gandallab / gene-list

📚List of curated gene sets for enrichment analyses

gene-list

The goal of this repository is to maintain a list of genes implicated in a range of neurodevelopmental and neuropsychiatric disorders. This list was generated from various human genetics study designs—for example, GWAS surveying common variants and whole-exome sequencing (WES) studies surveying rare variants.

Important files

• list - Directory containing downloaded lists.
• output/risk_genes_brain.tsv - The final merged list.
• munge-gene-list.Rmd An R Markdown document that imports downloaded lists and generates the merged list.

Sources

Short name	Desc	Count	Path	Ref
SFARI	ASD syndromic	328	SFARI-Gene_genes_01-13-2021release_02-05-2021export.csv	SFARI
ASD_Sanders	ASD de novo	65	mmc7.xlsx	Sanders et al. 2015
ASD_Satterstrom	ASD de novo	102	Satterstrom.xlsx	Satterstrom et al. 2020
ASD_Ruzzo	ASD rare inehrited	69	mmc3.xlsx	Ruzzo et al. 2019
DDD	DD de novo	285	41586_2020_2832_MOESM4_ESM.xlsx	Kaplanis et al. 2020
SCZ_SCHEMA	SCZ rare	10	meta_results_2021_02_04_20_01_48.csv	SCHEMA
SCZ_PsychENCODE	SCZ GWAS PsychENCODE	321	INT-17_SCZ_High_Confidence_Gene_List.csv	Wang et al. 2018
SCZ_HiC	SCZ GWAS Hi-C	455	1-s2.0-S0920996419300891-mmc1.txt	Mah et al. 2018
ASD_ID_DDD_Coe	ASD/ID/DD de novo	253	41588_2018_288_MOESM3_ESM.xlsx	Coe et al. 2018
FMRP	FMRP binding RNA	842	mmc2.xls	Darnell et al. 2011
CELF4	CELF4 binding RNA	2,803	mmc2.xls	Wagnon et al. 2012
RBFOX	RBFOX1 binding RNA	2,049	pgen.1003067.s004.xlsx	Weyn-Vanhentenryck et al. 2014
Cancer	Cancer genes	576	Census_all.tsv	COSMIC
GenCC	General disease genes	2,754	gencc-submissions.tsv	GenCC
Housekeeping	Housekeeping genes	3,804	HK_genes.txt	Eisenberg et al. 2013
MDEM	MDEM	70	MDEM.txt	Fahrner et al. 2019
UKBB_rare	Disease genes from UKBB WES	564	41586_2021_4103_MOESM5_ESM.xlsx	Backman et al. 2021

How to add genes

1. Clone this repository, e.g. git clone [e-mail]:gandallab/gene-list.git.
2. Download a tsv, csv, xlsx, or other tabular data file to the list directory.
3. Under Import Data in the Rmd, add a brief code snippet that shows how to import your data and filter it to significant/unique genes.
4. If you want your genes to appear in the output file, add a line that pulls the gene symbol column from your data into the geneset list under Combine Data.
5. Add a row to the Markdown table above. Make sure the short name column matches the variable name you chose in R.
6. Push your changes, e.g. git add .; git commit -m "added genes from [study name]"; git push.