[转载]人类和其他脊椎动物基因组

7. Human and other Vertebrate Genomes
7.1. Model organisms, comparative genomics
ABA	Ascidian body atlas: digital 3D model of ascidian development	http://ciona.lab.nig.ac.jp/ascidian/top.html
AgBase	GO annotations for agriculturally important plants and animals	http://www.agbase.msstate.edu/
AllGenes	Human and mouse gene, transcript and protein annotation	http://www.allgenes.org
Animal Genome Size Database	Genome sizes of vertebrates and invertebrates	http://www.genomesize.com
AnimalQTLdb	Quantitative trait loci in livestock animals	http://www.animalgenome.org/QTLdb/
ArkDB	Genome databases for farm and other animals	http://www.thearkdb.org/
BodyMap	Human and mouse gene expression data	http://bodymap.ims.u-tokyo.ac.jp/
BodyMap-Xs	Cross-species comparison of vertebrate gene expression	http://bodymap.jp/
ChickVD	Sequence variation in the chicken genome	http://chicken.genomics.org.cn
Cre Transgenic DB	Cre transgenic mouse lines with links to publications	http://www.mshri.on.ca/nagy/
CORG	COmparative Regulatory Genomics: conserved non-coding blocks	http://corg.molgen.mpg.de
DBTGR	Database of tunicate Ciona gene regulation	http://dbtgr.hgc.jp/
DED	Database of evolutionary distances	No longer maintained
Edinburgh Mouse Atlas	Digital atlas of mouse embryonic development	http://genex.hgu.mrc.ac.uk
EGO	Eukaryotic Gene Orthologs	http://compbio.dfci.harvard.edu/tgi/ego/
Ensembl	Annotated information on eukaryotic genomes	http://www.ensembl.org/
euGenes	Genomic Information for Eukaryotic Organisms	http://eugenes.org/
EuroPhenome	Large-scale phenotyping of knockout mouse lines	http://www.europhenome.eu
GALA	Genomic alignment, annotation and experimental results	http://gala.cse.psu.edu/
Gallus Gbrowse	Genomic information on chicken and other avian species	http://birdbase.net/
GEISHA	Gallus expression in situ hybridization analysis	http://geisha.arizona.edu
GXD	Mouse Gene Expression Database	http://www.informatics.jax.org/menus/expression_menu.shtml
HomoloGene	Automatically detected homologous genes in complete eukaryotic genomes	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
Homophila	Drosophila homologs of human disease genes	http://superfly.ucsd.edu/homophila/
KOG	Eukaryotic Orthologous Groups of proteins	http://www.ncbi.nlm.nih.gov/COG/
MamPol	Mammalia Polymorphism Database	http://mampol.uab.es
MFunGD	MIPS mouse functional genomics database	http://mips.gsf.de/genre/proj/mfungd
Mouse Genome DB	Formerly mouse genome database	http://www.informatics.jax.org
Mouse Phenome DB	phenotypic and genotypic data from inbred strains of mice	http://www.jax.org/phenome
Mouse SAGE	SAGE libraries from various mouse tissues and cell lines	http://mouse.biomed.cas.cz/sage
Mouse Transposon Insertion Database	Mouse Transposon Insertion Database	http://mouse.ccgb.umn.edu/transposon/
Mouse Tumor Biology	Tumor types, genes, classification, incidence, pathology	http://tumor.informatics.jax.org
Non-Human Genome Segmental Duplication DB	Segmental duplications in mouse, dog and chicken genomes	http://projects.tcag.ca/xenodup
OMIA	Online Mendelian Inheritance in Animals	http://omia.angis.org.au/
ParaDB	Paralogy mapping in human genomes	http://abi.marseille.inserm.fr/paradb/
PathBase	European mutant mice histopathology database: images	http://www.pathbase.net/
PBmice	piggyBac transposon insertions in the mouse genome.	http://www.scbit.org/PBmice/
PEDE	Pig Expression Data Explorer: Pig cDNA libraries and ESTs	http://pede.dna.affrc.go.jp
PigGIS	Pig genome mapping, genes and ESTs	http://pig.genomics.org.cn/
Rat Genome Database	Rat genetic and genomic data	http://rgd.mcw.edu
RatMap	Rat genome tools and data	http://ratmap.org
RTCGD	Retroviral Tagged Cancer Gene Database	http://rtcgd.ncifcrf.gov/
SPEED	Searchable prototype experimental evolutionary database	http://bioinfobase.umkc.edu/speed/speed_main.htm
TAED	The Adaptive Evolution Database: plant and chordate gene families	http://www.bioinfo.no/tools/TAED
TreeFam	Tree families database: phylogenetic trees of animal genes	http://www.treefam.org
UniTrap	Unambiguous insertions in the same subgenic regions of annotated mouse genes	http://unitrap.cbm.fvg.it/
