Paper Info
Title
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors.
Abstract
BACKGROUND: Genome annotation plays an essential role in the interpretation and use of genome sequence information. While great strides have been made in the annotation of coding regions of genes, less success has been achieved in the annotation of the regulatory regions of genes, including promoters, enhancers/silencers, and other regulatory elements. One reason for this disparity in annotated information is that coding regions can be assessed using high-throughput techniques such as EST sequencing, while annotation of regulatory regions often requires a gene-by-gene approach. RESULTS: The NFI-Regulome database http://nfiregulome.ccr.buffalo.edu was designed to promote easy annotation of the regulatory regions of genes that contain binding sites for the NFI (Nuclear Factor I) family of transcription factors, using data from the published literature. Binding sites are annotated together with the sequence of the gene, obtained from the UCSC Genome site, and the locations of all binding sites for multiple genes can be displayed in a number of formats designed to facilitate inter-gene comparisons. Classes of genes based on expression pattern, disease involvement, or types of binding sites present can be readily compared in order to assess common "architectural" structures in the regulatory regions. CONCLUSIONS: The NFI-Regulome database allows rapid display of the relative locations and number of transcription factor binding sites of individual or defined sets of genes that contain binding sites for NFI transcription factors. This database may in the future be expanded into a distributed database structure including other families of transcription factors. Such databases may be useful for identifying common regulatory structures in genes essential for organ development, tissue-specific gene expression or those genes related to specific diseases.
Year
DOI
Venue
2011
10.1186/2043-9113-1-4
J. Clinical Bioinformatics
Keywords
Field
DocType
distributed database,binding site,biomedical research,high throughput,organization development,transcription factor,genome annotation,gene expression,bioinformatics,genome sequence,health informatics,transcription factor binding site,gene regulation
ChIA-PET,Genome project,DNA binding site,Biology,NFI Transcription Factors,Gene prediction,Regulome,Bioinformatics,Genetics,Enhancer,Vertebrate and Genome Annotation Project,Database
Journal
Volume
Issue
ISSN
1
1
2043-9113
Citations 
PageRank 
References 
3
0.38
10
Authors
4
Name
Order
Citations
PageRank
Richard M. Gronostajski130.38
Joseph Guaneri230.38
Dong Lee330.38
Steven M. Gallo418624.88