release-updates

Data

This page lists all data sources loaded along with the date the data was downloaded and related publication. NOTE: All external links open in a new window.

Data CategoryDescriptionOrganismSourcePubMedLink

Genes

Maize Community Gene Set Z. mays (B73_RefGen_v4) Release 36 - Jun 2017 Lawrence et al - PubMed 14681441
Jiao et al. - PubMed 28605751
maizeGDB Genomes
Maize Community Gene Set Z. mays (B73_RefGen_v3) Release 21 - Dec 2013 Law et al - PubMed 25384563
Lawrence et al - PubMed 14681441
maizeGDB Genomes
NCBI Annotation Z. mays (B73_RefGen_v4) RefSeq AR102 - Dec 2017 O'Leary et al - PubMed 26553804 NCBI FTP

Homology

Orthologue and paralogue relationships A. tauschii
A. thaliana
B. distachyon
H. vulgare
O. barthii
O. brachyantha
O. glaberrima
O. glumaepatula
O. indica
O. longistaminata
O. meridionalis
O. nivara
O. punctata
O. rufipogon
O. sativa
S. italica
T. aestivum
T. urartu
S. bicolor
Z. mays
Plant Ensembl Compara, Version 36 - Jun 2017 Howe et al - PubMed 31598706 http://plants.ensembl.org/index.html

Proteins

Protein Annotations from UniProt Z. mays UniProt Version 70, release 2018-10 - Nov 2018 UniProt Consortium - PubMed 30395287 UniProt FTP
Protein family and domain assignments to proteins from InterPro Z. mays InterPro release 71, 2018-10 - Nov 2018 Mitchell et al - PubMed 30398656 InterPro FTP

Ontologies

Evidence Ontology Release 2017-08-04 Chibucos et al - PubMed 25052702 ECO
Gene Ontology Release 2017-05-20 The Gene Ontology Consortium - PubMed 30395331 GO
Plant Ontology Release 2017-02-02 Cooper et al - PubMed 23220694 PO
Sequence Ontology Release Nov 2019 Eilbeck et al - PubMed 15892872 SO

Gene Ontology

GO annotations Z. mays GOA at UniProt - 2018-11-06 Huntley et al - PubMed 25378336
GO Consortium Annotation FTP

Pathways

Pathway information A. thaliana
Z. mays
(B73_RefGen_v4)
Plant Reactome, release 52 - Nov 2016 Tello-Ruiz MK et al - PubMed 26553803 Reactome Gramene FTP
Pathway information Z. mays (RefSeq) KEGG - Nov 2017 Kanehisa M et al - PubMed 30321428 KEGG
Pathway information Z. mays (B73_RefGen_v4) CornCyc 8.0 - Dec 2018 Walsh JR et al - PubMed 27899149 CornCyc FTP

Publications

A mapping from genes to publications Z. mays UniProt publications - Nov 2018 UniProt Knowledgebase - PubMed 28150232

Gene Expression

Gene expression computed on reference gene set RefSeq, AGPv3 and AGPv4 Z. mays NCBI SRA - Nov 2017 Stelpflug et al - PubMed 27898762
Sekhon et al - PubMed 23637782
NCBI BioProject 171684

Variation

SNP data for Zea mays Z. mays (B73_RefGen_v4) dbSNP build 151 - Oct 2017 Sherry et al - PubMed 11125122 NCBI FTP

Genome Assembly

Chromosome Assembly Z. mays (B73_RefGen_v4) B73_RefGen_v4 (GCF_000005005.2) - Feb 2017 Jiao et al - PubMed 28605751 NCBI FTP
Chromosome Assembly Z. mays (B73_RefGen_v3) B73_RefGen_v3 (GCF_000005005.1) - Oct 2013 Schnable et al - PubMed 19965430 Ensembl Genomes FTP

Maize Community Datasets

maize-Gamer GO Annotations Z. mays (B73_RefGen_v3) maize-Gamer - Apr 2018 Wimalanathan et al - PubMed 31245718 https://download.maizegdb.org/GeneFunction_and_Expression/Maize-GAMER/
Ds insertion sites Z. mays (B73_RefGen_v3) Brutnell Lab Ds Insertions - Dec 2013 Vollbrecht et al - PubMed 20581308 https://download.maizegdb.org/Insertions/AcDs_Vollbrecht/
UniformMu Flanking Sequence Tags Z. mays (B73_RefGen_v3) McCarty Lab UniformMU FSTs, release 8 - Mar 2016 Settles et al - PubMed 17490480 https://download.maizegdb.org/Insertions/UniformMu/
Mu insertion sites Z. mays Barkan Lab Mu Insertions
B73_RefGen_v3 - Dec 2013
B73_RefGen_v4 - Jun 2017
Williams-Carrier et al - PubMed 20409008 https://download.maizegdb.org/Insertions/Mu_Illumina/
EMS mutation sites Z. mays Zhang Lab EMS mutations
B73_RefGen_v3 - Mar 2018
B73_RefGen_v4 - Jun 2018
Lu et al - PubMed 29223623 https://download.maizegdb.org/Diversity_and_Maps/Mutations/EMS/
SNP alias ids Z. mays Illumina 50K SNP Chip
B73_RefGen_v3 - Dec 2013
B73_RefGen_v4 - Jun 2017
Ganal et al - PubMed 22174790 https://download.maizegdb.org/Diversity_and_Maps/SNPs/50KSNP_Illumina_v3/