Use Case 4: Identify the Tissue Activity for a TF based on its Targets

Version 1

The workflow starts with selecting KLF4 as the search term. Gene sets with set labels containing KLF4 were queried from Enrichr[1]. Identified matching terms from the ENCODE TF ChIP-seq 2015[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ENCODE_TF_ChIP-seq_2015. Identified matching terms from the ChEA 2022[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ChEA_2022. Identified matching terms from the ARCHS4 TF Co-Expression[5] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ARCHS4_TFs_Coexp. Multiple GMTs were combined into one GMT. A consensus gene set was created by only retaining genes that appear in at least two sets. The gene set was submitted to Enrichr[1]. The gene set was enriched against the GTEx Tissues V8 2023[6] library to identify statistically significant GTEx Tissue Signatures.

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3. Keenan, A. B. et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research vol. 47 W212–W224 (2019). doi:10.1093/nar/gkz446
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5. Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nature Genetics vol. 45 580–585 (2013). doi:10.1038/ng.2653