Publications (128)831.32 Total impact
-
Article: Whole-Genome rVISTA: A Tool to Determine Enrichment of Transcription Factor Binding Sites in Gene Promoters from Transcriptomic Data.
[show abstract] [hide abstract]
ABSTRACT: We have developed a web-based query tool, Whole Genome rVISTA (WGRV) that determines enrichment of transcription factors (TFs) and associated target genes in sets of co-regulated genes. WGRV enables users to query databases containing pre-computed genome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promoters (from 100 bp up to 5kb upstream) of human, mouse and Drosophila genomes. TF binding sites are based on position weight matrices from the TRANSFAC Professional database. For a given set of coregulated genes WGRV returns statistically enriched and evolutionarily conserved binding sites, mapped by the rVISTA (Regulatory VISTA) algorithm. Users can then retrieve a list of genes from the query set containing the enriched TF binding sites and their location in the query set promoters. Results are exported in a .bed format for rapid visualization in the UCSC genome browser. Flat files of mapped conserved sites and their genomic coordinates are also available for analysis with stand-alone software. AVAILABILITY: http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl CONTACT: azambon@ucsd.edu, ildubchak@lbl.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.Bioinformatics 06/2013; · 5.47 Impact Factor -
Article: RegTransBase -- a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
[show abstract] [hide abstract]
ABSTRACT: BACKGROUND: Due to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly remains a field of semi-manual examination since absence of a knowledgebase and informatics platform for automated and systematic investigation restricts opportunities for computational prediction. Additionally, confirming computationally inferred regulons by experimental data is critically important.Description: RegTransBase is an open-access platform with a user-friendly web interface that is publicly available at http://regtransbase.lbl.gov. It consists of two databases -- a manually collected hierarchical regulatory interactions database based on more than 7000 scientific papers which can serve as a knowledgebase for verification of predictions, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools. RegTransBase captures the knowledge from published scientific literature using controlled vocabularies and contains various types of experimental data, such as: the activation or repression of transcription by an identified direct regulator; determination of the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA; mapping of binding sites for a regulatory protein; characterization of regulatory mutations. Analysis of the data collected from literature resulted in the creation of Putative Regulons from Experimental Data that are also available in RegTransBase. CONCLUSIONS: RegTransBase is a powerful user-friendly platform for the investigation of regulation in prokaryotes. It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation of transcriptional regulation data.BMC Genomics 04/2013; 14(1):213. · 4.07 Impact Factor -
Dataset: nature01262-s4
-
Dataset: nature01262-s12
-
Dataset: nature01262-s1
-
Dataset: nature01262-s14
-
Dataset: nature01262-s16
-
Dataset: nature01262-s5
-
Dataset: nature01262-s11
-
Dataset: nature01262-s6
-
Dataset: nature01262-s2
-
Dataset: nature01262-s10
-
Dataset: nature01262-s7
-
Dataset: nature01262-s4-1
-
Dataset: nature01262-s12
-
Dataset: nature01262-s5
-
Dataset: nature01262-s15
-
Dataset: nature01262-s5
-
Dataset: nature01262-s16
-
Dataset: nature01262-s9
Top co-authors
Top Journals
- Nucleic Acids Research (14)
- Genome Research (8)
- Nature (6)
- Science (4)
- Journal of bacteriology (4)
Institutions
-
2011
-
Sanford-Burnham Medical Research Institute
La Jolla, CA, USA
-
-
2006–2011
-
University of California, Berkeley
- • Energy Biosciences Institute
- • Department of Molecular and Cell Biology
Berkeley, MO, USA
-
-
2002–2011
-
Lawrence Berkeley National Laboratory
- • Physical Biosciences Division
- • Biological Data Management and Technology Center (BDMTC)
- • Life Sciences Division
Berkeley, CA, USA
-
-
2004–2010
-
DOE Joint Genome Institute
Walnut Creek, CA, USA -
University of California, Davis
- Department of Computer Science
Davis, CA, USA
-
-
2009
-
University of Georgia
- Plant Genome Mapping Laboratory
Athens, GA, USA -
Monterey Bay Aquarium Research Institute
Moss Beach, CA, USA
-
-
2004–2008
-
Russian Academy of Sciences
- Institute of Problems of Information Transmission
Moscow, Moscow, Russia
-
-
2007
-
University of California, San Diego
San Diego, CA, USA -
University of Toronto
- Department of Computer Science
Toronto, Ontario, Canada -
The Institute for Information Transmission Problems
Moscow, Moscow, Russia -
CSU Mentor
Long Beach, CA, USA
-
-
2004–2007
-
U.S. Department of Energy
Washington, D. C., DC, USA
-
