Table 2

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


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.

Peng et al. BMC Bioinformatics 2013 14(Suppl 2):S15   doi:10.1186/1471-2105-14-S2-S15

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