Gene Co-expression graph

Gene Co-expression graph

= Gene Co-expression graph
:neo4j-version: 2.3.0
:author: Kai Wang
:twitter: @kaiwang2009

We are building a Gene Co-expression network and neo4j is ued to store graph data and backbone support of drawing graph on the web


image::https://pbs.twimg.com/media/CZEH6d6UkAAPz2y.png:large[]

//A Cypher query to setup the database
//setup
//hide
[source,cypher]
----
CREATE
	(a1:Gene{GeneName:'LOC_Os01g01010',Species:'rice',Annotation:'TBC%20domain%20containing%20protein%2C%20expressed'}),
	(a2:Gene{GeneName:'LOC_Os11g39710',Species:'rice',Annotation:'retrotransposon%20protein%2C%20putative%2C%20Ty3-gypsy%20subclass%2C%20expressed'}),
	(a3:Gene{GeneName:'LOC_Os11g06580',Species:'rice',Annotation:'OsFBX397%20-%20F-box%20domain%20containing%20protein%2C%20expressed'}),
	(a4:Gene{GeneName:'LOC_Os09g39240',Species:'rice',Annotation:'expressed%20protein'}),
	(a5:Gene{GeneName:'LOC_Os08g02180',Species:'rice',Annotation:'expressed%20protein'}),
	(a6:Gene{GeneName:'LOC_Os06g15550',Species:'rice',Annotation:'ubiquitin%20carboxyl-terminal%20hydrolase%2C%20family%201%2C%20putative%2C%20expressed'}),
	(a7:Gene{GeneName:'LOC_Os05g26870',Species:'rice',Annotation:'CAMK_KIN1%2FSNF1%2FNim1_like.21%20-%20CAMK%20includes%20calcium%2Fcalmodulin%20depedent%20protein%20kinases%2C%20expressed'}),
	(a8:Gene{GeneName:'LOC_Os04g58210',Species:'rice',Annotation:'N-acetylglucosaminyl-phosphatidylinositol%20de-N-acetylase%2C%20putative%2C%20expressed'}),
	(a9:Gene{GeneName:'LOC_Os04g08340',Species:'rice',Annotation:'OsSigP3%20-%20Putative%20Type%20I%20Signal%20Peptidase%20homologue%3B%20employs%20a%20putative%20Ser%2FLys%20catalytic%20dyad%2C%20expressed'}),
	(a10:Gene{GeneName:'LOC_Os02g39060',Species:'rice',Annotation:'RNA%20recognition%20motif%20containing%20protein%2C%20putative%2C%20expressed'}),
	(a11:Gene{GeneName:'LOC_Os01g60250',Species:'rice',Annotation:'pentatricopeptide%2C%20putative%2C%20expressed'}),
	(a12:Gene{GeneName:'LOC_Os01g31940',Species:'rice',Annotation:'purine%20permease%2C%20putative%2C%20expressed'}),
	(a13:Gene{GeneName:'LOC_Os01g26080',Species:'rice',Annotation:'expressed%20protein'}),
	(a14:Gene{GeneName:'LOC_Os01g01030',Species:'rice',Annotation:'monocopper%20oxidase%2C%20putative%2C%20expressed'}),
	(a15:Gene{GeneName:'LOC_Os05g42270',Species:'rice',Annotation:'acyltransferase%2C%20putative%2C%20expressed'}),
	(a16:Gene{GeneName:'LOC_Os03g22960',Species:'rice',Annotation:'expressed%20protein'}),
	(a17:Gene{GeneName:'LOC_Os03g17170',Species:'rice',Annotation:'zinc%20finger%2C%20C3HC4%20type%20domain%20containing%20protein%2C%20expressed'}),
	(a18:Gene{GeneName:'LOC_Os01g01040',Species:'rice',Annotation:'expressed%20protein'}),
