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Resource:Gene Index Project

Name: Resource:Gene Index Project
Description: The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products. The promise of genome projects has been a complete catalog of genes in a wide range of organisms. While genome projects have been successful in providing reference genome sequences, the problem of finding genes and their variants in genomic sequence remains an ongoing challenge. TGI has created an inventory that contains genes and their variants together with description.

In addition, this resource is attempting to use these catalogs to find links between genes and pathways in different species and to provide lists of features within completed genomes that can aid in the understanding of how gene expression is regulated.

DATABASES

  • Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment): Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group.
  • GeneChip Oncology Database (GCOD):Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers. Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control. You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID.
  • Gene Indices: As of July 1, 2008, there are 111 publicly available gene indices. They are separated into 4 categories for better organization and easier access. Animal: 41, Plant: 45, Protist: 15, Fungal: 10
  • Genomic Maps: Human, mouse, rat, chicken, drosophila melanogaster, zebrafish, mosquito, caenorhabditis elegans, Arabidopsis thaliana, rice, yeast, fission yeast

Dana-Farber Cancer Institute (DFCI) Gene Indices Software Tools:

  • TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets.
  • GICL: this package contains the scripts and all the necessary pre-compiled binaries for 32bit Linux systems.
  • clview: an assembly file viewer.
  • SeqClean:a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.
  • cdbfasta/cdbyank: fast indexing/retrieval of fasta records from flat file databases.
  • DAS/XML Genomic Viewer The Genomic viewer borrows modules from http://www.biodas.org (lstein (at) cshl.org) & http://webreference.com.
Other Name(s): DFCI Gene Index Project, Gene Index Project
Abbreviation: TGI, DFCI TGI
Parent Organization: Resource:Dana-Farber Cancer Institute
Supporting Agency: National Science Foundation, U.S. Department of Energy
Grant: DBI-0552416
Resource Type(s): Topical portal, Downloadable database, Web accessible database, Software resource
Resource: Resource
URL: http://compbio.dfci.harvard.edu/tgi/
Id: nif-0000-20942
PMID: PMID 7566098
Keywords: functional, gene, genome, index, organism, pathway, product, role, sequence, species, transcript, variant
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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Notes

This page uses this default form:Resource

Contributors

Aarnaud, Ccdbuser, Zaidaziz



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Facts about Resource:Gene Index ProjectRDF feed
AbbrevTGI, DFCI TGI  +
CurationStatuscurated  +
DefiningCitationhttp://compbio.dfci.harvard.edu/tgi/  +
DefinitionThe goal of The Gene Index Project is to u The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products. The promise of genome projects has been a complete catalog of genes in a wide range of organisms. While genome projects have been successful in providing reference genome sequences, the problem of finding genes and their variants in genomic sequence remains an ongoing challenge. TGI has created an inventory that contains genes and their variants together with description.

In addition, this resource is attempting to use these catalogs to find links between genes and pathways in different species and to provide lists of features within completed genomes that can aid in the understanding of how gene expression is regulated.

DATABASES

  • Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment): Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group.
  • GeneChip Oncology Database (GCOD):Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers. Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control. You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID.
  • Gene Indices: As of July 1, 2008, there are 111 publicly available gene indices. They are separated into 4 categories for better organization and easier access. Animal: 41, Plant: 45, Protist: 15, Fungal: 10
  • Genomic Maps: Human, mouse, rat, chicken, drosophila melanogaster, zebrafish, mosquito, caenorhabditis elegans, Arabidopsis thaliana, rice, yeast, fission yeast

Dana-Farber Cancer Institute (DFCI) Gene Indices Software Tools:

  • TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets.
  • GICL: this package contains the scripts and all the necessary pre-compiled binaries for 32bit Linux systems.
  • clview: an assembly file viewer.
  • SeqClean:a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.
  • cdbfasta/cdbyank: fast indexing/retrieval of fasta records from flat file databases.
  • DAS/XML Genomic Viewer The Genomic viewer borrows modules from http://www.biodas.org (lstein (at) cshl.org) & http://webreference.com. (at) cshl.org) & http://webreference.com.
ExampleImageGene Index Project.PNG  +
GrantCategory:DBI-0552416   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleTopical portal  +, Downloadable database  +, Web accessible database  +, and Software resource  +
Idnif-0000-20942  +
Is part ofResource:Dana-Farber Cancer Institute  +
KeywordsFunctional  +, Gene  +, Genome  +, Index  +, Organism  +, Pathway  +, Product  +, Role  +, Sequence  +, Species  +, Transcript  +, and Variant  +
LabelResource:Gene Index Project  +
ModifiedDate23 October 2012  +
PMID7566098  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
Supporting AgencyNational Science Foundation  +, and U.S. Department of Energy  +
SynonymDFCI Gene Index Project  +, and Gene Index Project  +