专栏名称: VG生信软件

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生信学者需要知道的100个数据库|NAR

VG生信软件 · 公众号 · · 2017-09-30 14:29

正文

16年底，Nucleic Acids Research ( NAR ) 上共收录152篇与数据库相关的文章，其中，有54个数据库是之前没有新开发出来的，98个数据库进行升级，还有16篇处于待发表状态，这些数据库涵盖基因组结构、基因表达及其调控、蛋白质、蛋白质结构域和蛋白质-蛋白质相互作用等。近年来，数据库的一个趋势倾向于处理人类健康从癌症突变到药物和药物靶标，由此也可以看出来，已开始从科研层面向应用层面转变，越来越贴近人们健康。同时，NAR评审员和编辑选定三个数据库作为“突破性贡献”，它们主要是涵盖人类从头基因变型，模式生物中的疾病相关表型和用于治疗靶标识别和验证的生物信息学平台，预计这些数据库将会吸引更多的遗传学和基因组学领域工作的研究人员的关注。

以下是最新发表的50多个数据库的链接地址及功能描述。

Database name	Brief descriptiona	URL
3DSNP	Human noncoding SNPs: interactions with genes and other SNPs	http://biotech.bmi.ac.cn/3dsnp/
AAgAtlas	Human AutoAntigen database	http://aagatlas.ncpsb.org
ADPriboDB	ADP-ribosylated proteins and sites	http://adpribodb.leunglab.org/
antiSMASH	antibiotics and Secondary Metabolite Analysis SHell	http://antismash-db.secondarymetabolites.org
AraPheno	Phenotypic data for Arabidopsis thaliana	https://arapheno.1001genomes.org
ccNET	Co-expression networks for diploid and polyploid Gossypium	http://structuralbiology.cau.edu.cn/gossypium/
CeNDR	C. elegans Natural Diversity Resource	http://www.elegansvariation.org
CGDB	Circadian Gene database	http://cgdb.biocuckoo.org/
CistromeDB	ChIP-Seq and DNase-Seq data in human and mouse	http://cistrome.org/db
Coexpedia	Gene co-expression data mapped to medical subject headings (MeSH).	http://www.coexpedia.org
dbSAP	Single Amino acid Polymorphisms: SNP-derived variation in human proteins	http://www.megabionet.org/dbSAP
denovo-db	Human de novo gene variants detected by parent-child sequencing	http://denovo-db.gs.washington.edu
DrugCentral	Active ingredients of approved pharmaceutical products, indications and mode of action	http://drugcentral.org
EURISCO	European catalogue for plant genetic resources	http://eurisco.ecpgr.org/
ExAC browser	Exome Aggregation Consortium sequence data	http://exac.broadinstitute.org
Exposome-Explorer	Biomarkers of exposure to disease risk factors	http://exposome-explorer.iarc.fr
FAIRDOMHub	Findable, Accessible, Interoperable and Reusable Data, Operating procedures and Models	https://fairdomhub.org/
FuzDB	Database of fuzzy protein complexes	http://protdyn-database.org
GenomeCRISPR	High-throughput screening using the CRISPR/Cas-9 system	http://genomecrispr.org
GTRD	Gene Transcription Regulation Database	http://gtrd.biouml.org
HieranoiDB	Ortholog groups and trees inferred by Hieranoid2 software	http://hieranoidb.sbc.su.se/
IGSR	International Genome Sample Resource	http://www.1000genomes.org/data-portal
IMG/VR	DOE Joint Genome Institute Viral Resource	https://img.jgi.doe.gov/vr/
JET2 Viewer	viewer/ Joint Evolutionary Trees: protein-protein interaction patches in known structures	http://www.lcqb.upmc.fr/jet2
jPOSTrepo	Japanese ProteOme STandard repository	https://repository.jpostdb.org/
KERIS	Kaleidoscope of gEne Responses to Inflammation among Species	http://igenomed.org/KERIS
