C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.66666667, 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\"Degree\": 2, \"SUID\": 1488}}, {\"position\": {\"y\": 1920.2575087591072, \"x\": 1075.518730002661}, \"selected\": false, \"data\": {\"id_original\": \"2188\", \"name\": \"YFL017C\", \"Eccentricity\": 19, \"IsSingleNode\": false, \"COMMON\": \"GNA1\", \"selected\": false, \"BetweennessCentrality\": 0.0426128, \"gal1RGsig\": 0.0017854, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"nucleus\"], \"alias\": [\"GNA1\", \"PAT1\", \"S000001877\", \"glucosamine-phosphate N-acetyltransferase\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"glucosamine 6-phosphate N-acetyltransferase activity\"], \"gal4RGsig\": 0.0055302, \"TopologicalCoefficient\": 0.2, \"shared_name\": \"YFL017C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.10575693, \"AverageShortestPathLength\": 9.45564516, \"NeighborhoodConnectivity\": 1.6, \"gal80Rexp\": 0.124, \"gal1RGexp\": 0.131, \"gal80Rsig\": 0.050323, \"Stress\": 6282.0, \"id\": \"1487\", \"gal4RGexp\": 0.122, 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1.7601e-05, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"nucleus\"], \"alias\": [\"CNR1\", \"CST17\", \"GSP1\", \"GTP-binding protein\", \"S000004284\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"GTPase activity\"], \"gal4RGsig\": 0.00067968, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YLR293C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.6, \"AverageShortestPathLength\": 1.66666667, \"NeighborhoodConnectivity\": 3.0, \"gal80Rexp\": -0.128, \"gal1RGexp\": -0.242, \"gal80Rsig\": 0.012703, \"Stress\": 0.0, \"id\": \"1484\", \"gal4RGexp\": -0.247, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"nuclear organization and biogenesis\", \"nucleocytoplasmic transport\", \"rRNA processing\"], \"Radiality\": 0.66666667, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1484}}, {\"position\": {\"y\": 3783.684403900709, \"x\": 1548.9363172829344}, \"selected\": false, 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\"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1483}}, {\"position\": {\"y\": 3777.1561293645764, \"x\": 1454.728950339575}, \"selected\": false, \"data\": {\"id_original\": \"2193\", \"name\": \"YPR080W\", \"Eccentricity\": 2, \"IsSingleNode\": false, \"COMMON\": \"TEF1\", \"selected\": false, \"BetweennessCentrality\": 0.16666667, \"gal1RGsig\": 0.00098725, \"annotation_GO_CELLULAR_COMPONENT\": [\"eukaryotic translation elongation factor 1 complex\", \"ribosome\"], \"alias\": [\"translational elongation factor EF-1 alpha\", \"EF-1 alpha\", \"S000006284\", \"TEF1\", \"eEF1A\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"translation elongation factor activity\"], \"gal4RGsig\": 0.89728, \"TopologicalCoefficient\": 1.0, \"shared_name\": \"YPR080W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.75, \"AverageShortestPathLength\": 1.33333333, \"NeighborhoodConnectivity\": 2.0, \"gal80Rexp\": -0.278, \"gal1RGexp\": -0.138, \"gal80Rsig\": 0.00067798, \"Stress\": 2.0, \"id\": \"1482\", \"gal4RGexp\": 0.009, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"translational elongation\"], \"Radiality\": 0.83333333, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 2.0, \"Degree\": 2, \"SUID\": 1482}}, {\"position\": {\"y\": 3871.6342711492443, \"x\": 1457.6393965065672}, \"selected\": false, \"data\": {\"id_original\": \"2194\", \"name\": \"YLR249W\", \"Eccentricity\": 2, \"IsSingleNode\": false, \"COMMON\": \"YEF3\", \"selected\": false, \"BetweennessCentrality\": 0.16666667, \"gal1RGsig\": 2.713e-08, \"annotation_GO_CELLULAR_COMPONENT\": [\"ribosome\"], \"alias\": [\"Translation elongation factor 3 (EF-3)\", \"EF-3\", \"S000004239\", \"TEF3\", \"YEF3\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"translation elongation factor activity\"], \"gal4RGsig\": 0.04747, \"TopologicalCoefficient\": 1.0, \"shared_name\": \"YLR249W\", 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\"gal4RGsig\": 0.31268, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YOR204W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.6, \"AverageShortestPathLength\": 1.66666667, \"NeighborhoodConnectivity\": 3.0, \"gal80Rexp\": -0.91, \"gal1RGexp\": -0.033, \"gal80Rsig\": 8.349e-16, \"Stress\": 