Volume 41, Issue D1
1 January 2013
ISSN 0305-1048
EISSN 1362-4962
Issue navigation
Volume 41, Issue D1, 1 January 2013
Database issue
Articles
The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1–D7, https://doi.org/10.1093/nar/gks1297
Tags:
dna, genome, genomics, molecular biology, nucleic acids
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D8–D20, https://doi.org/10.1093/nar/gks1189
The International Nucleotide Sequence Database Collaboration
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D21–D24, https://doi.org/10.1093/nar/gks1084
DDBJ new system and service refactoring
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D25–D29, https://doi.org/10.1093/nar/gks1152
Facing growth in the European Nucleotide Archive
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D30–D35, https://doi.org/10.1093/nar/gks1175
GenBank
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D36–D42, https://doi.org/10.1093/nar/gks1195
Update on activities at the Universal Protein Resource (UniProt) in 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D43–D47, https://doi.org/10.1093/nar/gks1068
Ensembl 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D48–D55, https://doi.org/10.1093/nar/gks1236
ENCODE Data in the UCSC Genome Browser: year 5 update
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D56–D63, https://doi.org/10.1093/nar/gks1172
Tags:
datasets, genome, genome, human, mice, encode consortium
The UCSC Genome Browser database: extensions and updates 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D64–D69, https://doi.org/10.1093/nar/gks1048
Dfam: a database of repetitive DNA based on profile hidden Markov models
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D70–D82, https://doi.org/10.1093/nar/gks1265
Tags:
benchmarking, consensus sequence, dna, genome, genome, human
SINEBase: a database and tool for SINE analysis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D83–D89, https://doi.org/10.1093/nar/gks1263
DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D90–D93, https://doi.org/10.1093/nar/gks990
Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D94–D100, https://doi.org/10.1093/nar/gks955
UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D101–D109, https://doi.org/10.1093/nar/gks1092
Tags:
genome, vertebrates, genes, candidate disease gene
APPRIS: annotation of principal and alternative splice isoforms
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D110–D117, https://doi.org/10.1093/nar/gks1058
Tags:
genes, protein isoforms
HEXEvent: a database of Human EXon splicing Events
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D118–D124, https://doi.org/10.1093/nar/gks969
SpliceAid-F: a database of human splicing factors and their RNA-binding sites
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D125–D131, https://doi.org/10.1093/nar/gks997
Tags:
rna, rna splicing, genes, rna splicing factors, binding sites
Spliceosome Database: a tool for tracking components of the spliceosome
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D132–D141, https://doi.org/10.1093/nar/gks999
Tags:
complex, genes, spliceosomes, rna splicing
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D142–D151, https://doi.org/10.1093/nar/gks1041
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D152–D156, https://doi.org/10.1093/nar/gks1062
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D157–D164, https://doi.org/10.1093/nar/gks1233
TFClass: an expandable hierarchical classification of human transcription factors
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D165–D170, https://doi.org/10.1093/nar/gks1123
Tags:
dna, genes, transcription factor, protein isoforms, genome
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D171–D176, https://doi.org/10.1093/nar/gks1221
Tags:
cell lines, chromatin, datasets, encode consortium, histones
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D177–D187, https://doi.org/10.1093/nar/gks1060
CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D188–D194, https://doi.org/10.1093/nar/gks1165
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D195–D202, https://doi.org/10.1093/nar/gks1089
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D203–D213, https://doi.org/10.1093/nar/gks1201
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D214–D220, https://doi.org/10.1093/nar/gks1145
Tags:
genome, oncogenes, mice, binding sites
NCBI Epigenomics: What’s new for 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D221–D225, https://doi.org/10.1093/nar/gks1171
Tags:
biotechnology, datasets, epigenetics, gene expression, genes
Rfam 11.0: 10 years of RNA families
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D226–D232, https://doi.org/10.1093/nar/gks1005
BSRD: a repository for bacterial small regulatory RNA
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D233–D238, https://doi.org/10.1093/nar/gks1264
Tags:
rna, genome, bacteria, host (organism), transcription factor
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D239–D245, https://doi.org/10.1093/nar/gks1246
Tags:
micrornas, verification, mice
LNCipedia: a database for annotated human lncRNA transcript sequences and structures
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D246–D251, https://doi.org/10.1093/nar/gks915
miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D252–D257, https://doi.org/10.1093/nar/gks1168
Darned in 2013: inclusion of model organisms and linking with Wikipedia
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D258–D261, https://doi.org/10.1093/nar/gks961
MODOMICS: a database of RNA modification pathways—2013 update
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D262–D267, https://doi.org/10.1093/nar/gks1007
Tags:
rna, nucleosides, enzymes, ribonucleosides, transfer rna
RNApathwaysDB—a database of RNA maturation and decay pathways
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D268–D272, https://doi.org/10.1093/nar/gks1052
Tags:
rna, molecule, catabolism, complex, enzymes
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D273–D279, https://doi.org/10.1093/nar/gks935
Voronoia4RNA—a database of atomic packing densities of RNA structures and their complexes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D280–D284, https://doi.org/10.1093/nar/gks1061
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D285–D294, https://doi.org/10.1093/nar/gks1238
Tags:
micrornas, rna, small, arm
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D295–D305, https://doi.org/10.1093/nar/gks1229
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D306–D311, https://doi.org/10.1093/nar/gks1230
MetalPDB: a database of metal sites in biological macromolecular structures
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D312–D319, https://doi.org/10.1093/nar/gks1063
Tags:
metals
eProS—a database and toolbox for investigating protein sequence–structure–function relationships through energy profiles
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D320–D326, https://doi.org/10.1093/nar/gks1079
SwissSidechain: a molecular and structural database of non-natural sidechains
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D327–D332, https://doi.org/10.1093/nar/gks991
Tags:
amino acids, biochemistry, bioinformatics, drug design, peptides
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D333–D337, https://doi.org/10.1093/nar/gks998
ValidNESs: a database of validated leucine-rich nuclear export signals
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D338–D343, https://doi.org/10.1093/nar/gks936
Tags:
leucine, chromosomes
New and continuing developments at PROSITE
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D344–D347, https://doi.org/10.1093/nar/gks1067
CDD: conserved domains and protein three-dimensional structure
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D348–D352, https://doi.org/10.1093/nar/gks1243
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D353–D357, https://doi.org/10.1093/nar/gks1239
Tags:
amino acid sequence, archaea, bacteria, eukaryotic cells, genes
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D358–D365, https://doi.org/10.1093/nar/gks1116
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D366–D376, https://doi.org/10.1093/nar/gks1241
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D377–D386, https://doi.org/10.1093/nar/gks1118
Tags:
genes, trees (plant), genome, inference, gene duplication
TIGRFAMs and Genome Properties in 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D387–D395, https://doi.org/10.1093/nar/gks1234
Tags:
genome
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D396–D401, https://doi.org/10.1093/nar/gks1091
ClusterMine360: a database of microbial PKS/NRPS biosynthesis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D402–D407, https://doi.org/10.1093/nar/gks993
DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D408–D414, https://doi.org/10.1093/nar/gks1177
Tags:
biosynthesis, gene clusters, genes, metabolites, enzymes
EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D415–D422, https://doi.org/10.1093/nar/gks1144
Tags:
dna, endonuclease, engineering, knowledge bases, peptides
ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D423–D429, https://doi.org/10.1093/nar/gks1154
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D430–D440, https://doi.org/10.1093/nar/gks1218
PeroxiBase: a database for large-scale evolutionary analysis of peroxidases
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D441–D444, https://doi.org/10.1093/nar/gks1083
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D445–D451, https://doi.org/10.1093/nar/gks1103
Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D452–D455, https://doi.org/10.1093/nar/gks1167
Tags:
dna, engineering, zinc fingers, persistence
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D456–D463, https://doi.org/10.1093/nar/gks1146
ChemProt-2.0: visual navigation in a disease chemical biology database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D464–D469, https://doi.org/10.1093/nar/gks1166
Glycan fragment database: a database of PDB-based glycan 3D structures
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D470–D474, https://doi.org/10.1093/nar/gks987
Tags:
polysaccharides, carbohydrates
The RCSB Protein Data Bank: new resources for research and education
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D475–D482, https://doi.org/10.1093/nar/gks1200
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D483–D489, https://doi.org/10.1093/nar/gks1258
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D490–D498, https://doi.org/10.1093/nar/gks1211
Tags:
catheterization
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D499–D507, https://doi.org/10.1093/nar/gks1266
Tags:
catheterization, genome, dissociative fugue, consensus
D2P2: database of disordered protein predictions
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D508–D516, https://doi.org/10.1093/nar/gks1226
Tags:
batteries, consensus, genome, proteome, trees (plant)
NPIDB: nucleic acid—protein interaction database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D517–D523, https://doi.org/10.1093/nar/gks1199
Tags:
complex, databases, dna, molecule, nucleic acids
PDBTM: Protein Data Bank of transmembrane proteins after 8 years
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D524–D529, https://doi.org/10.1093/nar/gks1169
Gene Ontology Annotations and Resources
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D530–D535, https://doi.org/10.1093/nar/gks1050
Tags:
genes, bioinformatics, community, internet, reasoning
dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D536–D544, https://doi.org/10.1093/nar/gks1080
Tags:
phenotype, genome, enzymes, genes, protein domains
Genenames.org: the HGNC resources in 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D545–D552, https://doi.org/10.1093/nar/gks1066
Tags:
