KnockTF 2.0: a comprehensive gene expr profile database with knockdown / knockout of transcription (co-)factors in multiple species

Chenchen Feng, Chao Song, Shuang Song, Guorui Zhang, Mingxue Yin, Yuexin Zhang, Fengcui Qian, Qiuyu Wang, Maozu Guo, Chunquan Li

Nucleic Acids Research; 2024 Jan 5; 52(D1):D183-D193. doi: 10.1093/nar/gkad1016.

Abstract

Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.

See https://pubmed.ncbi.nlm.nih.gov/37956336/

Figure 1: Database content and construction. KnockTF 2.0 provides a large number of manually curated T(co)F knockdown/knockout datasets in humans, mice, A. thaliana and Z. mays. Detailed and abundant (epi)genetic annotation information for TF target genes can be collected, including super-enhancers, enhancers, TFBSs, common SNPs, risk SNPs, CRISPR/Cas9 target sites and so forth. KnockTF 2.0 contains a variety of functions to browse, search, analyze, and download T(co)F knockdown/knockout datasets.