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Table 6 MultiFun cellular function assignments.

From: Stringent response of Escherichia coli: revisiting the bibliome using literature mining

MultiFun Concepts Frequency of Ontology Annotation Brief Description Genes Gene Products
    Name Frequency of Assignment Frequency of Annotation Name Frequency of Annotation
BC-1.7.33 Nucleotide and nucleoside conversions 76% The chemical reactions involved in the central carbon metabolism by which a nucleobase, nucleoside or nucleotide is converted from another nucleobase, nucleoside or nucleotide. relA 68% 72% RelA 79%
    spoT 28% 46% SpoT 31%
BC- Proteases, cleavage of compounds 55% Proteins that hydrolysates a peptide bond or bonds within a protein during posttranscriptional regulatory processes. spoT 91% 46% SpoT 31%
BC-2.2.2 Transcription related functions 51% The information transfer related functions involved in the synthesis of RNA on a template of DNA. fis 22% 6% Fis 9%
    rpoB 17% 16% RpoB 18%
BC-2.3.2 Translation 48% The cellular metabolic process by which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. dksA 23% 3% DksA 8%
    rplK 17% 6% RplK 7%
    rpsG 12% 18% RpsG NA
    rpsL 11% 19% RpsL 3%
BC-5.5.3 Starvation 47% A state or activity of a cell or an organism as a result to the adaptation to starvation. spoT 85% 46% SpoT 31%
    dksA 12% 3% DksA 8%
BC-1.1.1 Carbon compounds 46% The metabolic reactions by which living organisms utilises carbon compounds. lacZ 49% 26% LacZ 28%
    ptsG 22% 16% PtsG 1%
BC-2.3.8 Ribosomal proteins 44% Proteins that associate to form a ribosome involved in genetic information transfer in cells. rplK 24% 6% RplK 7%
    rpsG 18% 18% RpsG NA
    rpsL 17% 19% RpsL 3%
BC- Repressor 40% Any transcription regulator that prevents or downregulates transcription. fis 41% 6% Fis 9%
BC- Activator 32% Any transcription regulator that induces or upregulates transcription. fis 45% 6% Fis 9%
  1. MultiFun terms were assigned to annotated concepts associated with genes. A threshold of 30% of documents was considered for ontology assignment and a threshold of 10% was used to point out the genes that most contributed to such assignment.
  2. NA: corresponds to non-annotated gene products in the corpus.