Center for Systems and Computational Biology || Databases

Databases

Mammalian Promoter Database (MPromDb) is an informational resource containing an integrated description of the gene transcription regulation supported by experiment and mapped on the mammalian genomes. MPromDb (release 1.0) currently contains 32,994 promoters and first exons (16,094 of human, 12,710 of mouse & 4,190 of rat), 4,527 transcription factor (TF) binding sites (2,585 of human, 1,291 mouse & 651 Rat) and 1,503 transcription factors with links to PubMed and GenBank references. The database can be searched based on promoter, gene and transcription factor information. We have implemented in house developed Java application framework called Genome Data Visualization Tool Kit (GDVTK) for MPromDb database management and information presentation in the form of an image map of gene regulatory regions with interactive contextual menus for easy navigation.
Sun, H., Palaniswamy, S.K., Pohar, T.T., Jin, V.X.and Davuluri, R.V.

The Hematopoiesis Promoter Database, (HemoPDB) is an information resource for the scientific research community focusing on hematopoiesis, the regulation thereof, and hematologic malignancies. HemoPDB is composed of experimentally-defined promoters and the associated annotations of cis-regulatory sequences. In addition to annotations that are included in publicly available databases, data acquired from comprehensive literature reviews are continuously being added. HemoPDB may be searched by gene symbol, GenBank accession ID or transcription factor. For each gene, one may obtain information including the lineage(s) in which it is expressed, annotated cis-regulatory elements, description of it's role in hematopoietic regulation and respective literature references. Target genes, annotations and respective functional classes are an example of obtainable information for each transcription factor.

Pohar, T.T., Sun, H., Davuluri, R.V.
HemoPDB: An information resource of transcriptional regulation in blood c ell development.
Nucleic Acids Research. 2004 32: D86-D90.
Abstract | Full Text | PDF

Orthologous Mammalian Gene Promoter datababse (OMGProm) is an integrated resource of mammalian gene promoters. The current version of OMGProm, following a stringent filtering process, contains promoters of 5,717 unique human mouse orthologous genes which contains 8,347 promoters including alternative promoters for the orthologous genes. All of the data acquired from the several sources are primarily associated with their UniGene ID. OMGProm can be searched by Gene Symbol, Unigene Id & Genbank Accession Number.

Palaniswamy, S.K., Jin, V.X., Sun, H. and Davuluri, R.V.
OMGProm: A Database of Orthologous Mammalian Gene Promoters.
Bioinformatics.2005 21(6):835-6.
Abstract | PDF

The Arabidopsis cis-regulatory element database (AtcisDB) provides a comprehensive resource for the scientific community working with gene regulatory information of Arabidopsis thaliana, a widely used model plant. AtcisDB consists of a searchable relational database, which includes many different datatypes, such as transcription factor binding site information, promoter sequence and related annotations. The data can be viewed using our interactive browser developed by Genome Data Visualization Toolkit (GDVTK), and analyzed with our pattern recognition tools. The AtcisDB can be searched by Gene Symbol, Locus ID and GenBank Accession Number.

Davuluri R.V., Sun H., Palaniswamy S.K., Matthews N., Molina C., Kurtz M., Grotewold E.
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
BMC Bioinformatics. 2003 Jun 23;4(1):25.

Arabidopsis transcription factor database (AtTFDB) is a comprehensive and public Arabidopsis transcription factor database. From this page, users may search the database for transcription factors in two ways: a) By utilizing a specific LocusID or gene name search. b) Browse Families.

As part of the Integrative Cancer Biology Program of the National Cancer Institute, we are developing an integrative computational and high-throughput experimental approach to characterize the epigenetic mechanisms involved in the target genes of the ER pathway. ERTargetDB integrates information from the ongoing Chip-on-chip experiments in our laboratory and promoter sequence conservation from the OMGProm database. We will add methylation and acetylation patterns across the target gene promoters in the future versions of the database.

Jin, V.X., Sun, H. Pohar, T.T., Liyanarachchi, S., Palaniswamy, S.K., Davuluri, R.V.
ERTargetDb: An integral information resource of transcription regulation of ER Target Genes.
Journal of Molecular Endocrinology 2005. In Press.
Abstract | Full Text | PDF

First Exon Annotations (FEAnnotations) contains annotations of promoters and first exons annotated by an automated system, called FexAnnotator (First exon Annotator). FexAnnotator combines the predictions of FirstEF and genomic similarities to mRNAs and ESTs. FEXannotator is a suit of perl programs that automatically merges overlapping BLAT alignments of mRNAs and ESTs to get different transcriptional units, and combines with FirstEF predictions. The database includes the first exons and promoters in the human genome (June, 2002 Freeze) by using FexAnnotator and present these annotations along with the nearest CpG windows for all of the 24 chromosomes.

Davuluri R.V., Grosse I., Zhang M.Q.
Annotation of Promoters and First Exons in the Human Genome.
Submitted

One of the objectives of the Integrative Cancer Biology Program is focused on the development of statistical approaches to model the interaction between SMAD complexes and altered chromatin structure and the definition of unique epigenetic signatures in ovarian cancer cells. KbTSMAD is an information resource exclusively focused on addressing the need for a better understanding of the TGF-β/SMAD regulatory mechanism. This database currently contains information about the TGF-β/SMAD signaling pathway and its target gene promoters and a map of experimentally known binding sites of SMADs and transcription factors involved in their regulation. A graphical platform, which contains a representative overview of the signaling pathway, is also linked to functional information and regulatory preferences.