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Table 3 Inference rules for gene classification

From: CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations

Rule # CGE CCS IGE PT Gene class
1 increased normal- >cancer * causality oncogene
2 decreased cancer- >normal unidentifiable causality oncogene
3 decreased cancer- >normal up-regulated * oncogene
4 decreased normal- >cancer * causality tumor suppressor gene
5 increased cancer- >normal unidentifiable causality tumor suppressor gene
6 increased cancer- >normal down-regulated * tumor suppressor gene
7 * normal- >cancer * observation biomarker
8 * cancer- >normal unidentifiable observation biomarker
9 decreased cancer- >cancer up-regulated observation biomarker
10 increased cancer- >cancer down-regulated observation biomarker
  1. The rules are not symmetric to each other. For instance, Rule 4 states that a gene can be classified as a 'tumor suppressor gene’ when a decreased expression level of the gene causes cancer progression, regardless of the IGE value. Rule 2 is about a similar case, where a decreased expression level of a gene causes cancer regression. However, Rule 2 requires IGE to be 'unidentifiable’ to infer the gene as an 'oncogene’. Rule 3, not Rule 2, covers the case where CGE is 'up-regulated’ and PT is 'causality’. Also, Rule 2 does not cover the cases where IGE is 'down-regulated’ or 'unchanged’ since we expect such cases to be rarely reported in biology articles (cf. Section on Inference rule development). Rules 5 and 8 are designed in a similar way. The asterisk denotes all the pre-defined values for the corresponding concept.