54. glycolysis

Similarity values obtained by G-SESAME

Clustering results obtained by G-SESAME

Similarity values obtained by Resnik's method

Clustering results obtained by Resnik's method

Analysis:

Genes TDH1, TDH2, and TDH3 are annotated by the same molecular function term GO:0004365: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity. Genes ENO1 and ENO2 are annotated by the same molecular function term GO:0004634: phosphopyruvate hydratase activity. Genes PFK1 and PFK2 are annotated by the same molecular function term GO:0003872: 6-phosphofructokinase activity. Genes PYK2 and CDC19 are annotated by the same molecular function term GO:0004743: pyruvate kinase activity.

Thus, TDH1, TDH2, and TDH3 have the same molecular function. ENO1 and ENO2 have the same molecular function. PFK1 and PFK2 have the same molecular function. PYK2 and CDC19 have the same molecular function. The similarity values and clustering results obtained by G-SESAME are consistent with these observations.

However, based on Resnik's method, the similarity among genes TDH1, TDH2, and TDH3 is greater than the similarity between PFK1 and PFK2. The similarity between PFK1 and PFK2 is greater than the similarity between ENO1 and ENO2. The similarity between ENO1 and ENO2 is greater than the similarity between PYK2 and CDC19. These results are inconsistent with the human perception.

Furthermore, there are other results obtained by Resnik's method are not consistent with human perspectives. For instance, Genes TPI1 and PGI1 are annotated by two different terms, GO:0004807: triose-phosphate isomerase activity and GO:0004347: glucose-6-phosphate isomerase activity respectively. Therefore, the difference between TPI1 and PGI1 should be greater than the difference between PYK2 and CDC19. However, based on Resnik's method, the similarity value between TPI1 and PGI1 is greater than the similarity between PYK2 and CDC19, two genes annotated by the same molecular function term.

Conclusions:

G-SESAME is better.