genes, symbols, rna, pseudogenes, bioinformatics
The disease and gene annotations (DGA): an annotation resource for human disease
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D553–D560, https://doi.org/10.1093/nar/gks1244
BioGPS and MyGene.info: organizing online, gene-centric information
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D561–D565, https://doi.org/10.1093/nar/gks1114
HBVdb: a knowledge database for Hepatitis B Virus
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D566–D570, https://doi.org/10.1093/nar/gks1022
The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D571–D578, https://doi.org/10.1093/nar/gks984
ViralZone: recent updates to the virus knowledge resource
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D579–D583, https://doi.org/10.1093/nar/gks1220
HAMAP in 2013, new developments in the protein family classification and annotation system
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D584–D589, https://doi.org/10.1093/nar/gks1157
Tags:
uniprot knowledgebase
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D590–D596, https://doi.org/10.1093/nar/gks1219
Tags:
datasets, genes, rrna, taxonomic classification, internet, genes
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D597–D604, https://doi.org/10.1093/nar/gks1160
EcoCyc: fusing model organism databases with systems biology
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D605–D612, https://doi.org/10.1093/nar/gks1027
Tags:
genes, genome, systems biology, escherichia coli
EcoGene 3.0
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D613–D624, https://doi.org/10.1093/nar/gks1235
Tags:
genbank, genes, genome, pseudogenes, codon, initiator
ECMDB: The E. coli Metabolome Database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D625–D630, https://doi.org/10.1093/nar/gks992
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D631–D635, https://doi.org/10.1093/nar/gks1006
Tags:
genome
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D636–D647, https://doi.org/10.1093/nar/gks1194
Tags:
genes, genome, microscopes
metaMicrobesOnline: phylogenomic analysis of microbial communities
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D648–D654, https://doi.org/10.1093/nar/gks1202
Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D655–D659, https://doi.org/10.1093/nar/gks1137
SecReT4: a web-based bacterial type IV secretion system resource
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D660–D665, https://doi.org/10.1093/nar/gks1248
Tags:
bacteria, bodily secretions, dna, genes, genetics
The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D666–D675, https://doi.org/10.1093/nar/gks1119
Tags:
antibiotics, bacteria, clone cells, dna, engineering
dictyBase 2013: integrating multiple Dictyostelid species
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D676–D683, https://doi.org/10.1093/nar/gks1064
EuPathDB: The Eukaryotic Pathogen database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D684–D691, https://doi.org/10.1093/nar/gks1113
GenColors-based comparative genome databases for small eukaryotic genomes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D692–D699, https://doi.org/10.1093/nar/gks1176
Tags:
genome
Genomicus: five genome browsers for comparative genomics in eukaryota
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D700–D705, https://doi.org/10.1093/nar/gks1156
Tags:
genes, genome, plants, protists, vertebrates
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D706–D713, https://doi.org/10.1093/nar/gks1139
Tags:
apicomplexa, genes, genome, host (organism), libraries
CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D714–D719, https://doi.org/10.1093/nar/gks1163
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D720–D727, https://doi.org/10.1093/nar/gks1106
SchistoDB: an updated genome resource for the three key schistosomes of humans
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D728–D731, https://doi.org/10.1093/nar/gks1087
WDDD: Worm Developmental Dynamics Database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D732–D737, https://doi.org/10.1093/nar/gks1107
Tags:
cell growth, chromosomes, embryo, genes, helminthiasis
WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D738–D743, https://doi.org/10.1093/nar/gks1124
Tags:
caenorhabditis, genetics, genotype, helminthiasis, helminths
FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D744–D750, https://doi.org/10.1093/nar/gks1141
FlyBase: improvements to the bibliography
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D751–D757, https://doi.org/10.1093/nar/gks1024
Tags:
datasets, drosophila, drosophila melanogaster, genes, funding
MonarchBase: the monarch butterfly genome database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D758–D763, https://doi.org/10.1093/nar/gks1057
Tags:
butterflies, genome, genes
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D764–D772, https://doi.org/10.1093/nar/gks1049
The EBI enzyme portal
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D773–D780, https://doi.org/10.1093/nar/gks1112
Tags:
enzymes
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D781–D786, https://doi.org/10.1093/nar/gks1004
Tags:
metabolites, metabolomics, metadata, diet, arabidopsis
WholeCellKB: model organism databases for comprehensive whole-cell models
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D787–D792, https://doi.org/10.1093/nar/gks1108
The ConsensusPathDB interaction database: 2013 update
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D793–D800, https://doi.org/10.1093/nar/gks1055
Tags:
genes, graphical displays, metabolites, complex
HMDB 3.0—The Human Metabolome Database in 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D801–D807, https://doi.org/10.1093/nar/gks1065
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D808–D815, https://doi.org/10.1093/nar/gks1094
Tags:
internet, mining, transfer technique, genes
The BioGRID interaction database: 2013 update
