ArticleGenome research2001
A predictive model for regulatory sequences directing liver-specific transcription.
Article in Genome research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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Who cites it
102 citing papers in PubMed, 204 citations in OpenAlex.
- 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 binding site orientation and order are major drivers of gene regulatory activity.Nature communications · 2023Article
- Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers.BMC medical genomics · 2017Article
- Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Mechanisms of mutational robustness in transcriptional regulation.Frontiers in genetics · 2015Review
- Article
- Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors.Nucleic acids research · 2013Article
- Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.Nature genetics · 2013Article
- MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters.BMC bioinformatics · 2013Article
- A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks.BMC genomics · 2013Article
- Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.BMC bioinformatics · 2012Article
- Detection of interacting transcription factors in human tissues using predicted DNA binding affinity.BMC genomics · 2012Article
- Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules.BMC genomics · 2011Article
- Towards resolving the transcription factor network controlling myelin gene expression.Nucleic acids research · 2011Article
- Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development.PLoS genetics · 2011Article
- Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.BMC bioinformatics · 2011Article
- Functional characterization of liver enhancers that regulate drug-associated transporters.Clinical pharmacology and therapeutics · 2011Article
- Assessing computational methods of cis-regulatory module prediction.PLoS computational biology · 2010Article
- Multivariate Hawkes process models of the occurrence of regulatory elements.BMC bioinformatics · 2010Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of sequence-specific signals, protein-protein interactions and chromatin structure. We present here a new procedure to identify clusters of transcription factor binding sites characteristic of sequence modules experimentally verified to direct transcription selectively to liver cells. This algorithm is sufficiently specific to identify known regulatory sequences in genes selectively expressed in liver, promising acceleration of experimental promoter analysis. In combination with phylogenetic footprinting, this improvement in the specificity of predictions is sufficient to motivate a scan of the human genome. Potential regulatory modules were identified in orthologous human and rodent genomic sequences containing both known and uncharacterized genes.
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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.