0.0, \"id\": \"1480\", \"gal4RGexp\": -0.056, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"RNA splicing\", \"translational initiation\"], \"Radiality\": 0.66666667, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1480}}, {\"position\": {\"y\": 3863.618310455885, \"x\": 1244.8050611794188}, \"selected\": false, \"data\": {\"id_original\": \"2196\", \"name\": \"YGL097W\", \"Eccentricity\": 1, \"IsSingleNode\": false, \"COMMON\": \"SRM1\", \"selected\": false, \"BetweennessCentrality\": 1.0, \"gal1RGsig\": 0.0021913, \"annotation_GO_CELLULAR_COMPONENT\": [\"nuclear chromatin\", 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\"IsSingleNode\": false, \"COMMON\": \"CRM1\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.61381, \"annotation_GO_CELLULAR_COMPONENT\": [\"nucleus\"], \"alias\": [\"CRM1\", \"KAP124\", \"S000003450\", \"XPO1\", \"chromosome region maintenance protein\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"protein carrier activity\"], \"gal4RGsig\": 0.9794, \"TopologicalCoefficient\": 0.0, \"shared_name\": \"YGR218W\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.6, \"AverageShortestPathLength\": 1.66666667, \"NeighborhoodConnectivity\": 3.0, \"gal80Rexp\": -0.018, \"gal1RGexp\": -0.018, \"gal80Rsig\": 0.80969, \"Stress\": 0.0, \"id\": \"1478\", \"gal4RGexp\": -0.001, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"mRNA export from nucleus\", \"protein export from nucleus\", \"ribosomal large subunit export from nucleus\"], \"Radiality\": 0.66666667, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 1.0, \"Degree\": 1, \"SUID\": 1478}}, {\"position\": {\"y\": 2678.9541029973884, \"x\": 3333.076591330786}, \"selected\": false, \"data\": {\"id_original\": \"2198\", \"name\": \"YGL122C\", \"Eccentricity\": 25, \"IsSingleNode\": false, \"COMMON\": \"NAB2\", \"selected\": false, \"BetweennessCentrality\": 0.02406295, \"gal1RGsig\": 0.00087295, \"annotation_GO_CELLULAR_COMPONENT\": [\"cytoplasm\", \"nucleus\"], \"alias\": [\"NAB2\", \"S000003090\", \"polyadenylated RNA binding protein\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"poly(A) binding\"], \"gal4RGsig\": 0.61707, \"TopologicalCoefficient\": 0.33333333, \"shared_name\": \"YGL122C\", \"PartnerOfMultiEdgedNodePairs\": 0.0, \"SelfLoops\": 0.0, \"ClosenessCentrality\": 0.06956522, \"AverageShortestPathLength\": 14.375, \"NeighborhoodConnectivity\": 1.66666667, \"gal80Rexp\": 0.187, \"gal1RGexp\": 0.174, \"gal80Rsig\": 0.0059966, \"Stress\": 5902.0, \"id\": \"1477\", \"gal4RGexp\": 0.02, \"annotation_GO_BIOLOGICAL_PROCESS\": [\"mRNA polyadenylation\", \"poly(A)+ mRNA export from nucleus\"], \"Radiality\": 0.50462963, \"ClusteringCoefficient\": 0.0, \"NumberOfUndirectedEdges\": 0.0, \"NumberOfDirectedEdges\": 3.0, \"Degree\": 3, \"SUID\": 1477}}, {\"position\": {\"y\": 2725.676393036451, \"x\": 3441.2708051979735}, \"selected\": false, \"data\": {\"id_original\": \"2199\", \"name\": \"YKR026C\", \"Eccentricity\": 26, \"IsSingleNode\": false, \"COMMON\": \"GCN3\", \"selected\": false, \"BetweennessCentrality\": 0.0, \"gal1RGsig\": 0.00091177, \"annotation_GO_CELLULAR_COMPONENT\": [\"eukaryotic translation initiation factor 2B complex\", \"guanyl-nucleotide exchange factor complex\"], \"alias\": [\"AAS2\", \"GCN3\", \"S000001734\", \"eIF2B 34 kDa alpha subunit\"], \"annotation_GO_MOLECULAR_FUNCTION\": [\"enzyme regulator activity\", \"guanyl-nucleotide exchange factor activity\", \"translation initiation factor activity\"], \"gal4RGsig\": 3.5692e-06, 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" },\n",
"\n",
" layout: {\n",
" name: 'preset'\n",
" },\n",
"\n",
" boxSelectionEnabled: true,\n",
"\n",
" ready: function() {\n",
" window.cy = this;\n",
" cy.fit();\n",
" cy.style().fromJson([{\"selector\": \"node\", \"css\": {\"text-opacity\": 1.0, \"height\": 55.0, \"text-valign\": \"center\", \"font-weight\": \"normal\", \"background-color\": \"rgb(106,172,184)\", \"border-color\": \"rgb(0,0,0)\", \"color\": \"rgb(85,85,85)\", \"width\": 55.0, \"border-opacity\": 1.0, \"content\": \"data(COMMON)\", \"font-family\": \"SansSerif\", \"shape\": \"ellipse\", \"background-opacity\": 1.0, \"text-halign\": \"center\", \"border-width\": 0.0, \"font-size\": 12}}, {\"selector\": \"node[Degree > 18]\", \"css\": {\"width\": 100.0}}, {\"selector\": \"node[Degree = 18]\", \"css\": {\"width\": 100.0}}, {\"selector\": \"node[Degree > 1][Degree < 