ArticleCell systems2017
Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds.
Article in Cell systems, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 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
25 citing papers in PubMed, 47 citations in OpenAlex.
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity.bioRxiv : the preprint server for biology · 2025Article
- Transcriptome analysis reveals role of transcription factor WRKY70 in early N-hydroxy-pipecolic acid signaling.Plant physiology · 2024Article
- DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.Nature communications · 2024Article
- A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia.Blood advances · 2023Article
- Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.Nucleic acids research · 2023Article
- Anterior-posterior patterning of segments in Anopheles stephensi offers insights into the transition from sequential to simultaneous segmentation in holometabolous insects.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2023Article
- Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements.Molecular systems biology · 2022Article
- EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma.Cancer discovery · 2022Article
- A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.Genome research · 2021Article
- Base-resolution models of transcription-factor binding reveal soft motif syntax.Nature genetics · 2021Article
- Computational biology approaches for mapping transcriptional regulatory networks.Computational and structural biotechnology journal · 2021Review
- Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits.Nature genetics · 2020Article
- Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model.Genome research · 2020Article
- MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates.BMC bioinformatics · 2020Article
- LIN28B regulates transcription and potentiates MYCN-induced neuroblastoma through binding to ZNF143 at target gene promotors.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.Molecular cell · 2020Article
- Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.Nature communications · 2020Article
- 6mA-RicePred: A Method for Identifying DNAFrontiers in plant science · 2020Article
- Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.Nucleic acids research · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Transcription factors (TFs) control cellular processes by binding specific DNA motifs to modulate gene expression. Motif enrichment analysis of regulatory regions can identify direct and indirect TF binding sites. Here, we created a glossary of 108 non-redundant TF-8mer "modules" of shared specificity for 671 metazoan TFs from publicly available and new universal protein binding microarray data. Analysis of 239 ENCODE TF chromatin immunoprecipitation sequencing datasets and associated RNA sequencing profiles suggest the 8mer modules are more precise than position weight matrices in identifying indirect binding motifs and their associated tethering TFs. We also developed GENRE (genomically equivalent negative regions), a tunable tool for construction of matched genomic background sequences for analysis of regulatory regions. GENRE outperformed four state-of-the-art approaches to background sequence construction. We used our TF-8mer glossary and GENRE in the analysis of the indirect binding motifs for the co-occurrence of tethering factors, suggesting novel TF-TF interactions. We anticipate that these tools will aid in elucidating tissue-specific gene-regulatory programs.
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Registered trials
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.