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GenBank®

http://www.ncbi.nlm.nih.gov/

Description :
GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 300 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage using the link provided.

Osteo-Promoter Database

http://www.opd.tau.ac.il/

Description :
Genes involved in osteogenic proliferation and differentiation

Plant Stress-Responsive Gene Catalog

http://dayhoff.generationcp.org/

Description :
Stress-responsive gene in various plant species

HGNC Database

http://www.genenames.org/

Description :
Genew, the Human Gene Nomenclature Database, is the only resource that provides data for all human genes which have approved symbols. It is managed by the HUGO Gene Nomenclature Committee (HGNC) as a confidential database, containing over 16,000 records, 80% of which are represented on the Web by searchable text files. The data in Genew are highly curated by HGNC editors and gene records can be searched on the Web by symbol or name to directly retrieve information on gene symbol, gene name, cytogenetic location, OMIM number and PubMed ID. Data are integrated with other human gene databases e.g. GDB, LocusLink and SWISS-PROT and approved gene symbols are carefully co-ordinated with the Mouse Genome Database (MGD). Approved gene symbols are available for querying and browsing at: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl.

Recent develoments :
The Genew search engine was updated in July 2002. You can now search using free text, as well as some new fields including: HGNC IDs, location, PMID, sequence accession IDs, other database IDs, previous gene names and symbols. Also, it is now possible to link directly through to the gene record using either the HGNC ID, or gene symbol. For example, the link for CFTR is: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=1884 or http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?match=CFTR.

Aknowledgement :
The HGNC is supported by NIH contract N01-LM-9- 3533 and by the UK Medical Research Council. Many thanks to John Attwood (Sanger Centre), Julia White (Open University) and Gary Walsh for their past contributions to the maintenance and development of Genew. Thanks are also due to the HGNC editors Drs Elspeth Bruford, Ruth Lovering and Mathew Wright whose accurate curation and attention to detail ensure the validity of the gene records.

SuperCAT

http://mlstoslo.uio.no/

Description :
A database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria

The Cell Cycle DB

http://www.itb.cnr.it/cellcycle

Description :
Genes and proteins involved in human and yeast cell cycle

EVOG

http://neobio.cs.pusan.ac.kr/evog/

Description :
Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. We have implemented EVOG (Evolution Visualizer for Overlapping Genes), a Web-based database with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Here we study comparatively the extent of overlapping genes in thirteen genomes by analyzing the public databases of expressed sequences using a set of computational tools designed to identify overlapping genes on opposite DNA strands of the same genomic locus. Using this technique, we collected and analyzed all overlapping genes in human, chimpanzee, orangutan, marmoset, rhesus, cow, dog, mouse, rat, chicken, Xenopus, zebrafish, and Drosophila. This integrated service provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG database components included a number of overlapping genes (10074 in human, 10009 in chimpanzee, 67039 in orangutan, 51001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10700 in mouse, 7987 in rat, 1439 in chicken, 597 in Xenopus, 2457 in zebrafish and 4115 in Drosophila). The EVOG database is very effective and easy to use for the analysis of the evolutionary process of overlapping genes when comparing different species. Therefore, EVOG could potentially be used as the main tool to investigate the evolution of the human genome in relation disease by comparing the expression profiles of overlapping genes.

References :
Yelin, R., Dahary, D., Sorek, R., Levanon, E. Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., Nemzer, S., Pinner, E., Walach, S., Bernstein, J., Savitsky, K. and Rotman, G. (2003) Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol., 21, 379-386.

PhyloPat

http://www.cmbi.ru.nl/phylopat

Description :
Phylogenetic patterns of genes from the Ensembl database

Human PAML Browser

http://mendel.gene.cwru.edu/adamslab/pbrowser.py

Description :
Positive selection in human genes detected through genome comparison

Tumor Associated Gene database

http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php

Description :
The completion of human genome sequence has advanced a gigantic step toward a new era of biomedical research. Though the sequence itself is not the key for many currently unanswered questions related to human diseases, it sheds light on potential genetic solution of these diseases. We believe that the available annotations including physical characterization and functional protein domains of known tumor-related genes can be used to study the mechanisms underlying tumorigenesis. The tumor-associated gene (TAG; http://www.binfo.ncku.edu.tw/TAG) database was designed to utilize information from well-characterized oncogenes and tumor suppressor genes to facilitate cancer research. All target genes were identified through text-mining approach from the PubMed database. A semi-automatic information retrieving engine was built to collect specific information of these target genes from various resources and store in the TAG database. The information are arranged into five tables including ¡§Gene content¡¨, ¡§Protein domain/family¡¨, ¡§Gene Ontology¡¨, ¡§Disorder & Mutation¡¨, and ¡§Cross reference¡¨. At current stage, TAG database contains information for 198 oncogenes and 167 tumor suppressor genes that were known to be involved in the tumorigenesis in at least one cancer type. In addition, 151 genes that are known to be involved in oncogenesis but the genes actions have not been classified were also collected in the TAG database. We have designed user-friendly web interfaces that provide functions in searching and analysis of TAG information. Furthermore, we categorized all TAG domains and generate a weight matrix table to provide additional analysis in "oncogenic potential" for any customer-provided protein. The TAG is an integrated database that collected only well studied gene in related to oncogenesis. Beside to provide comprehensive information of well-known tumor-related genes to promote biomedical studies, our final goal is to identify novel TAG and study their role in tumorigenesis using a more systemic approach.

Aknowledgement :
This study was supported by grant of National research program for genomic medicine (NRPGM) from National Science Council, Taiwan

ERGR

http://bioinfo.vipbg.vcu.edu/ERGR/

Description :
Ethanol-related genes in human and model organisms

G2Cdb

http://www.genes2cognition.org/

Description :
Genes to Cognition

PBIL

http://pbil.univ-lyon1.fr/

Description :
Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.

ENDEAVOUR

http://www.esat.kuleuven.be/endeavourweb

Description :
ENDEAVOUR is a computational approach to prioritizing candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server now supports multiple species (i.e. human, rat, mouse) and makes use of data from various databases (i.e. ontologies, annotations, protein-protein interactions, text mining data) to generate the prioritization.

ProdoNet

http://www.prodonet.tu-bs.de/

Description :
A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

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