KnockTF

KnockTF provides a curated database of human gene expression profiles from 570 manually curated RNA-seq and microarray datasets to study the effects of transcription factor knockdown and knockout across 308 transcription factors and multiple tissue and cell types.

Key Features:

• Extensive Dataset Collection: Contains 570 manually curated RNA-seq and microarray datasets linked to 308 transcription factors disrupted by knockdown or knockout across multiple tissue and cell types.
• Tissue/Cell Type-Specific Annotation: Annotates transcription factors and their target genes with tissue- and cell type-specific information.
• Pathway and Functional Annotations: Integrates upstream pathway information for transcription factors and functional annotation results for downstream target genes.
• Gene Binding Details: Provides transcription factor binding information including interactions with promoters, super-enhancers, and typical enhancers of target genes.
• Network Construction and Analysis: Constructs networks linking transcription factors to differentially expressed genes for network-based analysis of TF effects.

Scientific Applications:

• Target Gene Identification: Identify genes regulated by specific transcription factors using differential expression after knockdown or knockout.
• Functional Impact Assessment: Explore downstream functional consequences and pathway perturbations resulting from TF knockdown or knockout.
• Regulatory Network Analysis: Analyze TF–gene regulatory networks and interaction patterns derived from differential expression data.
• Tissue-Specific Regulatory Studies: Investigate tissue- and cell type-specific roles of transcription factors to inform precision medicine hypotheses.

Methodology:

Manual curation of 570 RNA-seq and microarray datasets; annotation of TFs and target genes by tissue and cell type; integration of upstream pathway and functional annotations; construction of networks linking transcription factors to differentially expressed genes.