18]\", \"css\": {\"width\": \"mapData(Degree,1,18,10.0,100.0)\"}}, {\"selector\": \"node[Degree = 1]\", \"css\": {\"width\": 10.0}}, {\"selector\": \"node[Degree < 1]\", \"css\": {\"width\": 10.0}}, {\"selector\": \"node[Degree > 18]\", \"css\": {\"font-size\": 100}}, {\"selector\": \"node[Degree = 18]\", \"css\": {\"font-size\": 100}}, {\"selector\": \"node[Degree > 1][Degree < 18]\", \"css\": {\"font-size\": \"mapData(Degree,1,18,10,100)\"}}, {\"selector\": \"node[Degree = 1]\", \"css\": {\"font-size\": 10}}, {\"selector\": \"node[Degree < 1]\", \"css\": {\"font-size\": 10}}, {\"selector\": \"node[Degree > 18]\", \"css\": {\"height\": 100.0}}, {\"selector\": \"node[Degree = 18]\", \"css\": {\"height\": 100.0}}, {\"selector\": \"node[Degree > 1][Degree < 18]\", \"css\": {\"height\": \"mapData(Degree,1,18,10.0,100.0)\"}}, {\"selector\": \"node[Degree = 1]\", \"css\": {\"height\": 10.0}}, {\"selector\": \"node[Degree < 1]\", \"css\": {\"height\": 10.0}}, {\"selector\": \"node[Degree > 18]\", \"css\": {\"background-color\": \"rgb(106,172,184)\"}}, {\"selector\": \"node[Degree = 18]\", \"css\": {\"background-color\": \"rgb(106,172,184)\"}}, {\"selector\": \"node[Degree > 1][Degree < 18]\", \"css\": {\"background-color\": \"mapData(Degree,1,18,rgb(255,255,255),rgb(106,172,184))\"}}, {\"selector\": \"node[Degree = 1]\", \"css\": {\"background-color\": \"rgb(255,255,255)\"}}, {\"selector\": \"node[Degree < 1]\", \"css\": {\"background-color\": \"rgb(255,255,255)\"}}, {\"selector\": \"node:selected\", \"css\": {\"background-color\": \"rgb(255,255,0)\"}}, {\"selector\": \"edge\", \"css\": {\"source-arrow-color\": \"rgb(0,0,0)\", \"content\": \"\", \"source-arrow-shape\": \"none\", \"line-style\": \"solid\", \"font-weight\": \"normal\", \"text-opacity\": 1.0, \"color\": \"rgb(0,0,0)\", \"width\": 2.0, \"target-arrow-shape\": \"none\", \"line-color\": \"rgb(51,51,51)\", \"target-arrow-color\": \"rgb(0,0,0)\", \"font-family\": \"SansSerif\", \"opacity\": 0.39215686274509803, \"font-size\": 10}}, {\"selector\": \"edge:selected\", \"css\": {\"line-color\": \"rgb(255,0,0)\"}}]).update();\n",
" }\n",
" });\n",
" }\n",
"\n",
" var before_render = function(){\n",
" if(window['cytoscape'] === undefined){\n",
" console.log(\"Waiting for Cyjs...\");\n",
" window.addEventListener(\"load_cytoscape\", before_render);\n",
" } else {\n",
" console.log(\"Ready to render graph!\");\n",
" render();\n",
" }\n",
" }\n",
"\n",
" before_render();\n",
"\n",
" })();\n",
" </script>\n",
"</head>\n",
"\n",
"<body>\n",
" <div id=\"cya6312872-861b-4b6a-82a2-b83352c19254\"></div>\n",
" <!-- When only #uuid div is placed on this page,\n",
" the height of output-box on ipynb will be 0px.\n",
" One line below will prevent that. -->\n",
" <div id=\"dummy\" style=\"width:1098px;height:700px\">\n",
"</body>\n",
"\n",
"</html>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# Step 5: (Optional) Embed as interactive Cytoscape.js widget\n",
"yeast_net_view = yeast_net.get_first_view()\n",
"style_for_widget = cy.style.get(my_yeast_style.get_name(), data_format='cytoscapejs')\n",
"renderer.render(yeast_net_view, style=style_for_widget['style'], background='radial-gradient(#FFFFFF 15%, #DDDDDD 105%)')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Long Description\n",
"From version 0.4.0, ___py2cytoscape___ has wrapper modules for [cyREST](http://apps.cytoscape.org/apps/cyrest) RESTful API. This means you can access Cytoscape features in more _Pythonic_ way instead of calling raw REST API via HTTP. \n",
"\n",
"\n",
"## Features\n",
"\n",
"### Pandas for basic data exchange\n",
"Since [pandas](http://pandas.pydata.org/) is a standard library for data mangling/analysis in Python, this new version uses its [DataFrame](http://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html#pandas.DataFrame) as its basic data object.\n",
"\n",
"### Embedded Cytoscaep.js Widget\n",
"You can use Cytoscape.js widget to embed your final result as a part of your notebook.\n",
"\n",
"### Simpler Code to access Cytoscape\n",
"cyREST provides language-agnostic RESTful API, but you need to use a lot of template code to access raw API. Here is an example. Both of the following do the same task, which is creating an empty network in Cytoscape. You will notice it is significantly simpler if you use _py2cytoscape_ wrapper API.\n",
"\n",
