Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and Fugu genomes. It is freely accessible at http://ecrbase.dcode.org
ECRbase was supported in part by grants from the Lawrence Livermore National Laboratory
G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1):122-4 (2007)
Coexpressed genes and networks in human and mouse
G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes
Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease
Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat
SysZNF provides a systematic catalogue of (until now) human and mouse C2H2 zinc finger genes/proteins based on HMM profile searches of the whole proteomes with the PFAM profile of the C2H2 domain (accession number: PF00096; http://pfam.sanger.ac.uk/). C2H2 zinc-finger proteins often contain additional conserved domains, such as KRAB, SCAN, BTB, and SET. These effector domains are usually found in the amino-terminal region of the proteins and often serve different roles in transcriptional regulation through their ability to interact with other cellular molecules.A comprehensive database has been developed with a web interface that i) arranges C2H2 gene information based on physical localization in the respective genome, ii) provides downloadable and visual information on gene organization and protein domain composition, iii) serves as starting point to search and examine ortholog and paralog relationships in different species and iv) contains direct links from a particular data set to other resources of the scientific community. In SysZNF, each C2H2-ZNF gene is represented as a card to integrate the related information from public databases. A graphical gene model system, a protein display system and a gene cluster display system were developed for these genes.The database should help in i) quickly gathering information on gene models, protein organization of particular ZNF genes/proteins, ii) providing the user with quick links to other biological databases, iii) suggesting orthologs and paralogs between species, and iv) generally providing basic information and leads for further experimentation. Thus, SysZNF should facilitate the research on C2H2 type ZNF genes under an integrative view in comparative genomic approaches.
Human Metabolome Database
Database for integration of human functional interactions
Human protein interaction database
High-throughput experiments are being performed at an ever-increasing rate to systematically elucidate protein-protein interaction (PPI) networks for model organisms, while similar experiments for human networks have lagged far behind. The Online Predicted Human Interaction Database (OPHID) is a web-based database of predicted interactions between human proteins. It combines the literature-derived human PPIs from BIND, HPRD and MINT, with predictions made from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Mus musculus. The 23,889 predicted interactions currently listed in OPHID are evaluated using protein domains, gene co-expression and Gene Ontology terms. OPHID can be queried using single IDs or batch queries, and using multiple supported ID types. The results can be displayed as text, HTML, or visualized using our custom graph visualization program. In addition, the entire database is available for download in tab-delimited text or PSI-compliant XML format.
Recent develoments :
OPHID continues to expand in the number and type of interactions it contains. While the initial focus was on predictions, experimentally-verified human interactions have been growing in abundance. Recent data directly testing human proteins been added to the database, including datasets from Barrios-Rodiles et al., (PMID: 15761153), Rual et al., (PMID: 16189514), and Stelzl et al., (PMID: 16169070).
We acknowledge the hardware and software support from IBM Life Sciences through a Shared University Research Grant, and support from the National Science and Engineering Research Council, the Institute for Robotics and Intelligent Systems, Precarn Inc., Genome Canada, the Princess Margaret Hospital Foundation through funds raised by the Toronto Women s Fashion Show Committee and Younger Foundation.
1. Brown, K.R., and Jurisica, I. (2005) Online Predicted Human Interaction Database. Bioinformatics 21: 2076-2082.
Network approach to human protein kinases and their substrate proteins
Human protein interactions mediated by phosphoprotein-binding domains
Predicted human protein-protein interactions
Genes and proteins involved in human and yeast cell cycle
Human genes and their vertebrate orthologs