Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature

Table 5C.

Performance on Genes Using BLASTObtained Articles

Category Num Exact match Partial match
Rank Rank
1 2 3 1 2 3
Metabolism 286 24.48% 15.73% 19.58% 32.87% 20.98% 21.68%
Cell_cycle 47 40.43% 29.79% 4.26% 57.45% 31.91% 14.89%
Signal_transduction 10 70.00% 20.00% 0.00% 70.00% 30.00% 0.00%
Meiosis 0 N/A N/A N/A N/A N/A N/A
Intracellular_protein_traffic 20 45.00% 15.00% 10.00% 80.00% 20.00% 15.00%
Sporulation 3 0.00% 0.00% 0.00% 0.00% 33.33% 0.00%
Cell_fusion 6 0.00% 0.00% 0.00% 0.00% 50.00% 0.00%
Stress_response 6 0.00% 0.00% 16.67% 66.67% 16.67% 16.67%
Biogenesis 60 21.67% 15.00% 10.00% 50.00% 28.33% 18.33%
Invasive_growth 0 N/A N/A N/A N/A N/A N/A
Transport 12 66.67% 0.00% 16.67% 75.00% 25.00% 33.33%
Ion_homeostasis 6 16.67% 0.00% 0.00% 16.67% 16.67% 16.67%
  • Only those genes with more than three but less than twenty-five articles were annotated.   For each table we list only the categories for which there was at least one gene with it as its annotation by the GO Consortium. Each row focuses on only the genes for which the category in the first column is a GO Consortium annotation. The “Num” column indicates the number of genes annotated by GO Consortium that we attempted to classify. The exact match columns are specific to a ranked prediction and list the percentage of times that the category in the first column was predicted with the rank. Partial match is similar, except we include other categories that are correct predictions for the gene in the percentage.

This Article

  1. Genome Res. 12: 203-214

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