LinkProt	Topologically complex protein structures	http://linkprot.cent.uw.edu.pl/
LNCediting	RNA editing sites in lncRNAs from human, monkey, mouse and fly	http://bioinfo.life.hust.edu.cn/LNCediting/
MEGaRes	Mechanisms of antimicrobial resistance	https://meg.colostate.edu/MEGaRes/
Membranome	A database of single-pass membrane proteins	http://membranome.org/
MethSMRT	DNA methylation data from Single Molecule, Real-Time sequencing	http://sysbio.sysu.edu.cn/methsmrt
mirDNMR	Background de novo mutation rates in human genes	https://www.wzgenomics.cn/mirdnmr/
Monarch Initiative	Human disease-related genotypes and phenotypes in model organisms	http://monarchinitiative.org
MRPrimerV	PCR primer pairs for detecting RNA virus-mediated infectious diseases	http://infolab.dgist.ac.kr/MRPrimerV
mutLBSgeneDB	Mutations in Ligand Binding Sites gene DataBase	http://www.zhaobioinfo.org/mutLBSgeneDB/
NSDNA	Nervous System Disease NcRNA Atlas	http://www.bio-bigdata.net/nsdna/
Ontobee	Ontology database server of OBO Foundry	http://www.ontobee.org/
Open Targets	Target validation platform: links between potential drug targets and diseases	https://targetvalidation.org
pathDIP	Pathway data integration and analysis portal	http://ophid.utoronto.ca/pathDIP
PathoYeastract	Transcription regulation in pathogenic yeasts	http://pathoyeastract.org/index.php
PceRBase	Plant competing endogenous RNAs	http://bis.zju.edu.cn/pcernadb/index.jsp
Pharos	Data on unstudied and understudied drug targets	https://pharos.nih.gov/idg/index
PLaMoM	Plant Mobile Macromolecules: Extracellular siRNAs, microRNAs, mRNAs and proteins in plants	http://www.byanbioinfo.org/plamom/
Plant Reactome	Plant metabolic, regulatory and signaling pathways	http://plantreactome.gramene.org/
PMDBase	Plant microsatellites and marker development	http://www.sesame-bioinfo.org/PMDBase
POSTAR	Post-transcriptional regulation by RNA-binding proteins	http://POSTAR.ncrnalab.org
proGenomes	Consistently annotated bacterial and archaeal genomes	http://van.embl.de/progene/
Proteome-pI	Pre-computed isoelectric points for >5000 proteomes	http://isoelectricpointdb.org/
REDIportal	A-to-I RNA editing events in human	http://srv00.recas.ba.infn.it/atlas/
RNALocate	RNA localization in the cell	http://www.rna-society.org/rnalocate/
SNP2TFBS	Regulatory SNPs affecting predicted transcription factor binding sites	http://ccg.vital-it.ch/snp2tfbs/:
SoyNet	Co-functional networks for soy bean Glycine max	http://www.inetbio.org/soynet/
TFBSbank	Transcription Factor Binding Site profiles deduced from ChIP-seq or ChIP-chip data	http://tfbsbank.co.uk/
TSTMP	Target Selection database for human TransMembrane Proteins	http://tstmp.enzim.ttk.mta.hu
Uniclust	Clustered protein sequences and multiple sequence alignments	http://uniclust.mmseqs.com/
WERAM	Writers, Erasers and Readers of histone Acetylation and Methylation	http://weram.biocuckoo.org/

