Identifying cross-category relations in gene ontology and constructing genome-specific term association networks

Peng, Jiajie; Chen, Jin; Wang, Yadong

doi:10.1186/1471-2105-14-S2-S15

BMC Bioinformatics

Table 2 Top 20 term associations in category "overlap but not identical" that were identified by CroGO.

From: Identifying cross-category relations in gene ontology and constructing genome-specific term association networks

MF Name	BP Name	Evidence
polynucleotide adenylyltransferase activity	ncRNA polyadenylation	NEW
TFIIF-class binding TF activity	regulation of transcription-coupled nucleotide-excision repair	REF [37]
TFIIF-class binding TF activity	positive regulation of transcription elongation from Pol I promoter	REF [38]
TFIIF-class binding TF activity	regulation of transcription elongation from Pol I promoter	REF [38]
TFIIF-class binding TF activity	positive regulation of histone H3-K36 trimethylation	NEW
TFIIF-class binding TF activity	regulation of histone H3-K36 trimethylation	NEW
TFIIF-class binding TF activity	positive regulation of histone H3-K36 methylation	NEW
TFIIF-class binding TF activity	regulation of nucleotide-excision repair	REF [39]
TFIIF-class binding TF activity	regulation of histone H2B ubiquitination	REF [40]
TFIIF-class binding TF activity	positive regulation of phosphorylation of Pol II C-terminal domain serine 2 residues	NEW
TFIIF-class binding TF activity	regulation of phosphorylation of Pol II C-terminal domain serine 2 residues	NEW
TFIIF-class binding TF activity	regulation of histone H2B conserved C-terminal lysine ubiquitination	NEW
IMP dehydrogenase activity	GTP biosynthetic process	REF [41]
hydrogen ion transporting ATP synthase activity, rotational mechanism	ATP biosynthetic process	LEXICAL
RNA-directed RNA polymerase activity	tRNA transcription from Pol III promoter	LEXICAL
RNA-directed RNA polymerase activity	tRNA transcription	NEW
protein prenyltransferase activity	protein geranylgeranylation	REF [42]
second spliceosomal transesterification activity	generation of catalytic spliceosome for second transesterification step	NEW
oxoglutarate dehydrogenase activity	2-oxoglutarate metabolic process	LEXICAL
peptide alpha-N-acetyltransferase activity	N-terminal protein amino acid acetylation	REF [43]

Top 20 term associations in category "overlap but not identical" that were identified by CroGO. In the list, 8 term associations are supported by the existing biological studies, 3 are supported by the lexical matching on term definition, and the rest 7 are new conceptual connections that cannot be found in any literature. Only 3 of the term associations can be identified by the VSM or ASR based measures.

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ISSN: 1471-2105

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