ArticleNucleic acids research2018
Towards a map of cis-regulatory sequences in the human genome.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
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- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.Briefings in bioinformatics · 2023Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
- Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice.BMC biology · 2022Article
- 44 Current Challenges in miRNomics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- regCNN: identifyingComputational and structural biotechnology journal · 2022Article
- The Role of the CREB Protein Family Members and the Related Transcription Factors in Radioresistance Mechanisms.Life (Basel, Switzerland) · 2021Review
- Accurate prediction ofNAR genomics and bioinformatics · 2021Article
- Profiling Chromatin Accessibility at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2021Review
- Zebrafish models of skeletal dysplasia induced by cholesterol biosynthesis deficiency.Disease models & mechanisms · 2020Article
- Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data.PloS one · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs. Here, we integrated 620 TF ChIP-seq datasets produced by the ENCODE project for 168 TFs in 79 different cell/tissue types and predicted an unprecedentedly completely map of CREs in CRMs in the human genome at single nucleotide resolution. The map includes 305 912 CRMs containing a total of 1 178 913 CREs belonging to 736 unique TF binding motifs. The predicted CREs and CRMs tend to be subject to either purifying selection or positive selection, thus are likely to be functional. Based on the results, we also examined the status of available ChIP-seq datasets for predicting the entire regulatory genome of humans.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.