注：可能有些网站失效

下面是回顾汇总12年来全社会广泛使用的具有权威性，全面性和便利性的数据库。小编觉得数据库不仅可以提高个人知名度和权威性，还可以推动加速科研产出造福人类。

Database name	Current URL	Brief description
Annual updates
DDBJ	http://www.ddbj.nig.ac.jp	All known nucleotide and protein sequences
ENA	http://www.ebi.ac.uk/ena	All known nucleotide and protein sequences
GenBank	https://www.ncbi.nlm.nih.gov/genbank/	All known nucleotide and protein sequences
Ensembl	http://www.ensembl.org/	Annotated information on eukaryotic genomes
Mouse Genome Database	http://www.informatics.jax.org	Mouse genome database
UCSC Genome Browser	http://genome.ucsc.edu/	A universal genome viewing and analysis platform
UniProt	http://www.uniprot.org	A universal database of protein sequences (includes Swiss-Prot and TrEMBL)
Regular updates
ArrayExpress	http://www.ebi.ac.uk/arrayexpress	Array-based gene expression data
BioCycd	http://biocyc.org/	Pathway information for sequenced
BioGRID	http://www.thebiogrid.org	Genetic and physical interactions in yeast, worm and fly
BRENDA	http://www.brenda-enzymes.info	Enzyme names and biochemical properties
CGD	http://www.candidagenome.org/	Candida Genome Database
CanSAR	http://cansar.icr.ac.uk	Cancer research and drug discovery resource
CATH	http://www.cathdb.info	Protein domain structure database
CAZy	http://www.cazy.org	Carbohydrate-Active enZymes database
CDD	http://www.ncbi.nlm.nih.gov/cdd	Conserved Domain Database
ChEBI	http://www.ebi.ac.uk/chebi	Chemical Entities of Biological Interest
ChEMBL	https://www.ebi.ac.uk/chembldb	Interaction of drugs and compounds with their targets
ChimerDB	http://ercsb.ewha.ac.kr/fusiongene	Chromosome translocations and gene fusions
COG	http://www.ncbi.nlm.nih.gov/COG	Clusters of Orthologous Groups of proteins
Comparative Toxicogenomics Database	http://ctdbase.org	A knowledgebase for curated chemical-gene-disease networks
COSMIC	http://cancer.sanger.ac.uk	Catalogue of Somatic Mutations in Cancer
CyanoBase	http://genome.microbedb.jp/cyanobase	Cyanobacterial genomes
dbPTM	http://dbPTM.mbc.nctu.edu.tw/	Post-translational modification of proteins
DBTSS	http://dbtss.hgc.jp/	Database of transcriptional start sites
DEG	http://www.essentialgene.org	Database of essential genes
DictyBase	http://dictybase.org	Model organism database for Dictyostelium discoideum
DrugBank	http://www.drugbank.ca/	Drug and drug target database
EcoCyc	http://ecocyc.org/	E. coli K12 genes, metabolic pathways, transporters, and gene regulation
eggNOG	http://eggnog.embl.de/	Evolutionary genealogy of genes:Non-supervised Orthologous Groups
ELM	http://elm.eu.org/	Eukaryotic Linear Motif: functional sites in eukaryotic proteins
EMAGE	http://www.emouseatlas.org/emage/	e-Mouse Atlas of Gene Expression
ENCODE project at UCSC	http://genome.ucsc.edu/ENCODE	Encyclopedia of DNA Elements,functional elements in human genome
EPD	http://epd.vital-it.ch	Eukaryotic Promoter Database
EuPathD	http://eupathdb.org/	Unified genome databases on eukaryotic pathogens (includes PlasmoDB, ToxoDB, ApiDB,TrichDB, TriTrypDB, GiardiaDB,etc.)
Expression Atlas	http://www.ebi.ac.uk/gxa/	Dene expression patterns deduced from microarray and RNA-seq data
FANTOM	http://fantom.gsc.riken.jp/	Functional annotation of mouse full-length cDNA clones
FINDBase	http://www.findbase.org	Frequencies of INherited Disorders
FlyBase	http://flybase.org/	Drosophila sequences and genomic information
FlyRNAi	http://flyrnai.org/	Genome-wide RNAi analysis in Drosophila
Gene3D	http://gene3d.biochem.ucl.ac.uk	Structural domain assignments for protein sequences
Genenames	http://www.genenames.org/	The HGNC human gene nomenclature database
GenomeRNAi	http://www.genomernai.org	RNA interference data for human and Drosophila
GEO	http://www.ncbi.nlm.nih.gov/geo/	NCBI’s Gene Expression Omnibus
GO	http://www.geneontology.org	Gene Ontology Database
GOA	http://www.ebi.ac.uk/GOA	Gene Ontology annotations for proteins in UniProt
GOLD	https://gold.jgi.doe.gov/	Genomes online database: completed and ongoing genome projects
GPCRdb	http://gpcrdb.org/	Data and tools for studying G protein-coupled receptors
Gramene	http://www.gramene.org	Comparative genomics of crops and model plant species
GXD	http://www.informatics.jax.org/expression.shtml	Mouse Gene Expression Database
HAMAP	http://hamap.expasy.org/	High-quality Automated and Manual Annotation of Proteins
HMDB	http://www.hmdb.ca	Human Metabolome Database
IEDB	http://www.iedb.org/	Immune Epitope Database
IMG/M	http://img.jgi.doe.gov/m	JGI’s Integrated Microbial Genomics and Metagenomics
IMGT	http://www.imgt.org	International ImMunoGeneTics database.
InParanoid	http://InParanoid.sbc.su.se	Orthologous relationships between eukaryotic proteomes