	(a19:Gene{GeneName:'LOC_Os12g16490',Species:'rice',Annotation:'transposon%20protein%2C%20putative%2C%20unclassified%2C%20expressed'}),
	(a20:Gene{GeneName:'LOC_Os11g41600',Species:'rice',Annotation:'expressed%20protein'}),
	(a21:Gene{GeneName:'LOC_Os11g26900',Species:'rice',Annotation:'expressed%20protein'}),
	(a22:Gene{GeneName:'LOC_Os11g11050',Species:'rice',Annotation:'initiation%20factor%202%20subunit%20family%20domain%20containing%20protein%2C%20expressed'}),
	(a23:Gene{GeneName:'LOC_Os11g05690',Species:'rice',Annotation:'amino%20acid%20permease%20family%20protein%2C%20putative%2C%20expressed'}),
	(a24:Gene{GeneName:'LOC_Os11g02760',Species:'rice',Annotation:'histidine%20triad%20family%20protein%2C%20putative%2C%20expressed'}),
	(a25:Gene{GeneName:'LOC_Os11g01420',Species:'rice',Annotation:'ribosomal%20protein%20L10%2C%20putative%2C%20expressed'}),
	(a26:Gene{GeneName:'LOC_Os10g28690',Species:'rice',Annotation:'expressed%20protein'}),
	(a27:Gene{GeneName:'LOC_Os09g39594',Species:'rice',Annotation:'expressed%20protein'}),
	(a1)-[:COEXPRESS{SCORE:0.079329}]->(a2),
	(a1)-[:COEXPRESS{SCORE:0.077299}]->(a3),
	(a1)-[:COEXPRESS{SCORE:0.070923}]->(a4),
	(a1)-[:COEXPRESS{SCORE:0.074086}]->(a5),
	(a1)-[:COEXPRESS{SCORE:0.094865}]->(a6),
	(a1)-[:COEXPRESS{SCORE:0.070355}]->(a7),
	(a1)-[:COEXPRESS{SCORE:0.081508}]->(a8),
	(a1)-[:COEXPRESS{SCORE:0.044456}]->(a9),
	(a1)-[:COEXPRESS{SCORE:0.075488}]->(a10),
	(a1)-[:COEXPRESS{SCORE:0.072876}]->(a11),
	(a1)-[:COEXPRESS{SCORE:0.060132}]->(a12),
	(a1)-[:COEXPRESS{SCORE:0.066166}]->(a13),
	(a14)-[:COEXPRESS{SCORE:0.057100}]->(a15),
	(a14)-[:COEXPRESS{SCORE:0.079074}]->(a16),
	(a14)-[:COEXPRESS{SCORE:0.078053}]->(a17),
	(a18)-[:COEXPRESS{SCORE:0.059965}]->(a19),
	(a18)-[:COEXPRESS{SCORE:0.106168}]->(a20),
	(a18)-[:COEXPRESS{SCORE:0.069690}]->(a21),
	(a18)-[:COEXPRESS{SCORE:0.084286}]->(a22),
	(a18)-[:COEXPRESS{SCORE:0.085629}]->(a23),
	(a18)-[:COEXPRESS{SCORE:0.096186}]->(a24),
	(a18)-[:COEXPRESS{SCORE:0.105337}]->(a25),
	(a18)-[:COEXPRESS{SCORE:0.085612}]->(a26),
	(a18)-[:COEXPRESS{SCORE:0.116786}]->(a27),
	(a18)-[:COEXPRESS{SCORE:0.062686}]->(a4)

----

Display the whole graph:

//graph

 take a glance of the network

// A Cypher query to give table output
[source,cypher]
----
MATCH (n:Gene)-[r:COEXPRESS]->(m:Gene) RETURN n.GeneName as gene1,r.SCORE as CO_EXPRESSION_VALUE,m.GeneName as gene2 LIMIT 10;
----

//table

 Find genes that co-express with a target gene

// A Cypher query to give graph visualization output
[source,cypher]
----
MATCH (n:Gene{GeneName:"LOC_Os01g01040"})-[r:COEXPRESS*..2]->(m:Gene) WHERE all(x in r WHERE x.SCORE > 0.1) return n,r,m
----

//graph_result

 neo4j can be used to rapidly build a model and fit our case beautifully

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