"#### Raw cyREST Workflow Example"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"New network created with raw REST API. Its SUID is 2864\n"
]
}
],
"source": [
"# HTTP Client for Python\n",
"import requests\n",
"\n",
"# Standard JSON library\n",
"import json\n",
"\n",
"# Basic Setup\n",
"PORT_NUMBER = 1234\n",
"BASE = 'http://localhost:' + str(PORT_NUMBER) + '/v1/'\n",
"\n",
"# Header for posting data to the server as JSON\n",
"HEADERS = {'Content-Type': 'application/json'}\n",
"\n",
"# Define dictionary of empty network\n",
"empty_network = {\n",
" 'data': {\n",
" 'name': 'This is an empty network...'\n",
" },\n",
" 'elements': {\n",
" 'nodes':[],\n",
" 'edges':[]\n",
" }\n",
"}\n",
"\n",
"res = requests.post(BASE + 'networks?collection=My%20Collection', data=json.dumps(empty_network), headers=HEADERS)\n",
"new_network_id = res.json()['networkSUID']\n",
"print('New network created with raw REST API. Its SUID is ' + str(new_network_id))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### With py2cytoscape"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"New network created with py2cytoscape. Its SUID is 2876\n"
]
}
],
"source": [
"network = cy.network.create(name='Another empty network created by py2cy', collection='My network collection')\n",
"print('New network created with py2cytoscape. Its SUID is ' + str(network.get_id()))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Status\n",
"\n",
"As of 6/4/2015, this is still in alpha status and feature requests are always welcome. If youi have questions or feature requests, please send them to our Google Groups:\n",
"\n",
"* https://groups.google.com/forum/#!forum/cytoscape-discuss"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Quick Tour of py2cytoscape Features\n",
"\n",
"----\n",
"\n",
"## Create a client object to connect to Cytoscape"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# Create an instance of cyREST client. Default IP is 'localhost', and port number is 1234.\n",
"# cy = CyRestClient() - This default constructor creates connection to http://localhost:1234/v1\n",
"cy = CyRestClient(ip='127.0.0.1', port=1234)\n",
"\n",
"# Cleanup: Delete all existing networks and tables in current Cytoscape session\n",
"cy.session.delete()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Creating empty networks"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# Empty network\n",
"empty1 = cy.network.create()\n",
"\n",
"# With name\n",
"empty2 = cy.network.create(name='Created in Jupyter Notebook')\n",
"\n",
"# With name and collection name\n",
"empty3 = cy.network.create(name='Also created in Jupyter', collection='New network collection')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Load networks from files, URLs or web services"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>CyNetwork</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>file:////Users/kono/git/tsri-lecture/lecture2/data/sample_yeast_network.xgmml</th>\n",
" <td>&lt;py2cytoscape.data.cynetwork.CyNetwork object ...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif</th>\n",
" <td>&lt;py2cytoscape.data.cynetwork.CyNetwork object ...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" CyNetwork\n",
"file:////Users/kono/git/tsri-lecture/lecture2/d... <py2cytoscape.data.cynetwork.CyNetwork object ...\n",
"http://chianti.ucsd.edu/cytoscape-data/galFilte... <py2cytoscape.data.cynetwork.CyNetwork object ..."
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Load a single local file\n",
"net_from_local2 = cy.network.create_from('data/galFiltered.json')\n",
"net_from_local1 = cy.network.create_from('data/sample_yeast_network.xgmml', collection='My Collection')\n",
"net_from_local2 = cy.network.create_from('data/galFiltered.gml', collection='Human')\n",
"\n",
"# Load from multiple locations\n",
"network_locations = [\n",
" 'data/sample_yeast_network.xgmml', # Local file\n",
" 'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif', # Static file on a web server\n",
"]\n",
"\n",
"# This requrns Series\n",
"networks = cy.network.create_from(network_locations)\n",
"pd.DataFrame(networks, columns=['CyNetwork'])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Create networks from various types of data\n",
"Currently, py2cytoscape accepts the following data as input:\n",
"\n",
"* Cytoscape.js\n",
"* NetworkX\n",
"* Pandas DataFrame\n",
"\n",
"\n",
"* igraph (TBD)\n",
