Genomics, Proteomics, and Bioinformatics: NCSU Libraries

Featured Review:

The endo-beta-mannanase gene families in Arabidopsis, rice, and poplar

Yuan JS, Yang XH, Lai JR, Lin H, Cheng ZM, Nonogaki H, Chen F.
Functional & Integrative Genomics 7(1): 1-16, 2007

Resources for Information about Genes

Note: These web sites refer primarily to collections or groups of organisms. For a listing of genome and sequence information for specific organisms, or groups, such as families—please go the Organisms page.

Entrez Gene
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
The Entrez Gene project was designed to organize information about genes and to function as a major node in the integrated network of NCBI resources, including genomic map, sequence, expression, protein structure, function, and homology data. Gene records are established for known or predicted genes as defined by nucleotide sequence or map position.

EuGenes: Genomic Information for Eukaryotic Organisms
http://iubio.bio.indiana.edu:8089/
euGenes provides a summary of gene and genomic information from eukaryotic organism databases. A gene report includes the gene symbol, name, map information (chromosome, genetic, molecular), and gene product information (function, structure, and homologies), Gene information is available for these organisms: Drosophila, human, mouse, mosquito, rat, Arabidopsis, C. elegans, yeast, and, zebrafish.

Gene Search (BioCarta)
http://www.biocarta.com/search/index.asp
Search by gene name or symbol to locate gene-specific information. Results include links to BioCarta (pathways) and other resources to obtain: sequence data, publications and reviews, disease correlation, and interrelationship with other proteomic pathways. The database includes information on genes from drosophila, worm, yeast, mouse, rat, and human.

Gene Sorter (UCSC Genome Bioinformatics)
http://genome.ucsc.edu/cgi-bin/hgNear
Gene Sorter displays similarities between a chosen gene and other genes based one of several types, including protein homology, gene expression profiles, or genomic proximity. Gene information is available for human, mouse, rat, yeast, C. elegans, and Drosophila. Search results include links to gene location, a description of the gene, and nucleotide and protein sequence data.

GeneView --ENSEMBL (EMBL-European Bioinformatics Institute, Sanger Institute)
http://www.ensembl.org/index.html
The ENSEMBL project focuses on providing accurate, automatic analysis of genome data for vertebrates. Ensembl gene predictions are based on experimental evidence, which is imported from other major databases. A GeneView record summarizes information about a specific gene, including genomic location, prediction method for gene identification, transcripts, ortholog prediction, links to other resources, and alignments with other genes. Genes can be searched from the ENSEMBL home page.

H-Invitational Database (H-InvDB)
http://www.jbirc.aist.go.jp/hinv/ahg-db/index.jsp
H-InvDB is a curated database of human genes and transcripts. Each entry includes extensive annotations containing information about gene structures, splicing isoforms, protein functions and domains, metabolic pathways, protein structure, genetic polymorphisms relation with diseases, molecular evolutionary features, and other data.

TIGR Gene Index
http://www.tigr.org/tdb/tgi/index.shtml
The TIGR Gene Index integrates data from publicly available EST sequencing and gene research projects. The Gene Index Project creates organism specific databases with the goal of representing a non-redundant view of all of an organisms genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships. A Gene Index is available for a large number of species grouped as animals (30), plants (33), protests (15), and fungi (9).

UniGene (NCBI)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
UniGene automatically analyzes and groups GenBank sequences, including ESTs, into a non-redundant set of gene-related clusters. Each cluster contains sequences representing a unique gene along with related information (tissue expression, maps). UniGene clusters are available for animals (human, rat, mouse, cow, zebrafish, clawed frog, fruitfly, and mosquito) and plants (wheat, rice, barley, maize, and cress). These organisms were selected as they are representative of diverse species, and large amounts of EST data are available. When available, links are provided to other NCBI resources or external databases

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