ArticleComputational and structural biotechnology journal2022
TF-COMB - Discovering grammar of transcription factor binding sites.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Heroin addiction modulates transcription factor binding in regulatory regions of the human putamen.Scientific reports · 2026Article
- Dynamic changes in chromatin accessibility reveal the role of NF-Y targeting AURKB in mediating cell cycle during asynchronous oogenesis in the Chinese Alligator (Alligator sinensis).Frontiers in zoology · 2026Article
- Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.Protein & cell · 2025Article
- Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.Nature neuroscience · 2025Article
- The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.Biology open · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Transcription factor condensates and signaling driven transcription.Nucleus (Austin, Tex.) · 2023Review
- In vitro modeling of CD8Science immunology · 2023Article
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- Guidelines on the performance evaluation of motif recognition methods in bioinformatics.Frontiers in genetics · 2023Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cooperativity between transcription factors is important to regulate target gene expression. In particular, the binding grammar of TFs in relation to each other, as well as in the context of other genomic elements, is crucial for TF functionality. However, tools to easily uncover co-occurrence between DNA-binding proteins, and investigate the regulatory modules of TFs, are limited. Here we present TF-COMB (Transcription Factor Co-Occurrence using Market Basket analysis) - a tool to investigate co-occurring TFs and binding grammar within regulatory regions. We found that TF-COMB can accurately identify known co-occurring TFs from ChIP-seq data, as well as uncover preferential localization to other genomic elements. With the use of ATAC-seq footprinting and TF motif locations, we found that TFs exhibit both preferred orientation and distance in relation to each other, and that these are biologically significant. Finally, we extended the analysis to not only investigate individual TF pairs, but also TF pairs in the context of networks, which enabled the investigation of TF complexes and TF hubs. In conclusion, TF-COMB is a flexible tool to investigate various aspects of TF binding grammar.
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