"* Numpy adjacency matrix (binary or weighted) (TBD)\n",
"* GraphX (TBD)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# Cytoscape.js JSON\n",
"n1 = cy.network.create(data=cyjs.get_empty_network(), name='Created from Cytoscape.js JSON')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <th>source</th>\n",
" <th>interaction</th>\n",
" <th>target</th>\n",
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" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>YKR026C</td>\n",
" <td>pp</td>\n",
" <td>YGL122C</td>\n",
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" <th>1</th>\n",
" <td>YGR218W</td>\n",
" <td>pp</td>\n",
" <td>YGL097W</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>YGL097W</td>\n",
" <td>pp</td>\n",
" <td>YOR204W</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>YLR249W</td>\n",
" <td>pp</td>\n",
" <td>YPR080W</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>YLR249W</td>\n",
" <td>pp</td>\n",
" <td>YBR118W</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" source interaction target\n",
"0 YKR026C pp YGL122C\n",
"1 YGR218W pp YGL097W\n",
"2 YGL097W pp YOR204W\n",
"3 YLR249W pp YPR080W\n",
"4 YLR249W pp YBR118W"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Pandas DataFrame\n",
"\n",
"# Example 1: From a simple text table\n",
"df_from_sif = pd.read_csv('data/galFiltered.sif', names=['source', 'interaction', 'target'], sep=' ')\n",
"df_from_sif.head()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>#ID(s) interactor A</th>\n",
" <th>ID(s) interactor B</th>\n",
" <th>Alt. ID(s) interactor A</th>\n",
" <th>Alt. ID(s) interactor B</th>\n",
" <th>Alias(es) interactor A</th>\n",
" <th>Alias(es) interactor B</th>\n",
" <th>Interaction detection method(s)</th>\n",
" <th>Publication 1st author(s)</th>\n",
" <th>Publication Identifier(s)</th>\n",
" <th>Taxid interactor A</th>\n",
" <th>...</th>\n",
" <th>Checksum(s) interactor A</th>\n",
" <th>Checksum(s) interactor B</th>\n",
" <th>Interaction Checksum(s)</th>\n",
" <th>Negative</th>\n",
" <th>Feature(s) interactor A</th>\n",
" <th>Feature(s) interactor B</th>\n",
" <th>Stoichiometry(s) interactor A</th>\n",
" <th>Stoichiometry(s) interactor B</th>\n",
" <th>Identification method participant A</th>\n",
" <th>Identification method participant B</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>uniprotkb:Q8IZC7</td>\n",
" <td>uniprotkb:P11802</td>\n",
" <td>intact:EBI-5278328|uniprotkb:C9JU83|uniprotkb:...</td>\n",
" <td>intact:EBI-295644|uniprotkb:B2R9A0|uniprotkb:B...</td>\n",
" <td>psi-mi:zn101_human(display_long)|uniprotkb:ZNF...</td>\n",
" <td>psi-mi:cdk4_human(display_long)|uniprotkb:CDK4...</td>\n",
" <td>psi-mi:\"MI:0424\"(protein kinase assay)</td>\n",
" <td>Anders et al. (2011)</td>\n",
" <td>pubmed:22094256|imex:IM-16628</td>\n",
" <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
" <td>...</td>\n",
" <td>rogid:mZLXs/PbWbfgLzkjwZfoE2c6jy09606</td>\n",
" <td>rogid:pxIzF9EkX+gMz7zj/TDiytYtsOc9606</td>\n",
" <td>intact-crc:0486DE729E5A8158|rigid:3gdrHm0coV8S...</td>\n",
" <td>False</td>\n",
" <td>glutathione s tranferase tag:?-?</td>\n",
" <td>sufficient binding region:4-303|glutathione s ...</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>psi-mi:\"MI:0821\"(molecular weight estimation b...</td>\n",
" <td>psi-mi:\"MI:0821\"(molecular weight estimation b...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>uniprotkb:P01106</td>\n",
" <td>uniprotkb:Q00534</td>\n",
" <td>intact:EBI-447544|intact:EBI-1058440|uniprotkb...</td>\n",
" <td>intact:EBI-295663|uniprotkb:A4D1G0</td>\n",
" <td>psi-mi:myc_human(display_long)|uniprotkb:BHLHE...</td>\n",
" <td>psi-mi:cdk6_human(display_long)|uniprotkb:CDK6...</td>\n",
" <td>psi-mi:\"MI:0424\"(protein kinase assay)</td>\n",
" <td>Anders et al. (2011)</td>\n",
" <td>pubmed:22094256|imex:IM-16628</td>\n",
" <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
" <td>...</td>\n",
" <td>rogid:CCk+p9FN7JV6cTmJDlin2hRp1tg9606</td>\n",
" <td>rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606</td>\n",
" <td>intact-crc:20A3DCC8419B269E|rigid:bfSR2lJKa/lY...</td>\n",
" <td>False</td>\n",
" <td>glutathione s tranferase tag:?-?</td>\n",
" <td>his tag:n-n</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>psi-mi:\"MI:0821\"(molecular weight estimation b...</td>\n",