IntAct	http://www.ebi.ac.uk/intact/	Protein–Protein INTerACTion data
InterPro	http://www.ebi.ac.uk/interpro	Integrated resource of protein families, domains and functional sites
IPD	http://www.ebi.ac.uk/ipd	Immuno Polymorphism database (includes IMGT/HLA)
JASPAR	http://jaspar.genereg.net/	PSSMs for transcription factor DNA-binding sites
KEGG	http://www.genome.ad.jp/kegg	Kyoto Encyclopedia of Genes and Genomes: genes, proteins, pathways
MEROPS	http://merops.sanger.ac.uk/	Database of proteases (peptidases)
MetaCyc	http://metacyc.org/	Metabolic pathways and enzymes in various organisms
miRBase	http://www.mirbase.org/	MicroRNA sequences, names and predicted targets in animals
miRGator	http://mirgator.kobic.re.kr	MicroRNA expression profiles and mRNA targets
miRGen	http://www.microrna.gr/mirgen	MicroRNA promoters and transcription start sites
miRTarBase	http://miRTarBase.mbc.nctu.edu.tw/	Experimentally validated microRNA–target interactions
MMDB	http://www.ncbi.nlm.nih.gov/Structure	Molecular Modeling Database of protein structures
MODOMICS	http://genesilico.pl/modomics/	RNA modification pathways
Mouse Tumor Biology Database	http://tumor.informatics.jax.org/mtbwi/	Mouse as a model system of human cancers
neXtProt	https://www.nextprot.org/	A database of human proteins
NONCODE	http://noncode.org/	A database of noncoding RNAs
OMIM	http://www.omim.org	Online Mendelian inheritance in man: A catalog of human genetic and genomic disorders
OrthoDB	http://www.orthodb.org	An hierarchical catalog of orthologous proteins
PANTHER	http://www.pantherdb.org	Protein sequence evolution mapped to functions and pathways
PATRIC	http://www.patricbrc.org	PathoSystems Resource Integration Center
PDB	http://rcsb.org/pdb	Protein DataBank: All biological macromolecular structures
PDBe	http://www.ebi.ac.uk/pdbe/	Protein Databank in Europe
PDBsum	http://www.ebi.ac.uk/pdbsum	Summaries and analyses of PDB structures
Pfam	http://pfam.xfam.org	Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains
PHI-base	http://www4.rothamsted.bbsrc.ac.uk/phibase/	Genes affecting fungal pathogen–host interactions
PIR	http://pir.georgetown.edu/	Protein Information Resource, part of UniProt
PRIDE	http://www.ebi.ac.uk/pride/	Proteomics peptide identification database
PRINTS	http://www.bioinf.man.ac.uk/dbbrowser/PRINTS	Protein fingerprints, conserved motifs used to characterise a protein family
Prosite	http://www.expasy.org/prosite	Biologically-significant protein patterns and profiles
PubChem	http://pubchem.ncbi.nlm.nih.gov/	Structures and biological activities of small organic molecules
RGD	http://rgd.mcw.edu/	Rat Genome Database
RDP	http://rdp.cme.msu.edu	Ribosomal Database Project:Bacterial and archaeal 16S rRNA and fungal 28S rRNA sequences
Reactome	http://www.reactome.org	A database of metabolic and signaling pathways
REBASE	http://rebase.neb.com/rebase/	Restriction enzyme database
RefSeq	https://www.ncbi.nlm.nih.gov/refseq/	NCBI Reference Sequence Database
Rfam	http://rfam.xfam.org	RNA families with multiple sequence alignments
SCOP	http://scop.mrc-lmb.cam.ac.uk/	Structural Classification Of Proteins
SGD	http://www.yeastgenome.org	Saccharomyces Genome Database
SILVA	http://www.arb-silva.de/	Aligned small- and large subunit rRNA sequences
SIMAP	http://mips.gsf.de/simap/	Similarity Matrix of Proteins
SMART	http://smart.embl-heidelberg.de	Simple Modular Architecture Research Tool: signalling,extracellular and chromatin-associated protein domains
STITCH	http://stitch-db.org/	Search Tool for Interactions of Chemicals
STRING	http://string.embl.de/	Predicted functional associations between proteins
SUPERFAMILY	http://supfam.org	Genome-wide identification of protein domains of known structure
SWISS-MODEL	http://swissmodel.expasy.org/	3D models for proteins of unknown structure
TAIR	http://www.arabidopsis.org/	The Arabidopsis information resource
TarBase	http://microrna.gr/tarbase	Database of experimentally supported microRNA targets
TCDB	http://www.tcdb.org/	Transporter protein classification database
UCSC Cancer Genomics Browser	https://genome-cancer.ucsc.edu/	Visualization of cancer genomic datasets
VectorBase	https://www.vectorbase.org/	Invertebrate vectors of human pathogens
WormBase	http://www.wormbase.org	Community portal on all aspects of C. elegans biology
XenBase	http://www.xenbase.org	Xenopus frog database
YEASTRACT	http://www.yeastract.com	Transcriptional regulation in Saccharomyces cerevisiae
ZFIN	http://zfin.org/	Zebrafish information network

参考文献

1.Galperin M Y, Fernándezsuárez X M, Rigden D J. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes[J]. Nucleic Acids Research, 2017, 45(Database issue):D1-D11.