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hagenaue / Brain_GMT

Code and documentation for the brain-related gene set (Brain.GMT) curation project
MIT License
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Reading List & Background #4

Open hagenaue opened 9 months ago

hagenaue commented 9 months ago

Reading to provide background information about existing large gene set curation projects and how they are used in enrichment analyses to improve the interpretation of large genomic datasets.

hagenaue commented 9 months ago

MSigDB Gene Set Collection: https://www.gsea-msigdb.org/gsea/msigdb Liberzon_2011_MsigDB.pdf

hagenaue commented 9 months ago

Enrichr Gene Set Collection: https://maayanlab.cloud/Enrichr/ Xie_2021_Enrichr.pdf

hagenaue commented 9 months ago

Gene Set Enrichment Analysis: https://www.pnas.org/doi/10.1073/pnas.0506580102

hagenaue commented 9 months ago

Gene Ontology Resource: https://geneontology.org https://www.nature.com/articles/ng0500_25 https://academic.oup.com/genetics/article/224/1/iyad031/7068118?login=false

hagenaue commented 9 months ago

Kegg Pathway Database: https://www.genome.jp/kegg/pathway.html https://academic.oup.com/nar/article/49/D1/D545/5943834?login=false

hagenaue commented 9 months ago

Gemma Curated/Reanalyzed Gene Expression Studies: https://gemma.msl.ubc.ca/home.html Lim_2021_GemmaDatabase.pdf

hagenaue commented 9 months ago

GeneWeaver gene set database: https://www.geneweaver.org Bubier_2019_GeneWeaver_GeneSetCuration.pdf

hagenaue commented 9 months ago

Brain Ignoreome: Pandey_2014_BrainIgnorome.pdf