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

Last Reviewed on: 2010-03-02    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
RNA polymerase II transcription coactivator binding	IPI: Inferred from Physical Interaction with SGD:IFH1 Assigned on 2012-04-18	Martin DE, et al.  (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79	SGD
RNA polymerase II transcription corepressor binding	IPI: Inferred from Physical Interaction with SGD:CRF1 Assigned on 2012-04-18	Martin DE, et al.  (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-02-08	Martin DE, et al.  (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79	SGD
	IGI: Inferred from Genetic Interaction with SGD:IFH1 Assigned on 2010-02-08	Cherel I and Thuriaux P  (1995) The IFH1 gene product interacts with a fork head protein in Saccharomyces cerevisiae. Yeast 11(3):261-70	SGD
positive regulation of ribosomal protein gene transcription from RNA polymerase II promoter	IGI: Inferred from Genetic Interaction with SGD:IFH1 Assigned on 2012-04-18 IMP: Inferred from Mutant Phenotype Assigned on 2010-02-08	Schawalder SB, et al.  (2004) Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 432(7020):1058-61	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-02-08	Martin DE, et al.  (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
colocalizes_with CURI complex	IDA: Inferred from Direct Assay Assigned on 2010-02-05	Rudra D, et al.  (2007) Potential interface between ribosomal protein production and pre-rRNA processing. Mol Cell Biol 27(13):4815-24	SGD
nuclear chromatin	IDA: Inferred from Direct Assay Assigned on 2010-02-09	Martin DE, et al.  (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79	SGD
	IDA: Inferred from Direct Assay Assigned on 2007-08-28	Rudra D, et al.  (2005) Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J 24(3):533-42	SGD
nucleolus	IDA: Inferred from Direct Assay Assigned on 2004-10-29	Jorgensen P, et al.  (2004) A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 18(20):2491-505	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2004-10-29	Jorgensen P, et al.  (2004) A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 18(20):2491-505	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.

Molecular Function

High-throughput Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
sequence-specific DNA binding	IDA: Inferred from Direct Assay Assigned on 2009-02-05	Badis G, et al.  (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-05	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	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
DNA binding	IEA: Inferred from Electronic Annotation with EBI:KW-0238 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
double-stranded DNA binding	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Last updated 2011-10-06	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Last updated 2011-10-06	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
sequence-specific DNA binding	IEA: Inferred from Electronic Annotation with EBI:IPR001766, EBI:IPR018122 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
sequence-specific DNA binding transcription factor activity	IEA: Inferred from Electronic Annotation with EBI:IPR001766, EBI:IPR018122 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
regulation of sequence-specific DNA binding transcription factor activity	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Last updated 2011-10-06	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:IPR001766, EBI:IPR018122 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: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
transcription factor complex	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Last updated 2011-10-06	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome

*** 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)).