" <td>psi-mi:\"MI:0821\"(molecular weight estimation b...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>uniprotkb:Q00534</td>\n",
" <td>uniprotkb:P28698</td>\n",
" <td>intact:EBI-295663|uniprotkb:A4D1G0</td>\n",
" <td>intact:EBI-5278283|uniprotkb:M0QXU0|uniprotkb:...</td>\n",
" <td>psi-mi:cdk6_human(display_long)|uniprotkb:CDK6...</td>\n",
" <td>psi-mi:mzf1_human(display_long)|uniprotkb:MZF1...</td>\n",
" <td>psi-mi:\"MI:0424\"(protein kinase assay)</td>\n",
" <td>Anders et al. (2011)</td>\n",
" <td>pubmed:22094256|imex:IM-16628</td>\n",
" <td>taxid:9606(human)|taxid:9606(Homo sapiens)</td>\n",
" <td>...</td>\n",
" <td>rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606</td>\n",
" <td>rogid:1rq+ga/Uew705r63KlORpqBObbw9606</td>\n",
" <td>intact-crc:578214FA683591D0|rigid:8AADqx3NNAXF...</td>\n",
" <td>False</td>\n",
" <td>his tag:n-n</td>\n",
" <td>glutathione s tranferase tag:?-?</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>psi-mi:\"MI:0821\"(molecular weight estimation b...</td>\n",
" <td>psi-mi:\"MI:0821\"(molecular weight estimation b...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>3 rows × 42 columns</p>\n",
"</div>"
],
"text/plain": [
" #ID(s) interactor A ID(s) interactor B \\\n",
"0 uniprotkb:Q8IZC7 uniprotkb:P11802 \n",
"1 uniprotkb:P01106 uniprotkb:Q00534 \n",
"2 uniprotkb:Q00534 uniprotkb:P28698 \n",
"\n",
" Alt. ID(s) interactor A \\\n",
"0 intact:EBI-5278328|uniprotkb:C9JU83|uniprotkb:... \n",
"1 intact:EBI-447544|intact:EBI-1058440|uniprotkb... \n",
"2 intact:EBI-295663|uniprotkb:A4D1G0 \n",
"\n",
" Alt. ID(s) interactor B \\\n",
"0 intact:EBI-295644|uniprotkb:B2R9A0|uniprotkb:B... \n",
"1 intact:EBI-295663|uniprotkb:A4D1G0 \n",
"2 intact:EBI-5278283|uniprotkb:M0QXU0|uniprotkb:... \n",
"\n",
" Alias(es) interactor A \\\n",
"0 psi-mi:zn101_human(display_long)|uniprotkb:ZNF... \n",
"1 psi-mi:myc_human(display_long)|uniprotkb:BHLHE... \n",
"2 psi-mi:cdk6_human(display_long)|uniprotkb:CDK6... \n",
"\n",
" Alias(es) interactor B \\\n",
"0 psi-mi:cdk4_human(display_long)|uniprotkb:CDK4... \n",
"1 psi-mi:cdk6_human(display_long)|uniprotkb:CDK6... \n",
"2 psi-mi:mzf1_human(display_long)|uniprotkb:MZF1... \n",
"\n",
" Interaction detection method(s) Publication 1st author(s) \\\n",
"0 psi-mi:\"MI:0424\"(protein kinase assay) Anders et al. (2011) \n",
"1 psi-mi:\"MI:0424\"(protein kinase assay) Anders et al. (2011) \n",
"2 psi-mi:\"MI:0424\"(protein kinase assay) Anders et al. (2011) \n",
"\n",
" Publication Identifier(s) Taxid interactor A \\\n",
"0 pubmed:22094256|imex:IM-16628 taxid:9606(human)|taxid:9606(Homo sapiens) \n",
"1 pubmed:22094256|imex:IM-16628 taxid:9606(human)|taxid:9606(Homo sapiens) \n",
"2 pubmed:22094256|imex:IM-16628 taxid:9606(human)|taxid:9606(Homo sapiens) \n",
"\n",
" ... \\\n",
"0 ... \n",
"1 ... \n",
"2 ... \n",
"\n",
" Checksum(s) interactor A \\\n",
"0 rogid:mZLXs/PbWbfgLzkjwZfoE2c6jy09606 \n",
"1 rogid:CCk+p9FN7JV6cTmJDlin2hRp1tg9606 \n",
"2 rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606 \n",
"\n",
" Checksum(s) interactor B \\\n",
"0 rogid:pxIzF9EkX+gMz7zj/TDiytYtsOc9606 \n",
"1 rogid:IlAJCZ9bvB5RaBdS1rlPnqDL9xg9606 \n",
"2 rogid:1rq+ga/Uew705r63KlORpqBObbw9606 \n",
"\n",
" Interaction Checksum(s) Negative \\\n",
"0 intact-crc:0486DE729E5A8158|rigid:3gdrHm0coV8S... False \n",
"1 intact-crc:20A3DCC8419B269E|rigid:bfSR2lJKa/lY... False \n",
"2 intact-crc:578214FA683591D0|rigid:8AADqx3NNAXF... False \n",
"\n",
" Feature(s) interactor A \\\n",
"0 glutathione s tranferase tag:?-? \n",
"1 glutathione s tranferase tag:?-? \n",
"2 his tag:n-n \n",
"\n",
" Feature(s) interactor B \\\n",
"0 sufficient binding region:4-303|glutathione s ... \n",
"1 his tag:n-n \n",
"2 glutathione s tranferase tag:?-? \n",
"\n",
" Stoichiometry(s) interactor A Stoichiometry(s) interactor B \\\n",
"0 - - \n",
"1 - - \n",
"2 - - \n",
"\n",
" Identification method participant A \\\n",
"0 psi-mi:\"MI:0821\"(molecular weight estimation b... \n",
"1 psi-mi:\"MI:0821\"(molecular weight estimation b... \n",
"2 psi-mi:\"MI:0821\"(molecular weight estimation b... \n",
"\n",
" Identification method participant B \n",
"0 psi-mi:\"MI:0821\"(molecular weight estimation b... \n",
"1 psi-mi:\"MI:0821\"(molecular weight estimation b... \n",
"2 psi-mi:\"MI:0821\"(molecular weight estimation b... \n",
"\n",
"[3 rows x 42 columns]"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# By default, it uses 'source' for source node column, 'target' for target node column, and 'interaction' for interaction\n",
