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 AGPv4 Lawrence et al - PubMed 14681441
Jiao et al. - PubMed 28605751
MaizeGDB Genomes
Maize Community Gene Set Z. mays AGPv3 Law et al - PubMed 25384563
Lawrence et al - PubMed 14681441
MaizeGDB Genomes
NCBI Annotation (RefSeq and Gene) Z. mays RefSeq 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
(AGPv4)
Plant Ensembl Compara Howe et al - PubMed 31598706 Plant Ensembl Compara

Proteins

Protein Annotations from UniProt Z. mays UniProt - Release 2017-02 UniProt Consortium - PubMed 30395287 UniProt FTP
Protein family and domain assignments to proteins from InterPro Z. mays InterPro Version 62 Mitchell et al - PubMed 30398656 InterPro FTP

Ontologies

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

Gene Ontology

GO annotations Z. mays GOA at UniProt (GOC Validation Date: 12/16/2016) Huntley et al - PubMed 25378336
GO Consortium Annotation FTP

Pathways

Pathway information A. thaliana
Z. mays
(AGPv4)
Plant Reactome - release 52 Tello-Ruiz MK et al - PubMed 26553803 Reactome Gramene FTP
Pathway information Z. mays (RefSeq) KEGG data set Kanehisa M et al - PubMed 30321428 KEGG
Pathway information Z. mays (AGPv4) CornCyc 8.0 Walsh JR et al - PubMed 27899149 CornCyc 8.0 at MaizeGDB

Publications

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

Gene Expression

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

Variation

dbSNP data for Zea mays Z. mays dbSNP build 151 Sherry et al - PubMed 11125122 NCBI FTP

Genome Assembly

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

Maize Community Datasets

maize-Gamer GO Annotations Z. mays (AGPv4) maize-Gamer Wimalanathan et al - PubMed 31245718
Ds insertion sites Z. mays Brutnell Lab Ds Insertions Vollbrecht et al - PubMed 20581308
UniformMu Flanking Sequence Tags Z. mays McCarty Lab UniformMU FSTs Settles et al - PubMed 17490480
Mu insertion sites Z. mays Barkan Lab Mu Insertions Williams-Carrier et al - PubMed 20409008
EMS mutation sites Z. mays Zhang Lab EMS mutations Lu et al - PubMed 29223623
SNP alias ids Z. mays Illumina 50K SNP Chip Ganal et al - PubMed 22174790