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

Author:

Feng Chenchen1234,Song Chao2356,Song Shuang2378,Zhang Guorui2378,Yin Mingxue2378ORCID,Zhang Yuexin2356,Qian Fengcui2356,Wang Qiuyu12378,Guo Maozu9,Li Chunquan123105ORCID

Affiliation:

1. National Health Commission Key Laboratory of Birth Defect Research and Prevention & School of Computer, University of South China , Hengyang, Hunan, 421001, China

2. The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

3. Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China , Hengyang, Hunan, 421001, China

4. School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China

5. The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

6. The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China

7. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

8. Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

9. School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture , Beijing 100044, China

10. MOE Key Lab of Rare Pediatric Diseases, University of South China , Hengyang, Hunan, 421001, China

Abstract

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.

Funder

National Natural Science Foundation of China

Hospital of University of South China

China Postdoctoral Science Foundation

Natural Science Foundation of Hunan Province

Scientific Research Fund Project of Hunan Provincial Health Commission

Clinical Research 4310 Program of the University of South China

Natural Science Foundation of Heilongjiang Province

Publisher

Oxford University Press (OUP)

Subject

Genetics

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