ChEA (ChIP-X Enrichment Analysis) database contains manually extracted datasets of transcription-factor/target-gene interactions from over 100 experiments such as ChIP-chip, ChIP-seq, ChIP-PET applied to mammalian cells. We use the database to analyze mRNA expression data where we perform gene-list enrichment analysis as the prior biological knowledge gene-list library. The system is delivered as web-based interactive software. With this software users can input lists of mammalian genes for which the program computes over-representation of transcription factor targets from the ChEA database.
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ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma’ayan A.
Nucleic Acids Res. 2019 Jul 2;47(W1):W212-W224. doi: 10.1093/nar/gkz446.
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma’ayan A.
Bioinformatics. 2010 Oct 1;26(19):2438-44.