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 © 1997-2019 The Board of Trustees of Leland Stanford Junior University. SGD operates under the Creative Commons Attribution 4.0 International license (CC BY 4.0) . 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.