UTGB/medaka	University of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data	http://medaka.utgenome.org/
VEGA	Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences	http://vega.sanger.ac.uk/
XenBase	Xenopus genomics resource	http://www.xenbase.org
ZFIN	Zebrafish information network	http://zfin.org/
7.2. Human genome databases, maps and viewers
ENCODE Project	Encyclopedia of DNA Elements, all functional elements in the human genome	http://genome.ucsc.edu/ENCODE
GDB	Human genes and genomic maps	http://www.gdb.org
Gene Resource Locator	Alignment of ESTs with finished human sequence	No longer maintained
GeneAnnot	Revised annotation of Affymetrix human gene probe sets	http://genecards.weizmann.ac.il/geneannot/
GeneCards	Integrated database of human genes, maps, proteins and diseases	http://bioinfo.weizmann.ac.il/genecards/
GeneLoc	Gene location database	http://genecards.weizmann.ac.il/geneloc/
GenMapDB	Mapped human BAC clones	http://genomics.med.upenn.edu/genmapdb
HOWDY	Human organized whole genome database	http://www-alis.tokyo.jst.go.jp/HOWDY/
Human BAC Ends DB	Non-redundant human BAC end sequences	http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html
Human Genome Seg-mental Duplication DB	Segmental duplications in the human genome	http://projects.tcag.ca/humandup
IXDB	Physical maps of human chromosome X	http://ixdb.mpimg-berlin-dahlem.mpg.de
Map Viewer	Display of genomic information by chromosomal position	http://www.ncbi.nlm.nih.gov/mapview/
QTL Matchmaker	Quantitative trait loci mapping in human, mouse and rat	http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp
RHdb	Radiation hybrid map data	http://www.ebi.ac.uk/RHdb
SKY/M-FISH and CGH	Fluorescent images of chromosomes and cytogenetic data	http://www.ncbi.nlm.nih.gov/sky/
The Chromosome 7 Annotation Project	Human chromosome 7 sequence and annotation	http://www.chr7.org
TRBase	Tandem repeats in the human genome	http://trbase.ex.ac.uk/
UCSC Genome Browser	Genome assemblies and annotation	http://genome.ucsc.edu/
UniSTS	Unified view of sequence tagged sites with mapping data	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
X:MAP	Annotation and visualization of genome structure for Affymetrix exon array analysis	http://xmap.picr.man.ac.uk
7.3. Human proteins
Consensus CDS	Collaborative effort to identify a core set of human proteins	http://www.ncbi.nlm.nih.gov/projects/CCDS/
Evola	Human genes and their vertebrate orthologs	http://jbirc.jbic.or.jp/hinv/evola/
FANTOM	Functional annotation of mouse full-length cDNA clones	http://fantom2.gsc.riken.go.jp
FLJ-DB	Annotated full-length human cDNAs (formerly HUNT database)	http://fldb.hgc.jp/cgi-bin/cDNA3/public/publication/index.cgi
GeneSpeed	Protein domains in the expressed human, mouse, fly and worm genes	http://genespeed.ccf.org
H-InvDB	Full-length human cDNA clones	http://www.h-invitational.jp/
Hoppsigen	Human and mouse homologous processed pseudogenes	http://pbil.univ-lyon1.fr/databases/hoppsigen.html
HPRD	Human protein reference database: domain architecture, post-translational modifications, and disease association	http://www.hprd.org
HUGE	Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences	http://www.kazusa.or.jp/huge/
IPI	International Protein Index	http://www.ebi.ac.uk/IPI
LIFEdb	Localization, interaction and functions of human proteins	http://www.dkfz.de/LIFEdb
Mammalian Gene Collection	Full-length open reading frame clones for human, mouse, and rat genes	http://mgc.nci.nih.gov/
NetAffx	Public Affymetrix probesets and annotations	http://www.affymetrix.com/
ORFDB	Collection of ORFs that are sold by Invitrogen	http://orf.invitrogen.com/
PlasmID	A repository for collection and distribution of plasmid clones	http://plasmid.hms.harvard.edu/
STACK	Sequence tag alignment and consensus knowledgebase	http://www.sanbi.ac.za/Dbases.html
SYSTERS	Systematic re-searching and clustering of proteins	http://systers.molgen.mpg.de/
trome, trEST, trGEN	Databases of predicted human protein sequences	ftp://ftp.isrec.isb-sib.ch/pub/databases/
UniGene	Unified clusters of ESTs and full-length mRNA sequences	http://www.ncbi.nlm.nih.gov/UniGene/

 

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