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ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

E. Blanco
2006 Nucleic Acids Research  
ABS (http://genome. imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography  ...  We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences.  ...  D.F. is recipient of a predoctoral fellowship from Instituto Nacional de Bioinformática (Spain).  ... 
doi:10.1093/nar/gkj116 pmid:16381947 pmcid:PMC1347478 fatcat:l5guiiewg5c2zoqjpffgp637ca

Ab initio identification of putative human transcription factor binding sites by comparative genomics [article]

Davide Cora', Carl Herrmann, Christoph Dieterich, Ferdinando Di Cunto, Paolo Provero, Michele Caselle
2005 arXiv   pre-print
We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation.  ...  In this way we find various known motifs and also some new candidate binding sites.  ...  Acknowledgements P.P. is a Lagrange Fellow of the I.S.I. foundation. We thanks Enrico Curiotto for helpful discussion.  ... 
arXiv:q-bio/0505005v1 fatcat:jxjtlnlnjzgwbazd6gzut2ds2m

Ab initio identification of putative human transcription factor binding sites by comparative genomics

D Corà, C Herrmann, C Dieterich, F Di Cunto, P Provero, M Caselle
2005 BMC Bioinformatics  
We discuss here a simple and powerful approach for the ab initio identification of these cis-regulatory motifs.  ...  We have discussed a new integrated algorithm for the "ab initio" identification of transcription factor binding sites in the human genome.  ...  Acknowledgements P.P. is a Lagrange Fellow of the I.S.I. foundation. We thanks Enrico Curiotto for helpful discussion.  ... 
doi:10.1186/1471-2105-6-110 pmid:15865625 pmcid:PMC1097714 fatcat:jtt3p3rssfc5pnklftxa3phx6m

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites

Santi González, Bàrbara Montserrat-Sentís, Friman Sánchez, Montserrat Puiggròs, Enrique Blanco, Alex Ramirez, David Torrents
2012 Computer applications in the biosciences : CABIOS  
Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding  ...  Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts024 pmid:22253291 pmcid:PMC3307110 fatcat:6gcxqupm5bcprhnt32e5rmmzlu

Ab initio identification of functionally interacting pairs of cis-regulatory elements

B. A. Friedman, M. B. Stadler, N. Shomron, Y. Ding, C. B. Burge
2008 Genome Research  
Cooperatively acting pairs of cis-regulatory elements play important roles in many biological processes.  ...  of an intervening exon in a splicing reporter assay.  ...  This work was supported in part by grants from the NIH and NSF (C.B.B.).  ... 
doi:10.1101/gr.080085.108 pmid:18799692 pmcid:PMC2556269 fatcat:ezt5idvw7bddbpudrhzzetkbga

Genetic and molecular bases of photoperiod responses of flowering in soybean

Satoshi Watanabe, Kyuya Harada, Jun Abe
2012 Breeding Science  
We also discuss our identification of orthologs of Arabidopsis flowering genes from among the 46,367 genes annotated in the publicly available soybean genome database Phytozome Glyma 1.0.  ...  We emphasize the usefulness of a combined approach including QTL analysis, fine mapping, and use of candidate gene information from model plant species in genetic and molecular studies of soybean flowering  ...  We detected a total of 333 orthologs of 92 Arabidopsis genes from among a total of 46,367 annotated genes (Table 1, Supplemental Table 1 and Supplemental Fig. 1 ).  ... 
doi:10.1270/jsbbs.61.531 pmid:23136492 pmcid:PMC3406791 fatcat:4qjtx2qtfvhn3asoexw7ej23em

KBERG: KnowledgeBase for Estrogen Responsive Genes

S. Tang, Z. Zhang, S. L. Tan, M.-H. E. Tang, A. P. Kumar, S. K. Ramadoss, V. B. Bajic
2007 Nucleic Acids Research  
The motif detection is based on ab initio discovery of common cis-elements from the orthologous gene cluster from human, mouse and rat, thus reflecting a degree of promoter sequence preservation during  ...  The identified motifs are linked to transcription factor binding sites based on the TRANSFAC database.  ...  This allowed identification of TFBSs that potentially bind identified motifs. As a result, we found that SP1-binding site is the most frequent TFBS in promoter regions in our collection.  ... 
doi:10.1093/nar/gkl816 pmid:17090589 pmcid:PMC1669744 fatcat:2q4kab3h6vd6bl2lw5lotallgu

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

E. Barta
2004 Nucleic Acids Research  
DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species.  ...  Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters.  ...  start site of a gene), called transcription factor binding sites (TFBSs) (1) .  ... 
doi:10.1093/nar/gki097 pmid:15608291 pmcid:PMC540051 fatcat:ymmd33xca5budnlo7nn56s3itq

