ArticleNucleic acids research2006
cisRED: a database system for genome-scale computational discovery of regulatory elements.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
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- Epithelial RNase H2 Maintains Genome Integrity and Prevents Intestinal Tumorigenesis in Mice.Gastroenterology · 2019Article
- E2F transcription factors associated with up-regulated genes in glioblastoma.Cancer biomarkers : section A of Disease markers · 2017Article
- High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.BMC genomics · 2015Article
- Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data.Genome biology and evolution · 2014Article
- TNFα-mediated Hsd11b1 binding of NF-κB p65 is associated with suppression of 11β-HSD1 in muscle.The Journal of endocrinology · 2014Article
- Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis.Frontiers in genetics · 2014Article
- Interferon-beta therapy in multiple sclerosis: the short-term and long-term effects on the patients' individual gene expression in peripheral blood.Molecular neurobiology · 2013Article
- New insights in osteogenic differentiation revealed by mass spectrometric assessment of phosphorylated substrates in murine skin mesenchymal cells.BMC cell biology · 2013Article
- Article
- Functional characterization of motif sequences under purifying selection.Nucleic acids research · 2013Article
- Importance of different types of prior knowledge in selecting genome-wide findings for follow-up.Genetic epidemiology · 2013Article
- Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.Database : the journal of biological databases and curation · 2013Article
- TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription.PloS one · 2013Article
- Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach.PloS one · 2013Article
- Ensembl 2013.Nucleic acids research · 2013Article
- Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors.
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Abstract
We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred.org). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.
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