KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

Abstract Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF function...

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Bibliographic Details
Published in:Nucleic acids research 2020-01, Vol.48 (D1), p.D93-D100
Main Authors: Feng, Chenchen, Song, Chao, Liu, Yuejuan, Qian, Fengcui, Gao, Yu, Ning, Ziyu, Wang, Qiuyu, Jiang, Yong, Li, Yanyu, Li, Meng, Chen, Jiaxin, Zhang, Jian, Li, Chunquan
Format: Article
Language:English
Subjects:
Computational Biology - methods
Database Issue
Databases, Genetic
Gene Expression Profiling - methods
Gene Knockdown Techniques
Humans
Molecular Sequence Annotation
Software
Transcription Factors - genetics
Transcription Factors - metabolism
User-Computer Interface
Web Browser
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Summary:Abstract Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http://www.licpathway.net/KnockTF/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkz881