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Table 7 GO biological processes assignments.

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

Gene Ontology concepts Frequency of Ontology Annotation Brief Description Gene Products Coding Genes
    Name Frequency of Assignment Frequency of Annotation Name Frequency of Annotation
GO:0008152 Metabolic process 89% The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. RelA 80% 79% relA 72%
    LacZ 10% 24% lacZ 26%
GO:0015949 Nucleobase, nucleoside and nucleotide interconversion 80% The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide is synthesized from another nucleobase, nucleoside or nucleotide. RelA 80% 79% relA 72%
    SpoT 20% 31% spoT 46%
GO:0015969 Guanosine tetraphosphate metabolic process 80% The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates. RelA 80% 79% relA 72%
    SpoT 20% 31% spoT 46%
GO:0006350 Transcription 56% The synthesis of either RNA on a template of DNA or DNA on a template of RNA. RpoS 16% 22% rpoS 17%
    CRP 12% 6% crp 4%
    RpoB 10% 18% rpoB 16%
    Mfd 10% 2% mfd 2%
GO:0006355 Regulation of transcription, DNA-dependent 52% Any process that modulates the frequency, rate or extent of DNA-dependent transcription. RpoS 20% 22% rpoS 17%
    CRP 14% 6% crp 4%
    Mfd 12% 2% mfd 2%
GO:0006412 Translation 40% 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. RplK 28% 7% rplK 6%
    DksA 28% 8% dksA 3%
    EF-Tu 13% 14% tufB 3%
GO:0006950 Response to stress 39% A change in state or activity of a cell or an organism as a result of a disturbance in cellular homeostasis, usually, but not necessarily, exogenous. RecA 20% 16% recA 20%
    RelB 16% 4% relB 3%
    NusA 10% 5% nusA 4%
GO:0042594 Response to starvation 39% A change in state or activity of a cell or an organism as a result of a starvation stimulus, deprivation of nourishment. SpoT 67% 31% spoT 46%
    DksA 30% 8% dksA 3%
GO:0006970 Response to osmotic stress 38% A change in state or activity of a cell or an organism as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. RpoS 59% 22% rpoS 17%
    EF-Tu 34% 14% tufB 3%
GO:0005975 Carbohydrate metabolic process 36% The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. LacZ 94% 24% lacZ 26%
GO:0006974 Response to DNA damage stimulus 36% A change in state or activity of a cell or an organism as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. Mfd 28% 2% mfd 2%
    RecA 11% 16% recA 20%
    RecG 11% 3% recG NA
GO:0006281 DNA repair 36% The process of restoring DNA after damage that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. Mfd 28% 2% mfd 2%
    RecA 11% 16% recA 20%
    RecG 11% 3% recG NA
  1. GO terms were assigned to annotated concepts associated with gene products annotations. A threshold of 35% of documents was considered for ontology assignment and a threshold of 10% was used to point out the gene products that most contributed to such assignment.
  2. NA: corresponds to non-annotated genes in the corpus.