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D816–D823, https://doi.org/10.1093/nar/gks1158
2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D824–D827, https://doi.org/10.1093/nar/gks1002
Tags:
affinity, atom, biophysics, complex, datasets
PrePPI: a structure-informed database of protein–protein interactions
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D828–D833, https://doi.org/10.1093/nar/gks1231
SynSysNet: integration of experimental data on synaptic protein–protein interactions with drug-target relations
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D834–D840, https://doi.org/10.1093/nar/gks1040
The TissueNet database of human tissue protein–protein interactions
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D841–D844, https://doi.org/10.1093/nar/gks1198
Tags:
genes, proton pump inhibitors
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D845–D853, https://doi.org/10.1093/nar/gks1159
ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D854–D860, https://doi.org/10.1093/nar/gks938
Tags:
animals, transgenic, genes, phenotype, zebrafish, genome
The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D861–D864, https://doi.org/10.1093/nar/gks946
Xenbase: expansion and updates of the Xenopus model organism database
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D865–D870, https://doi.org/10.1093/nar/gks1025
Tags:
gene expression, genes, genome, xenopus, antibodies
Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D871–D879, https://doi.org/10.1093/nar/gks1150
Tags:
farm animals, genome, quantitative trait loci, genes, cattle
H2DB: a heritability database across multiple species by annotating trait-associated genomic loci
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D880–D884, https://doi.org/10.1093/nar/gks1216
The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D885–D891, https://doi.org/10.1093/nar/gks1115
RhesusBase: a knowledgebase for the monkey research community
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D892–D905, https://doi.org/10.1093/nar/gks835
Tags:
cercopithecidae, community, exons, functional genomics, genes
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D906–D914, https://doi.org/10.1093/nar/gks1268
Tags:
functional genomics, genome, primates, rna, genes
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D915–D919, https://doi.org/10.1093/nar/gks1245
Tags:
genes, genome, dna, complementary, mendelian disorders, complex
Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D920–D924, https://doi.org/10.1093/nar/gks1082
Tags:
cancer, cytogenetics, genes, genetics, hematology
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D925–D935, https://doi.org/10.1093/nar/gks1173
dbVar and DGVa: public archives for genomic structural variation
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D936–D941, https://doi.org/10.1093/nar/gks1213
CellLineNavigator: a workbench for cancer cell line analysis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D942–D948, https://doi.org/10.1093/nar/gks1012
The UCSC Cancer Genomics Browser: update 2013
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D949–D954, https://doi.org/10.1093/nar/gks1008
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D955–D961, https://doi.org/10.1093/nar/gks1111
Tags:
biological markers, cancer, cell lines, datasets, drug response
The TP53 website: an integrative resource centre for the TP53 mutation database and TP53 mutant analysis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D962–D969, https://doi.org/10.1093/nar/gks1033
Tags:
mutation, protein p53, tp53 gene, cancer, neoplasms
TSGene: a web resource for tumor suppressor genes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D970–D976, https://doi.org/10.1093/nar/gks937
Tags:
cancer, gene expression, genes, methylation, mice
SomamiR: a database for somatic mutations impacting microRNA function in cancer
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D977–D982, https://doi.org/10.1093/nar/gks1138
Tags:
cancer, micrornas, mutation, somatic, mutation, genome
LncRNADisease: a database for long-non-coding RNA-associated diseases
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D983–D986, https://doi.org/10.1093/nar/gks1099
Tags:
bioinformatics, disease association, genome, micrornas, rna
ArrayExpress update—trends in database growth and links to data analysis tools
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D987–D990, https://doi.org/10.1093/nar/gks1174
NCBI GEO: archive for functional genomics data sets—update
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D991–D995, https://doi.org/10.1093/nar/gks1193
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D996–D1008, https://doi.org/10.1093/nar/gks1042
Tags:
brain, genes, gene expression, mice, datasets
CircaDB: a database of mammalian circadian gene expression profiles
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1009–D1013, https://doi.org/10.1093/nar/gks1161
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1014–D1020, https://doi.org/10.1093/nar/gks1014
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1021–D1026, https://doi.org/10.1093/nar/gks1170
Tags:
genes, guidelines, phenotype, rna interference, id
Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1027–D1033, https://doi.org/10.1093/nar/gks1155
HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1034–D1039, https://doi.org/10.1093/nar/gks1021
INTERFEROME v2.0: an updated database of annotated interferon-regulated genes
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1040–D1046, https://doi.org/10.1093/nar/gks1215
Tags:
genes, interferons, datasets, metadata, mice
METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1047–D1054, https://doi.org/10.1093/nar/gks886
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining
Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1055–D1062, https://doi.org/10.1093/nar/gks1186
Tags:
data mining, genes, genome, spermatogenesis, mice