"yeast1 = cy.network.create_from_dataframe(df_from_sif, name='Yeast network created from pandas DataFrame')\n",
"\n",
"# Example 2: from more complicated table\n",
"df_from_mitab = pd.read_csv('data/intact_pubid_22094256.txt', sep='\\t')\n",
"df_from_mitab.head(3)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"source = df_from_mitab.columns[0]\n",
"target = df_from_mitab.columns[1]\n",
"interaction = 'Interaction identifier(s)'\n",
"title='A Systematic Screen for CDK4/6 Substrates Links FOXM1 Phosphorylation to Senescence Suppression in Cancer Cells.'\n",
"\n",
"human1 = cy.network.create_from_dataframe(df_from_mitab, source_col=source, target_col=target, interaction_col=interaction, name=title)\n",
"\n",
"\n",
"# Import edge attributes and node attributes at the same time (TBD)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# NetworkX\n",
"nx_graph = nx.scale_free_graph(100)\n",
"nx.set_node_attributes(nx_graph, 'Degree', nx.degree(nx_graph))\n",
"nx.set_node_attributes(nx_graph, 'Betweenness_Centrality', nx.betweenness_centrality(nx_graph))\n",
"scale_free100 = cy.network.create_from_networkx(nx_graph, collection='Generated by NetworkX')\n",
"\n",
"# TODO: igraph\n",
"# TODO: Numpy adj. martix\n",
"# TODO: GraphX"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Network from Cytoscape\n",
"\n",
"You can get network data in the following forms:\n",
"\n",
"* Cytoscape.js\n",
"* NetworkX\n",
"* DataFrame"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" \"elements\": {\n",
" \"edges\": [\n",
" {\n",
" \"data\": {\n",
" \"target_original\": \"YDL194W\",\n",
" \"Interaction_Type\": [],\n",
" \"Host_Organism_Taxonomy\": [],\n",
" \"interaction\": \"pp\",\n",
" \"Source_Biological_Role\": [],\n",
" \"Source_Biological_Role_ID\": [],\n",
" \"shared_interaction\": \"pp\",\n",
" \"Complex_Expansion\": [],\n",
" \"Detection_Method\": [],\n",
" \"Complex_Expansion_ID\": [],\n",
" \"Source_Participant_Detection_Method\": [],\n",
" \"Publication_DB\": [],\n",
" \"Source_Experimental_Role_ID\": [],\n",
" \"Host_Organism_Taxonomy_ID\": [],\n",
" \"Target_Participant_Detection_Method\": [],\n",
" \"Target_Experimental_Role_ID\": [],\n",
" \"selected\": false,\n",
" \"Author\": [],\n",
" \"Xref\": [],\n",
" \"Publication_ID\": [],\n",
" \"Xref_ID\": [],\n",
" \"id\": \"9345\",\n",
" \"Target_Biological_Role\": [],\n",
" \"Target_Experimental_Role\": [],\n",
" \"target\": \"8984\",\n",
" \"Source_Participant_Detection_Method_ID\": [],\n",
" \"source_original\": \"YDR277C\",\n",
" \"Source_Experimental_Role\": [],\n",
" \"Target_Biological_Role_ID\": [],\n",
" \"source\": \"8983\",\n",
" \"Target_Participant_Detection_Method_ID\": [],\n",
" \"Detection_Method_ID\": [],\n",
" \"SUID\": 9345,\n",
" \"Annotation\": []\n",
" }\n",
" },\n",
" {\n",
" \"data\": {\n",
" \"target_original\": \"YJR022W\",\n",
" \"Interaction_Type\": [],\n",
" \"Host_Organism_Taxonomy\": [],\n",
" \"interaction\": \"pp\",\n",
" \"Source_Biological_Role\": [],\n",
" \"Source_Biological_Role_ID\": [],\n",
" \"shared_interaction\": \"pp\",\n",
" \"Complex_Expansion\": [],\n",
" \"Detection_Method\": [],\n",
" \"Complex_Expansion_ID\": [],\n",
" \"Source_Participant_Detection_Method\": [],\n",
" \"Publication_DB\": [],\n",
" \"Source_Experimental_Role_ID\": [],\n",
" \"Host_Organism_Taxonomy_ID\": [],\n",
" \"Target_Participant_Detection_Method\": [],\n",
" \"Target_Experimental_Role_ID\": [],\n",
" \"selected\": false,\n",
" \"Author\": [],\n",
" \"Xref\": [],\n",
" \"Publication_ID\": [],\n",
" \"Xref_ID\": [],\n",
" \"id\": \"9344\",\n",
" \"Target_Biological_Role\": [],\n",
" \"Target_Experimental_Role\": [],\n",
" \"target\": \"8681\",\n",
" \"Source_Participant_Detection_Method_ID\": [],\n",
" \"source_original\": \"YDR277C\",\n",
" \"Source_Experimental_Role\": [],\n",
" \"Target_Biological_Role_ID\": [],\n",
" \"source\": \"8983\",\n",
" \"Target_Participant_Detection_Method_ID\": [],\n",
" \"Detection_Method_ID\": [],\n",
" \"SUID\": 9344,\n",
" \"Annotation\": []\n",
" }\n",
" },\n",
" {\n",
" \"data\": {\n",
" \"target_original\": \"YMR117C\",\n",
" \"Interaction_Type\": [],\n",
" \"Host_Organism_Taxonomy\": [],\n",
" \"interaction\": \"pp\",\n",
" \"Source_Biological_Role\": [],\n",
" \"Source_Biological_Role_ID\": [],\n",
