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 Category Description Link Source PubMed Link

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

EnsemblCompara Plant - Version 36 Monaco et al - PubMed 24217918 EnsemblCompara Plant

Proteins

Protein Annotations from UniProt

Z. mays

UniProt - Release 2017-02 UniProt Consortium - PubMed 25348405 UniProt FTP
Protein family and domain assignments to proteins from InterPro

Z. mays

InterPro Version 62 Mitchell et al - PubMed 25428371 InterPro FTP

Gene Ontology

GO annotations

Z. mays

GOA at UniProt (GOC Validation Date: 12/16/2016)

Huntley et al - PubMed 25378336

Gene Ontology Consortium - PubMed 25428369

GO Consortium Annotation FTP

Pathways

Pathway information

A. thaliana

Z. mays

Plant Reactome - release 52 Tello-Ruiz MK et al - PubMed 26553803 Reactome Gramene FTP
Pathway information Z. mays KEGG data set

Kanehisa M et al - PubMed22080510

KEGG
Pathway information Z. mays CornCyc 8.0

Walsh JR et al - PubMed 27899149

CornCyc FTP

Publications

A mapping from genes to publications Z. mays UniProt publications UniProt Knowledgebase 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

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