The transcription category provides six gene-set libraries that attempt to link differentially expressed genes with the transcriptional machinery. These six libraries include the ability to identify transcription factors that are enriched for target genes within the input list using four different options: 1) ChEA ; 2) position weight matrices (PWMs) from TRANSFAC  and JASPAR ; 3) target genes generated from PMWs downloaded from the UCSC genome browser ; and 4) transcription factor targets extracted from the ENCODE project [14, 15]. In addition, the two other gene-set libraries in the transcription category are gene sets associated with: 5) histone modifications extracted from the Roadmap Epigenomics Project ; and 6) microRNAs targets computationally predicted by TargetScan .
Transcription factor target genes inferred from PWMs for the human genome were downloaded from the UCSC Genome Browser  FTP site which contains many resources for gene and sequence annotations. We converted this file into a gene set library and included it in Enrichr since it produces different results compared with the other method to identify transcription factor/target interactions from PWMs as described above.
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