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

Last Reviewed on: 2012-03-12    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
DNA-dependent ATPase activity	IMP: Inferred from Mutant Phenotype Assigned on 2006-03-27 IDA: Inferred from Direct Assay Assigned on 2006-03-27	Laurent BC, et al.  (1993) The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev 7(4):583-91	SGD
	IDA: Inferred from Direct Assay Assigned on 2008-05-13	Cairns BR, et al.  (1994) A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci U S A 91(5):1950-4	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-05-13	Cote J, et al.  (1994) Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265(5168):53-60	SGD
histone acetyl-lysine binding	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-23	Hassan AH, et al.  (2002) Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111(3):369-79	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-03-12	Zhang Q, et al.  (2010) Biochemical profiling of histone binding selectivity of the yeast bromodomain family. PLoS One 5(1):e8903	SGD
nucleosomal DNA binding	IDA: Inferred from Direct Assay Assigned on 2012-03-05	Dechassa ML, et al.  (2008) Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol 28(19):6010-21	SGD
RNA polymerase II activating transcription factor binding	IPI: Inferred from Physical Interaction with SGD:GCN4, SGD:HAP4 Assigned on 2012-02-14	Neely KE, et al.  (2002) Transcription activator interactions with multiple SWI/SNF subunits. Mol Cell Biol 22(6):1615-25	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
ATP-dependent chromatin remodeling	IMP: Inferred from Mutant Phenotype Assigned on 2008-05-13 IDA: Inferred from Direct Assay Assigned on 2008-05-13	Cote J, et al.  (1994) Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265(5168):53-60	SGD
cellular alcohol catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-01	Peterson CL and Herskowitz I  (1992) Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell 68(3):573-83	SGD
chromatin remodeling	IGI: Inferred from Genetic Interaction with SGD:HTB1, SGD:HTA1 Assigned on 2012-02-15 IMP: Inferred from Mutant Phenotype Assigned on 2012-02-15	Hirschhorn JN, et al.  (1992) Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev 6(12A):2288-98	SGD
DNA-dependent DNA replication	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-02	Flanagan JF and Peterson CL  (1999) A role for the yeast SWI/SNF complex in DNA replication. Nucleic Acids Res 27(9):2022-8	SGD
double-strand break repair	IMP: Inferred from Mutant Phenotype Assigned on 2006-06-19	Chai B, et al.  (2005) Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. Genes Dev 19(14):1656-61	SGD
nucleosome mobilization	IDA: Inferred from Direct Assay Assigned on 2012-03-05	Yang X, et al.  (2007) Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement. Nat Struct Mol Biol 14(6):540-7	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-05	Smith CL and Peterson CL  (2005) A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol Cell Biol 25(14):5880-92	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-10-22	Ford J, et al.  (2007) A SWI/SNF- and INO80-dependent nucleosome movement at the INO1 promoter. Biochem Biophys Res Commun 361(4):974-9	SGD
positive regulation of mating type switching	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-02	Stern M, et al.  (1984) Five SWI genes are required for expression of the HO gene in yeast. J Mol Biol 178(4):853-68	SGD
positive regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-14	Breeden L and Nasmyth K  (1987) Cell cycle control of the yeast HO gene: cis- and trans-acting regulators. Cell 48(3):389-97	SGD
	IGI: Inferred from Genetic Interaction with SGD:SNF6, SGD:SNF5 Assigned on 2012-02-14	Laurent BC, et al.  (1991) Functional interdependence of the yeast SNF2, SNF5, and SNF6 proteins in transcriptional activation. Proc Natl Acad Sci U S A 88(7):2687-91	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-14	Cote J, et al.  (1994) Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265(5168):53-60	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-15	Peterson CL and Herskowitz I  (1992) Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell 68(3):573-83	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-10-22	Ford J, et al.  (2007) A SWI/SNF- and INO80-dependent nucleosome movement at the INO1 promoter. Biochem Biophys Res Commun 361(4):974-9	SGD
positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-23	Natarajan K, et al.  (1999) Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator. Mol Cell 4(4):657-64	SGD
strand invasion	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-05	Sinha M, et al.  (2009) Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling. Cell 138(6):1109-21	SGD
sucrose catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-02	Neigeborn L and Carlson M  (1984) Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics 108(4):845-58	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-01	Peterson CL and Herskowitz I  (1992) Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell 68(3):573-83	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IDA: Inferred from Direct Assay Assigned on 2008-05-08	Laurent BC, et al.  (1991) Functional interdependence of the yeast SNF2, SNF5, and SNF6 proteins in transcriptional activation. Proc Natl Acad Sci U S A 88(7):2687-91	SGD
SWI/SNF complex	IDA: Inferred from Direct Assay Assigned on 2009-10-15	Dechassa ML, et al.  (2008) Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol 28(19):6010-21	SGD
	IDA: Inferred from Direct Assay Assigned on 2008-05-13	Cairns BR, et al.  (1994) A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci U S A 91(5):1950-4	SGD
	IDA: Inferred from Direct Assay Assigned on 2008-05-13	Cote J, et al.  (1994) Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265(5168):53-60	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-05-12 IDA: Inferred from Direct Assay Assigned on 2008-05-12	Peterson CL, et al.  (1994) Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc Natl Acad Sci U S A 91(8):2905-8	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
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

** 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
ATP binding	IEA: Inferred from Electronic Annotation with EBI:IPR014978, EBI:IPR001650, EBI:IPR000330 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:KW-0067 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
DNA binding	IEA: Inferred from Electronic Annotation with EBI:IPR017956, EBI:IPR000330 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
helicase activity	IEA: Inferred from Electronic Annotation with EBI:IPR001650 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:KW-0347 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	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
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	IEA: Inferred from Electronic Annotation with EBI:IPR014978 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleic acid binding	IEA: Inferred from Electronic Annotation with EBI:IPR001650 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleotide binding	IEA: Inferred from Electronic Annotation with EBI:KW-0547 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 Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:IPR014978 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	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:IPR014978 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	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)).