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Cavadas et al., Scientific Reports, 2016 Supplements

This gist pre-processes supplementary data from Cavadas et al. paper in Scientific Reports, citation below:

Cavadas, M.A.S., Mesnieres, M., Crifo, B., Manresa, M.C., Selfridge, A.C., Keogh, C.E., Fabian, Z., Scholz, C.C., Nolan, K.A., Rocha, L.M.A., et al. (2016). REST is a hypoxia-responsive transcriptional repressor. Sci Rep-Uk 6, 31355

Each of the notebooks downloads the data directly from the journal, converts it into an easier-to-work tsv format, and augments it with uniprot, ensembl and entrez identifiers.

The notebooks make extensive use of MyGene.info which can be cited as:

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import pandas as pd

def transcript_to_tss(transcript_bed, tss_bed):
    """
        Convert transcript bed file to TSS bed file
        Strand aware
    """

    # Read bedfile to pandas
    df = pd.read_csv(transcript_bed,

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from matplotlib import pyplot as plt
import numpy as np
from scipy.interpolate import interpn

# Density scatterplots, based on https://stackoverflow.com/a/53865762
def density_scatterplot(x, y, bins=100, cmap='turbo', drop_na=True, ax=None, **kwargs):
    if ax is None:
        ax = plt.gca()
    x = np.asarray(x)
    y = np.asarray(y)

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Stoltzman et al. PNAS 2008 Figure S1

This Github gist contains a CSV file of manually transcribed gene names from Figure S1 of Stoltzman et al. 2008 PNAS paper.

Another file containing the ENSEMBL gene identifiers matched to these ids has been produced via mygene.info API (Xin,2016)

References

• Stoltzman, C., Peterson, C., Breen, K., Muoio, D., Billin, A., Ayer, D. (2008). Glucose sensing by MondoA:Mlx complexes: A role for hexokinases and direct regulation of thioredoxin-interacting protein expression Proceedings of the National Academy of Sciences 105(19), 6912-6917. https://dx.doi.org/10.1073/pnas.0712199105

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Converting deeptools matrix to pd.DataFrame

import matplotlib

# Deeptools will mess with matplotlib settings, fix that
_mpl_backend = matplotlib.rcParams['backend']
from deeptools.heatmapper import heatmapper as deeptools_heatmapper
matplotlib.use(_mpl_backend)
del _mpl_backend