ArticleBMC genomics2010
Identification of interacting transcription factors regulating tissue gene expression in human.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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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
18 citing papers in PubMed, 34 citations in OpenAlex.
- Developmental and tissue expression breadth define distinct but overlapping classes of housekeeping genes.PLoS computational biology · 2026Article
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Cooperation of ATF4 and CTCF promotes adipogenesis through transcriptional regulation.Cell biology and toxicology · 2022Article
- Long-Term Oral Administration of LLHK, LHK, and HK Alters Gene Expression Profile and Restores Age-Dependent Atrophy and Dysfunction of Rat Salivary Glands.Biomedicines · 2020Article
- Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer-enhancer interactions.Genes & development · 2019Article
- Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues.PloS one · 2019Article
- Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data.BMC genomics · 2018Article
- Full-Length Transcriptome Survey and Expression Analysis ofInternational journal of molecular sciences · 2018Article
- coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.PLoS computational biology · 2018Article
- Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations.Frontiers in genetics · 2018Article
- Predictive Models of Spatial Transcriptional Response to High Salinity.Plant physiology · 2017Article
- Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development.Frontiers in genetics · 2016Article
- Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets.PloS one · 2016Article
- PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information.BMC bioinformatics · 2015Article
- Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes.Bioinformatics and biology insights · 2014Article
- 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
- Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle.BMC genomics · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundTissue gene expression is generally regulated by multiple transcription factors (TFs). A major first step toward understanding how tissues achieve their specificity is to identify, at the genome scale, interacting TFs regulating gene expression in different tissues. Despite previous discoveries, the mechanisms that control tissue gene expression are not fully understood.
resultsWe have integrated a function conservation approach, which is based on evolutionary conservation of biological function, and genes with highest expression level in human tissues to predict TF pairs controlling tissue gene expression. To this end, we have identified 2549 TF pairs associated with a certain tissue. To find interacting TFs controlling tissue gene expression in a broad spatial and temporal manner, we looked for TF pairs common to the same type of tissues and identified 379 such TF pairs, based on which TF-TF interaction networks were further built. We also found that tissue-specific TFs may play an important role in recruiting non-tissue-specific TFs to the TF-TF interaction network, offering the potential for coordinating and controlling tissue gene expression across a variety of conditions.
conclusionThe findings from this study indicate that tissue gene expression is regulated by large sets of interacting TFs either on the same promoter of a gene or through TF-TF interaction networks.
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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.