Epigenetic factor associated gene serach

Question

[Confused_human]

Hello everyone,

I have a set of genes that I got from my RNA seq experiment.

This file looks like this :

gene    Symbol  baseMean    log2FoldChange  lfcSE   stat    pvalue  padj    UP_DOWN
ENSG00000001497 LAS1L   2669.490018 -1.11256317 0.276762731 63.9156085  4.35E-13    6.58E-12    DOWN
ENSG00000002726 AOC1    39.71640451 -2.490906864    0.773899659 20.0813272  0.000481272 0.001685566 DOWN
ENSG00000003096 KLHL13  66.52926768 -2.136937629    0.566770871 24.88279312 5.31E-05    0.000224519 DOWN
ENSG00000003393 ALS2    3272.900526 -1.774354339    0.311956488 80.22216375 1.56E-16    3.66E-15    DOWN
ENSG00000004399 PLXND1  1245.275705 -1.542591287    0.907299129 22.20880841 0.000182122 0.000692253 DOWN
ENSG00000004478 FKBP4   3879.49839  -1.270012868    0.258911852 160.1143558 1.38E-33    1.30E-31    DOWN
ENSG00000004777 ARHGAP33    430.519171  -1.283991814    0.449043224 12.95656292 0.011489997 0.02937801  DOWN
ENSG00000005156 LIG3    1637.429904 -1.025668201    0.207067717 43.24787418 9.19E-09    7.30E-08    DOWN
ENSG00000005187 ACSM3   185.1320761 -1.897450548    0.33205081  43.88622598 6.77E-09    5.52E-08    DOWN
ENSG00000005189 AC004381.6  532.5152679 -1.23488899 0.232013473 32.3331893  1.64E-06    9.01E-06    DOWN

The complete list has 2928 genes. How will I find the genes from this list which are involved in epigenetic factor?

Please help me on this. I am new to this.

Thank you

[Basti]

You could have a look at the EpiFactors database : https://epifactors.autosome.org

[Confused_human]

Thank you,

But How will I search for the gene set . I have 2928 genes.

[Basti]

You could download the database (https://epifactors.autosome.org/description) and you cross-check it with your gene list

[ATpoint]

There won't almost certainly not be that one geneset you think about. Epigenetic factors are a diverse group of genes/proteins, ranging from methylation factors, histone modifiers, pioneering factors, activating or repressing transcription factors, it can be anything. You need to better define the biological question you want to answer. Just "epigenetic" is not sufficient. And please don't ask how to do that, this is apparently the core of your project so you and your PI must sit and talk it over.