Annotated regulatory Binding Sites from Orthologous Promoters
Names
More detailed information about this field from each metasource.
Annotated regulatory Binding Sites from Orthologous Promoters
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ABS
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
abs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Names
More detailed information about this field from each metasource.
Annotated regulatory Binding Sites from Orthologous Promoters
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ABS
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
abs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Names
More detailed information about this field from each metasource.
Annotated regulatory Binding Sites from Orthologous Promoters
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ABS
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
abs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.
Description
More detailed information about this field from each metasource.
ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ABS (Annotated Binding Sites) is a public database of experimentally verified orthologous transcription factor binding sites (TFBSs). Annotations have been collected from the literature and are manually curated. For each gene, the TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) have been always extracted to form the collection of gene promoter sequences from human, mouse, rat and chicken. For each one of the annotated 650 regulatory sites, the position, the motif and the sequence in which the site is present are available in a very simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments, and graphical dotplots are also available. ABS is oriented to the study of regulatory regions in the context of pattern discovery programs. Thus, ABS provides two applications to aid during the automatical training of them: CONSTRUCTOR and EVALUATOR. CONSTRUCTOR automatically generates artificial benchmarks by planting motifs in random sequences. The user can customize the content of the background sequence, the number of motifs that are planted, the subset of the real sites that can be used, the density of motifs on each sequence, and the length and the number of the sequences. EVALUATOR uses the standard accuracy measures to assess the correctness of the predictions introduced by the user in contrast to the real sites also submitted. In the output, a table with the accuracy at both nucleotide and site level is supplied. The formal definitions of the values are always included to facilitate the interpretation.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Annotated regulatory binding sites from orthologous promoters.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Webpage:
http://genome.imim.es/datasets/abs2005/Webpage
More detailed information about this field from each metasource.
http://genome.imim.es/datasets/abs2005/
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
http://genome.crg.es/datasets/abs2005/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: GPL-2.0Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
PMID: 16381947
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkj116
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Publications
More detailed information about this field from each metasource.
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
PMID: 16381947
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkj116
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
-
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
PubMed citations: 24.
24 articles citing: ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
Sequence motif finder using memetic algorithm. PMID:29298679
An Entropy-Based Position Projection Algorithm for Motif Discovery. PMID:27882329
Compound hierarchical correlated beta mixture with an application to cluster mouse transcription factor DNA binding data. PMID:25964663
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. PMID:24680932
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. PMID:23282090
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species. PMID:22984403
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. PMID:22253291
On calculating the probability of a set of orthologous sequences. PMID:21918614
Towards resolving the transcription factor network controlling myelin gene expression. PMID:21729871
SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model. PMID:21342545
Discovering multiple realistic TFBS motifs based on a generalized model. PMID:19811641
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions. PMID:19786498
Probabilistic inference of transcription factor binding from multiple data sources. PMID:18364997
Text-mining assisted regulatory annotation. PMID:18271954
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. PMID:17916232
Multiple non-collinear TF-map alignments of promoter regions. PMID:17456238
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. PMID:17286865
SwissRegulon: a database of genome-wide annotations of regulatory sites. PMID:17130146 - http://dx.doi.org/10.1093/nar/gkj116
Tags:
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
promoter
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
regulation of gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 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
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
promoter
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
regulation of gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: ABS; Annotated regulatory Binding Sites from Orthologous Promoters; DOI: https://doi.org/10.25504/FAIRsharing.7mnebr; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 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
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
binding site biological regulation gene molecular interaction promoter regulation of gene expression nucleic acid sequence transcription transcription factors and regulatory sites
Need help integrating and/or managing biomedical data?