This page displays GO annotations in different sections according to the annotation method used to add that annotation to SGD.

Last Reviewed on: 2002-10-10    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
NAD-dependent histone deacetylase activity	IDA: Inferred from Direct Assay Assigned on 2002-10-10	Pijnappel WW, et al.  (2001) The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev 15(22):2991-3004	SGD
NAD-independent histone deacetylase activity	IDA: Inferred from Direct Assay Assigned on 2002-10-10	Pijnappel WW, et al.  (2001) The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev 15(22):2991-3004	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin organization	ISS: Inferred from Sequence or structural Similarity Assigned on 2001-01-18	Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8	SGD
histone deacetylation	IDA: Inferred from Direct Assay Assigned on 2002-10-10	Pijnappel WW, et al.  (2001) The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev 15(22):2991-3004	SGD
negative regulation of meiosis	IMP: Inferred from Mutant Phenotype Assigned on 2002-10-10	Pijnappel WW, et al.  (2001) The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev 15(22):2991-3004	SGD
positive regulation of stress-activated MAPK cascade	IMP: Inferred from Mutant Phenotype Assigned on 2008-09-05	Cohen TJ, et al.  (2008) Hos2p/Set3p deacetylase complex signals secretory stress through the Mpk1p cell integrity pathway. Eukaryot Cell 7(7):1191-9	SGD
regulation of transcription, DNA-dependent	ISS: Inferred from Sequence or structural Similarity Assigned on 2001-01-18	Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-10-21	Kim T and Buratowski S  (2009) Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. Cell 137(2):259-72	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
Set3 complex	IDA: Inferred from Direct Assay Assigned on 2008-09-08	Pijnappel WW, et al.  (2001) The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev 15(22):2991-3004	SGD

* Manually curated GO annotations reflect our best understanding of the basic molecular function, biological process, and cellular component for this gene product. Manually curated annotations are assigned by SGD curators based on published papers when available, or by curatorial statements if necessary. Curators periodically review all Manually curated GO annotations for accuracy and completeness. The "Last Reviewed on:" date at the top of this section indicates when these annotations were last reviewed.

Cellular Component

High-throughput Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm	IDA: Inferred from Direct Assay Assigned on 2012-12-12	Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2012-12-12	Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76	SGD
Rpd3L-Expanded complex	IDA: Inferred from Direct Assay Assigned on 2009-01-08	Shevchenko A, et al.  (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167	SGD

** GO annotations from High-throughput experiments are made based on a variety of large scale high-throughput experiments, including genome-wide experiments. Many of these annotations are made based on GO annotations (or mappings to GO annotations) assigned by the authors, rather than SGD curators. While SGD curators read these publications and often work closely with authors to incorporate the information, each individual annotation may not necessarily be reviewed by a curator. GO Annotations from high-throughput experiments will be assigned only when this type of data is available, and thus may not be assigned in all three aspects of the Gene Ontologies.

Molecular Function | Biological Process | Cellular Component

Computational Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
histone deacetylase activity	IEA: Inferred from Electronic Annotation with EBI:IPR003084 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
histone deacetylase activity (H3-K14 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
histone deacetylase activity (H3-K9 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
histone deacetylase activity (H4-K16 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
hydrolase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0378 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
NAD-dependent histone deacetylase activity (H3-K14 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
NAD-dependent histone deacetylase activity (H3-K18 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
NAD-dependent histone deacetylase activity (H3-K9 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
NAD-dependent histone deacetylase activity (H4-K16 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin modification	IEA: Inferred from Electronic Annotation with EBI:KW-0156 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
histone deacetylation	IEA: Inferred from Electronic Annotation with EBI:IPR003084 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
histone H3 deacetylation	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	GOC
histone H4 deacetylation	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	GOC
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0805 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0804 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

Computational Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IEA: Inferred from Electronic Annotation with EBI:SL-0191 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
	IEA: Inferred from Electronic Annotation with EBI:KW-0539 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

*** Computational GO Annotations are predictions. These annotations are NOT reviewed by a curator. Currently, all computational GO annotations for S. cerevisiae are assigned by an external source (for example, the Gene Ontology Annotation (GOA) project of the European Bioinformatics Institute (EBI)).