GenomeTraFaC
GenomeTraFaC is a database of conserved regulatory elements obtained by systematically analyzing the orthologous set of human and mouse genes. It mainly focuses on all of the high-quality mRNA entries of mouse and human genes in the Reference Sequence (RefSeq) database of the NCBI.
Description
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GenomeTraFaC is a database of conserved regulatory elements obtained by systematically analyzing the orthologous set of human and mouse genes. It mainly focuses on all of the high-quality mRNA entries of mouse and human genes in the Reference Sequence (RefSeq) database of the NCBI.
metasource: Fairsharing.orgversion: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Adopting a systematic gene-centric pipeline approach, GenomeTraFaC (http://genometrafac.cchmc.org) allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://genometrafac.cchmc.orgWebpage
More detailed information about this field from each metasource.
http://genometrafac.cchmc.org
metasource: Fairsharing.orgversion: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://genometrafac.cchmc.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
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GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
PMID: 17178752
metasource: Fairsharing.org
version: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
PMID: 17178752
metasource: Fairsharing.org
version: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
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GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
PubMed citations: 14.
14 articles citing: GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
Regulation of PLPP3 gene expression by NF-κB family transcription factors. PMID:31362988
An integrative approach to inferring gene regulatory module networks. PMID:23285197
Neuronal apoptosis by HIV-1 Vpr: contribution of proinflammatory molecular networks from infected target cells. PMID:22727020
Long range regulation of human FXN gene expression. PMID:21760943
KIT signaling regulates MITF expression through miRNAs in normal and malignant mast cell proliferation. PMID:21273305
Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. PMID:20092628
Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene. PMID:20049725
Transcription factor site dependencies in human, mouse and rat genomes. PMID:19835596
Gfi1 regulates miR-21 and miR-196b to control myelopoiesis. PMID:19278956
An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer. PMID:19087325
Mutations in growth factor independent-1 associated with human neutropenia block murine granulopoiesis through colony stimulating factor-1. PMID:18328744
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. PMID:17615082
Characterization of microRNA expression profiles in normal human tissues. PMID:17565689
Tags:
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene regulatory element
metasource: Fairsharing.org
version: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
messenger rna
metasource: Fairsharing.org
version: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 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
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene regulatory element
metasource: Fairsharing.orgversion: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
messenger rna
metasource: Fairsharing.orgversion: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: GenomeTraFaC; GenomeTraFaC; DOI: https://doi.org/10.25504/FAIRsharing.f8pqxt; Last edited: April 26, 2021, 8:41 a.m.; Last accessed: Jan 03 2022 7:07 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
biological regulation gene regulatory element messenger rna rna nucleic acid sequence transcription
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