cis-Regulatory Element Database
Names
More detailed information about this field from each metasource.
cis-Regulatory Element Database
metasource: Fairsharing.org
version: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cisRED
metasource: Fairsharing.org
version: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Databases of genome-wide regulatory module and element predictions
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cis - Regulatory element database
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cisred
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Names
More detailed information about this field from each metasource.
cis-Regulatory Element Database
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cisRED
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Databases of genome-wide regulatory module and element predictions
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cis - Regulatory element database
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cisred
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
Other names: cisRED, Databases of genome-wide regulatory module and element predictions, cis - Regulatory element database, cisred
Names
More detailed information about this field from each metasource.
cis-Regulatory Element Database
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cisRED
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Databases of genome-wide regulatory module and element predictions
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cis - Regulatory element database
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cisred
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
This source may no longer be available. No known URL could be resolved successfully.
The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.
Description
More detailed information about this field from each metasource.
The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cisRED (http://www.cisred.org) is a database for predicted regulatory elements that are identified and ranked by a computational system for genome-scale discovery of phylogenetically conserved motifs. The current version of the database, human v2, contains 386 000 motifs with lengths between 6 to ~30 base pairs. Motifs were predicted for ~18 000 human genes, using sequence search regions that extended from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons, which were masked. Many known transcription factor binding sites are located in such regions. Motifs were predicted using multiple de novo discovery methods applied to multi-species sequence sets that contained between 4 and 15 vertebrate species. An empirical p-value was assigned to each motif by applying motif discovery methods to randomized sequence sets that were adaptively derived from target sequence sets, and retaining motifs below a p-value threshold. Groups of similar motifs were identified using OPTICS hierarchical clustering; co-occurring patterns of motifs are being identified. Predicted regulatory elements can be viewed directly in cisRED's web user interface, and can be user-filtered by p-value or species composition. In addition, motifs can be viewed in the UCSC or Ensembl genome browsers, and in the Sockeye comparative genomics workspace. Methods are described by documentation on the cisRED web site. A schema diagram is available, and the data and SQL structure for the MySQL databases can be downloaded. The database can be queried directly at db.cisred.org, using "anonymous" as a username and leaving the password blank.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. A Nucleic Acids Research article describes the system architecture
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
cisRED is a database system for genome-scale computational discovery of regulatory elements.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
Webpage:
http://www.cisred.org/Webpage
More detailed information about this field from each metasource.
http://www.cisred.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Licence:
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other
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
Licence URL
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http://www.bcgsc.ca/data/data-release-open-access
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
Publications:
Publications
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cisRED: a database system for genome-scale computational discovery of regulatory elements
PMID: 16381958
metasource: Fairsharing.org
version: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Publications
More detailed information about this field from each metasource.
cisRED: a database system for genome-scale computational discovery of regulatory elements
PMID: 16381958
metasource: Fairsharing.org
version: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
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cisRED: a database system for genome-scale computational discovery of regulatory elements
PubMed citations: 59.
59 articles citing: cisRED: a database system for genome-scale computational discovery of regulatory elements
Distinct patterns of whole blood transcriptional responses are induced in mice following immunisation with adenoviral and poxviral vector vaccines encoding the same antigen. PMID:34717548
Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. PMID:32941995
Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells. PMID:31462142
Shifting Retroviral Vector Integrations Away from Transcriptional Start Sites via DNA-Binding Protein Domain Insertion into Integrase. PMID:30534579
Epithelial RNase H2 Maintains Genome Integrity and Prevents Intestinal Tumorigenesis in Mice. PMID:30273559
High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants. PMID:26654095
Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data. PMID:25349267
Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis. PMID:24478791
TNFα-mediated Hsd11b1 binding of NF-κB p65 is associated with suppression of 11β-HSD1 in muscle. PMID:24413279
Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach. PMID:24303025
New insights in osteogenic differentiation revealed by mass spectrometric assessment of phosphorylated substrates in murine skin mesenchymal cells. PMID:24148232
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. PMID:24089456
TBCK influences cell proliferation, cell size and mTOR signaling pathway. PMID:23977024
Genome-wide analysis of H4K5 acetylation associated with fear memory in mice. PMID:23927422
TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription. PMID:23874396
Interferon-beta therapy in multiple sclerosis: the short-term and long-term effects on the patients' individual gene expression in peripheral blood. PMID:23636981
Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. PMID:23307621
Functional characterization of motif sequences under purifying selection. PMID:23303791
Ensembl 2013. PMID:23203987
Transcriptional regulation of the Ufm1 conjugation system in response to disturbance of the endoplasmic reticulum homeostasis and inhibition of vesicle trafficking. PMID:23152784
Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species. PMID:22984403
GW8510 increases insulin expression in pancreatic alpha cells through activation of p53 transcriptional activity. PMID:22242153
cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression. PMID:22171029
Large-scale motif discovery using DNA Gray code and equiprobable oligomers. PMID:22057160
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. PMID:21910886
The regulatory epicenter of miRNAs. PMID:21857109
The differential disease regulome. PMID:21736759
TAFFEL: Independent Enrichment Analysis of gene sets. PMID:21592412
Preferential regulation of miRNA targets by environmental chemicals in the human genome. PMID:21592377
LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data. PMID:21422075
Predicting functionally important SNP classes based on negative selection. PMID:21247465
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data. PMID:20965971
The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. PMID:20943967
Genomic features of the human dopamine transporter gene and its potential epigenetic States: implications for phenotypic diversity. PMID:20548783
Touring Ensembl: a practical guide to genome browsing. PMID:20459808
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. PMID:20421737
Contrasting genetic paths to morphological and physiological evolution. PMID:20368429
Transcription factor site dependencies in human, mouse and rat genomes. PMID:19835596
Effect of dietary calcium and dairy proteins on the adipose tissue gene expression profile in diet-induced obesity. PMID:19776631
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes. PMID:19534755
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. PMID:19151087
A miRNA signature of prion induced neurodegeneration. PMID:18987751
Identification of transcripts with enriched expression in the developing and adult pancreas. PMID:18554416
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. PMID:18515841
The Innate Immune Database (IIDB). PMID:18321385
DBD--taxonomically broad transcription factor predictions: new content and functionality. PMID:18073188
TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. PMID:18045502
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection. PMID:17875205
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. PMID:17478504
From genes to functional classes in the study of biological systems. PMID:17407596
Large-scale discovery of promoter motifs in Drosophila melanogaster. PMID:17238282
Tissue-specific regulatory elements in mammalian promoters. PMID:17224917
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. PMID:17148480
VISTA Enhancer Browser--a database of tissue-specific human enhancers. PMID:17130149
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. PMID:16845052
Transcription factor map alignment of promoter regions. PMID:16733547
Practical strategies for discovering regulatory DNA sequence motifs. PMID:16683017
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. PMID:16606704
Tags:
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
c. elegans
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
dna
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
sage
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
human
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
mouse
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
rat
metasource: re3data.org
version: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
data mining
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
sequence sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:04.056589
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: cisRED; cis-Regulatory Element Database; DOI: https://doi.org/10.25504/FAIRsharing.rwd4wq; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
c. elegans
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
dna
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
sage
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
human
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
mouse
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
rat
metasource: re3data.orgversion: re3data.org: cisRED; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XK69 last accessed: 2022-11-04
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
data mining
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
sequence sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:04.056589
biological regulation genome nucleic acid sequence transcription c. elegans dna sage human mouse rat transcription factors and regulatory sites model organisms data mining sequence sites, features and motifs
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