ArticleDatabase : the journal of biological databases and curation2020
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.
Article in Database : the journal of biological databases and curation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes.BMC genomics · 2021Pooled it
- A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs.Animals : an open access journal from MDPI · 2025Article
- Whole-Genome Sequencing-Based Population Genetic Analysis of Wild and Domestic Rabbit Breeds.Animals : an open access journal from MDPI · 2025Article
- Identification of co-localised transcription factors based on paired motifs analysis.IET systems biology · 2024Article
- Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding.Nature communications · 2023Article
- Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans.BMC genomics · 2023Article
- Long Noncoding RNAs in the Pathogenesis of Insulin Resistance.International journal of molecular sciences · 2022Review
- proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.Nucleic acids research · 2022Article
- Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications.Genome biology · 2021Article
- Article
- Role of Transposable Elements in Gene Regulation in the Human Genome.Life (Basel, Switzerland) · 2021Review
- Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules.Frontiers in genetics · 2020Article
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Authors and funding
8 authors.
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Abstract
ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein-protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets.
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