Computational Design and Application of Endogenous Promoters for Transcriptionally Targeted Gene Therapy for Rheumatoid Arthritis

Jeroen Geurts, Leo AB Joosten, Nozomi Takahashi, Onno J Arntz, Anton Glück, Miranda B Bennink, Wim B van den Berg, Fons AJ van de Loo
2009 Molecular Therapy  
This research is supported by a VIDI grant (917.46.373) from the Netherlands Organization for Scientific Research and an IOP Genomics grant (IGE02032).  ...  AcknoWledGMents We are grateful to Martin Letzkus, Nicole Hartmann, and Frank Staedtler of the Genomics Factory, Novartis Institutes for BioMedical Research, Basel, Switzerland for performing the RNA isolation  ...  When multiple promoters existed for a gene, we selected either a promoter from the Eukaryotic Promoter Database or Database of Transcription Start Sites.  ... 
doi:10.1038/mt.2009.182 pmid:19690516 pmcid:PMC2835043 fatcat:kvbplmdkkfdkndfoexn5hazi3a

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

P. S. Novichkov, D. A. Rodionov, E. D. Stavrovskaya, E. S. Novichkova, A. E. Kazakov, M. S. Gelfand, A. P. Arkin, A. A. Mironov, I. Dubchak
2010 Nucleic Acids Research  
Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation  ...  RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs.  ...  the server and useful suggestions, Alex Poliakov for technical assistance, and to Tatiana Paley for assistance in web interface development, and to Tatiana Smirnova for web design of the home page.  ... 
doi:10.1093/nar/gkq531 pmid:20542910 pmcid:PMC2896116 fatcat:hifo7rl75vf7db2x5ngckp5gmu

Multiple non-collinear TF-map alignments of promoter regions

Enrique Blanco, Roderic Guigó, Xavier Messeguer
2007 BMC Bioinformatics  
The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements.  ...  We consider this kind of approach can be extremely useful in the future to annotate potential transcription factor binding sites on sets of co-regulated genes from high-throughput expression experiments  ...  This work was supported by grant BIO2003-05073 from the Spanish Ministerio de Ciencia y Tecnologia to RG.  ... 
doi:10.1186/1471-2105-8-138 pmid:17456238 pmcid:PMC1878506 fatcat:p4m26vusafbkjbyzyjsy55fbqi

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

Giulio Pavesi, Federico Zambelli, Graziano Pesole
2007 BMC Bioinformatics  
We also show examples on how the algorithm can be successfully employed when promoter annotations of the genes investigated are missing, or when regulatory sites and regions are located far away from the  ...  This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is  ...  Acknowledgements We thank David Horner for the help in the generation of the simulated datasets.  ... 
doi:10.1186/1471-2105-8-46 pmid:17286865 pmcid:PMC1803799 fatcat:7mvnzj5t7rex5dbwrievoahbmu

In Silico Identification of Regulatory Elements in Promoters [chapter]

Vikrant Nain, Shakti Sahi, Polumetla Ananda
2011 Computational Biology and Applied Bioinformatics  
ABS ABS is a database of known TF binding sites identified in promoters of orthologous vertebrate genes.  ...  It has 650 annotated and experimental validated binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat and chicken genome sequences.  ...  .), ISBN: 978-953-307-629-4, InTech, Available from: http://www.intechopen.com/books/computational-biology-and-appliedbioinformatics/in-silico-identification-of-regulatory-elements-in-promoters © 2011  ... 
doi:10.5772/22230 fatcat:wcruf4x7bvcsbaszaknsiejuxy

RSAT 2018: regulatory sequence analysis tools 20th anniversary

Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime A Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera (+1 others)
2018 Nucleic Acids Research  
), along with tools to extract sequences from a list of coordinates (retrieve-seqbed), to select motifs from motif collections (retrievematrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara  ...  RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences.  ...  Pattern matching crer-scan Transcription factor binding sites Cis-regulatory enriched regions (CRER) Given a set of cis-regulatory elements (predicted sites, annotated sites, ChIP-seq peaks  ... 
doi:10.1093/nar/gky317 pmid:29722874 pmcid:PMC6030903 fatcat:hau274l2trgfhhtpxtwsqftyna

Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation

Xi Wang, Georg Haberer, Klaus FX Mayer
2009 BMC Genomics  
The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter.  ...  In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited.  ...  Research in the laboratory of KFXM is supported by grants from the German Federal Ministry of Education and Research within the GABI Future programme (0315055C) and a grant from the Pact for Research and  ... 
doi:10.1186/1471-2164-10-284 pmid:19558665 pmcid:PMC2714861 fatcat:x6rnjjpbzncsplcs7j327wkzzm
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