Related External Links
Immunology Databases
Immunology Databases
- Resources
- Immunological Genome Project
@ USA
- This is a project to generate a complete microarray dissection of gene expression in the immune system of the mouse.
- IMGT
@ France
- The International Immunogenetics Information system is a high-quality integrated knowledge resource specialized in the immune related molecules.
- RAPID
@ Japan & India
- The Resource of Asian Primary Immunodeficiency Diseases has been constructed by the joint program with us and Institute of Bioinformatics, India.
- Innate Immunity
- InnateDB
@ Canada
- A public database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection.
Gene/cDNA/mRNA databases
Gene/cDNA/mRNA databases
- Comprehensive catalogs
- Entrez Gene
@NCBI, USA
- A searchable database of genes, from Refseq genomes,
and defined by sequence and/or located in the NCBI Map Viewer
- RefSeq
@NCBI, USA
- The reference sequence collection of genome, transcripts
and proteins.
- FANTOM3
@GSC, RIKEN, Japan
- A comprehensive annotation of mouse cDNA clones.
- H-Inv DB
@JBIRC, Japan
- Human gene database, with integrative annotation
validated by Full-Length cDNA clones.
- HUGE
@Kazusa DNA Research Institute, Japan
- A database of Human Unidentified Gene-Encoded large proteins
by Kazusa Human cDNA Project
Protein databases
Protein databases
- Comprehensive catalogs
- UniProt
@EBI, SIB and PIR
- The world's most comprehensive catalog of information on proteins.
- Human Protein Reference Database
@Institute of Bioinformatics, USA
- Integrated database of information on human proteins,
domain architecture,
post-transcriptional modifications, interaction networks and disease association.
- Protein families, domains
- InterPro
@EBI, UK
- the database of protein families, domains and functional sites.
- Pfam
@Sanger Institute, UK
- the database of protein families, domains and functional sites.
- SMART
@EMBL, Germany
- the database of protein domain architectures.
- Transcription factors
- TRANSFAC
@BIOBASE, Germany
- the database of known 3D structures of proteins and nucleic acids
- Protein tertiary/quarternary structures
- PDBsum
@EBI, UK
- the database of known 3D structures of proteins and nucleic acids
- GTOP database
@NIG, Japan
- database of sequence/3D structure search analysis of proteins identified by various genome sequencing projects
Gene/Protein expression databases
Gene/Protein expression databases
- Data repositories (mainly microarrays)
- Gene Expression Omnibus (GEO)
@NCBI, USA
- A gene expression/molecular abundance repository
- ArrayExpress
@EBI, UK
- A public repository for microarray data
- CIBEX
@NIG, Japan
- A gene expression database system
- PRIDE
@EBI, UK
- A public repository for proteomic data
- Expression profile analyses
- Riken Expression Array Database
@GSC, RIKEN, Japan
- expression data by FANTOM clone cDNA microarray
- RefExA
@The University of Tokyo, Japan
- A comprehensive database of Gene Expression Profiles of
various tissues,organs and experiments on human.
- GNF SymAtlas
@Genome Institute of Novartis Research Foundation, USA
- A web-application for publishing experimental gene functionalization datasets
integrated with a flexibly searchable gene-centric database of public and
proprietary annotations.
- GeneNote
@Weizmann Institute of Science, Israel
- A database of human genes and their expression profiles in healthy tissues.
- InGaP
@Kazusa DNA Research Institute, Japan
- A database for Gene/Protein expression profiles using mKIAA cDNA microarray
and anti-mKIAA antibodies.
- Cell Montage
@CBRC, Japan
- Tools for searching and comparing of gene expression profiles.
Microarray data analyses
Microarray data analyses
- Web applications
- Onto-Tools
@ISBL, USA
- Tools for gene list classification with Gene Ontology
- GOToolBox
@LGPD, France
- A Tool for gene list classification with Gene Ontology
- Softwares
- GOMiner
@NIH, USA
- A standalone program written in Java for gene list classification with Gene Ontology.
Any platform.
- Cluster
@Eisen Lab in UCB, USA
- Microarray data clustering, also several useful programs available from this site.
- Java Treeview
@Eisen Lab in UCB, USA
- An open source, extensible viewer for microarray data.
Pathway
Pathway
- Databases
- NetPath
@Johns Hopkins University, USA and
Institute of Bioinformatics, India
- A curated resource of signal transduction pathways in humans.
- KEGG PATHWAY
@Kyoto University, Japan
- A collection of manually drawn pathway maps representing their
knowledge on the molecular interaction and reaction networks.
- Signaling Pathway Database
@Kyushu University, Japan
- An integrated database for genetic information and signal transduction systems.
- Cytokine Signaling Pathway Database
@Kumamoto University, Japan
- A database of signaling pathways of cytokines.
- Applications
- GenMAPP
@UCSF, USA
- A free appplication designed to visuallize gene expression and other
genomic resource
on maps representing biological pathways and grouping of genes.
Miscellaneous
Miscellaneous
-
- Sequence Manipulation Suite
@Bioinformatics Organization, Inc., USA
- A collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.
- Gene's Now
@The University of Tokyo, Japan
- A collection of links to functional-genomics related sites.
