ArticleMolecular systems biology2007
Tissue-specific regulatory elements in mammalian promoters.
Article in Molecular systems biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 64 citations in OpenAlex.
- Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis.PloS one · 2011Pooled it
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- SpliceTransformer predicts tissue-specific splicing linked to human diseases.Nature communications · 2024Article
- Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs.Journal of animal science and biotechnology · 2022Article
- Distinctive regulatory architectures of germline-active and somatic genes inGenome research · 2020Article
- Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.Cell reports · 2018Article
- Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions.PLoS genetics · 2018Article
- Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis.Scientific reports · 2016Article
- Direct ChIP-Seq significance analysis improves target prediction.BMC genomics · 2015Article
- Efficient and graded gene expression in glia and neurons of primary cerebellar cultures transduced by lentiviral vectors.Histochemistry and cell biology · 2015Article
- Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.BMC bioinformatics · 2012Article
- Article
- Detection of interacting transcription factors in human tissues using predicted DNA binding affinity.BMC genomics · 2012Article
- Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.BMC bioinformatics · 2011Article
- Sequence features that drive human promoter function and tissue specificity.Genome research · 2010Article
- Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.PloS one · 2010Article
- A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.Molecular systems biology · 2010Article
- Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Transcription factor-binding sites and the cis-regulatory modules they compose are central determinants of gene expression. We previously showed that binding site motifs and modules in proximal promoters can be used to predict a significant portion of mammalian tissue-specific transcription. Here, we report on a systematic analysis of promoters controlling tissue-specific expression in heart, kidney, liver, pancreas, skeletal muscle, testis and CD4 T cells, for both human and mouse. We integrated multiple sources of expression data to compile sets of transcripts with strong evidence for tissue-specific regulation. The analysis of the promoters corresponding to these sets produced a catalog of predicted tissue-specific motifs and modules, and cis-regulatory elements. Predicted regulatory interactions are supported by statistical evidence, and provide a foundation for targeted experiments that will improve our understanding of tissue-specific regulatory networks. In a broader context, methods used to construct the catalog provide a model for the analysis of genomic regions that regulate differentially expressed genes.
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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.