Data

YeastMine integrates multiple data types from SGD. Datatypes that can be queried in YeastMine include: Genomic elements, DNA and protein sequences, Gene Ontology (GO) annotations, pathways, phenotypes, interaction data, expression data, and supporting literature. Comparative ortholog and paralog data for a select set of organisms (yeast, worm, fly, rat, zebrafish, mouse and human) are also available. This page provides a list of the data and data sources loaded into YeastMine.

Data Category Data Source

Genome

Genome annotation for Saccharomyces cerevisiae. Data loaded includes:
  • PrimaryIdentifier
  • SecondaryIdentifier
  • Symbol
  • Name
  • Length
  • Description
  • Feature type
  • Locations
  • Sequences
SGD

Homology

Homologs for Saccharomyces cerevisiae. Data loaded includes:
  • CGOB homologs
  • FungiDB homologs
  • S.pombe homologs
CGOB
FungiDB
Pombe
Ortholog and paralog relationships between MOD organisms: Yeast, Human, Mouse, Rat, Fly, Worm, Mosquito and Zebrafish Treefam
Homologene
PantherDB
Ensembl Compara

Complementation

Yeast Human gene functional complementation P_POD (via SGD)

Disease

Human disease gene annotations OMIM

Proteins

Protein annotations SGD

Complexes

Macromolecular Interaction Complexes IntAct-SGD

Function

Gene Ontology and Pathways SGD

Phenotypes

Phenotypes SGD

Interactions

Physical and Genetic Interactions BioGRID (via SGD)

Literature

All publications in SGD SGD

Expression

Microarray-based gene expression data SGD
SGD Integrated Transcript data SGD

Regulation

Transcription Factor and Target relationships SGD
YEASTRACT
YeTFaSCo


YeastMine is a collaboration between SGD and the Intermine project at the Cambridge Systems Biology Centre. YeastMine is funded by NHGRI grant 2R01HG004834.
Copyright © 1997-2016 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The SGD project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.