S' pombe

1
S. pombe

• Unicellular archiascomycete
• Diverged from S. cerevisiae 330- 1144 Ma
• Size 14 Mb, 3 chromosomes
• No synteny
• Data stored in GeneDB

2

Areas of interest

• Nomenclature
• Evolutionary relationships (orthology, paralogy,
  protein family and domain)
• Functional annotation (Using GO, from literature
  curation, functional transfer from orthologs,
  inferred electronically from protein
  family/domain)
• Genetic mapping data (minimal, small amount,
  mostly linked to physical sequence data)

3
Areas of expertise/collaborations

• Literature curation
• Ontology development (GO consortium)
• Ortholog/paralog resolution (and functional
  inference)
• Protein family identification (Pfam/Interpro)
• Functional mappings (e.g. Interpro2GO)
• Physical and genetic interactions (GO BioGRID
  consortiums)
• Functional prediction (Daniel Barker)

4
3
Orthologs
1
4
GO associations
GO curation
5
Domain /family
Family identification
2
Sequence and annotation updates
Interpro2Go
6
GOA
5
Biological process
101
494
537
2681
124
318
106
Cellular component
Molecular function
Gene count 4990 Dubious 67 No
GO S. pombe 567 11.5 (c.f. S. cerevisiae
612 10.5)
6

GO terms
Gene count 4990 Unassigned 456 Dubious
67 Conserved 57 No GO/Pf/Ort 341
No orthologs Of which 74
272
484
No S. cerevisiae ortholog
532
3161
41
27
38
S. cerevisiae orthologs
Pfam families
Distant ortholog detection
Pfam coverage S. pombe 75 c.f.S. cerevisiae 65
Submitted to Pfam
DUF mainly eukaryotic/fungal