" \"shared_interaction\": \"pp\",\n",
" \"Complex_Expansion\": [],\n",
" \"Detection_Method\": [],\n",
" \"Complex_Expansion_ID\": [],\n",
" \"Source_Participant_Detection_Method\": [],\n",
" \"Publication_DB\": [],\n",
" \"Source_Experimental_Role_ID\": [],\n",
" \"Host_Organism_Taxonomy_ID\": [],\n",
" \"Target_Participant_Detection_Method\": [],\n",
" \"Target_Experimental_Role_ID\": [],\n",
" \"selected\": false,\n",
" \"Author\": [],\n",
" \"Xref\": [],\n",
" \"Publication_ID\": [],\n",
" \"Xref_ID\": [],\n",
" \"id\": \"9340\",\n",
" \"Target_Biological_Role\": [],\n",
" \"Target_Experimental_Role\": [],\n",
" \"target\": \"8962\",\n",
" \"Source_Participant_Detection_Method_ID\": [],\n",
" \"source_original\": \"YPR145W\",\n",
" \"Source_Experimental_Role\": [],\n",
" \"Target_Biological_Role_ID\": [],\n",
" \"source\": \"8981\",\n",
" \"Target_Participant_Detection_Method_ID\": [],\n",
" \"Detection_Method_ID\": [],\n",
" \"SUID\": 9340,\n",
" \"Annotation\": []\n",
" }\n",
" },\n",
" {\n",
" \"data\": {\n",
" \"target_original\": \"YBR045C\",\n",
" \"Interaction_Type\": [],\n",
" \"Host_Organism_Taxonomy\": [],\n",
" \"interaction\": \"pp\",\n",
" \"Source_Biological_Role\": [],\n",
" \"Source_Biological_Role_ID\": [],\n",
" \"shared_interaction\": \"pp\",\n",
" \"Complex_Expansion\": [],\n",
" \"Detection_Method\": [],\n",
" \"Complex_Expansion_ID\": [],\n",
" \"Source_Participant_Detection_Method\": [],\n",
" \"Publication_DB\": [],\n",
" \"Source_Experimental_Role_ID\": [],\n",
" \"Host_Organism_Taxonomy_ID\": [],\n",
" \"Target_Participant_Detection_Method\": [],\n",
" \"Target_Experimental_Role_ID\": [],\n",
" \"selected\": false,\n",
" \"Author\": [],\n",
" \"Xref\": [],\n",
" \"Publication_ID\": [],\n",
" \"Xref_ID\": [],\n",
" \"id\": \"9339\",\n",
" \"Target_Biological_Role\": [],\n",
" \"Target_Experimental_Role\": [],\n",
" \"target\": \"8979\",\n",
" \"Source_Participant_Detection_Method_ID\": [],\n",
" \"source_original\": \"YER054C\",\n",
" \"Source_Experimental_Role\": [],\n",
" \"Target_Biological_Role_ID\": [],\n",
" \"source\": \"8980\",\n",
" \"Target_Participant_Detection_Method_ID\": [],\n",
" \"Detection_Method_ID\": [],\n",
" \"SUID\": 9339,\n",
" \"Annotation\": []\n",
" }\n",
" },\n",
" {\n",
" \"data\": {\n",
" \"target_original\": \"YER133W\",\n",
" \"Interaction_Type\": [],\n",
" \"Host_Organism_Taxonomy\": [],\n",
" \"interaction\": \"pp\",\n",
" \"Source_Biological_Role\": [],\n",
" \"Source_Biological_Role_ID\": [],\n",
" \"shared_interaction\": \"pp\",\n",
" \"Complex_Expansion\": [],\n",
" \"Detection_Method\": [],\n",
" \"Complex_Expansion_ID\": [],\n",
" \"Source_Participant_Detection_Method\": [],\n",
" \"Publication_DB\": [],\n",
" \"Source_Experimental_Role_ID\": [],\n",
" \"Host_Organism_Taxonomy_ID\": [],\n",
" \"Target_Participant_Detection_Method\": [],\n",
" \"Target_Experimental_Role_ID\": [],\n",
" \"selected\": false,\n",
" \"Author\": [],\n",
" \"Xref\": [],\n",
" \"Publication_ID\": [],\n",
" \"Xref_ID\": [],\n",
" \"id\": \"9338\",\n",
" \"Target_Biological_Role\": [],\n",
" \"Target_Experimental_Role\": [],\n",
" \"target\": \"8866\",\n",
" \"Source_Participant_Detection_Method_ID\": [],\n",
" \"source_original\": \"YER054C\",\n",
" \"Source_Experimental_Role\": [],\n",
" \"Target_Biological_Role_ID\": [],\n",
" \"source\": \"8980\",\n",
" \"Target_Participant_Detection_Method_ID\": [],\n",
" \"Detection_Method_ID\": [],\n",
" \"SUID\": 9338,\n",
" \"Annotation\": []\n",
" }\n",
" },\n",
" {\n",
" \"data\": {\n",
" \"target_original\": \"YOR178C\",\n",
" \"Interaction_Type\": [],\n",
" \"Host_Organism_Taxonomy\": [],\n",
" \"interaction\": \"pp\",\n",
" \"Source_Biological_Role\": [],\n",
" \"Source_Biological_Role_ID\": [],\n",
" \"shared_interaction\": \"pp\",\n",
" \"Complex_Expansion\": [],\n",
" \"Detection_Method\": [],\n",
" \"Complex_Expansion_ID\": [],\n",
" \"Source_Participant_Detection_Method\": [],\n",
" \"Publication_DB\": [],\n",
" \"Source_Experimental_Role_ID\": [],\n",
" \"Host_Organism_Taxonomy_ID\": [],\n",
" \"Target_Participant_Detection_Method\": [],\n",
" \"Target_Experimental_Role_ID\": [],\n",
" \"selected\": false,\n",
" \"Author\": [],\n",
" \"Xref\": [],\n",
" \"Publication_ID\": [],\n",
" \"Xref_ID\": [],\n",
" \"id\": \"9337\",\n",
" \"Target_Biological_Role\": [],\n",
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