36. glucose fermentation 

Similarity values obtained by G-SESAME

Clustering results by G-SESAME

Similarity values obtained by Resnik's method

Gene Clustering Result

Analysis:

Genes ALD5 and ALD6 are annotated by the same molecular function term GO:0004028: 3-chloroallyl aldehyde dehydrogenase activity. Genes TDH1, TDH2, and TDH3 are annotated by the same molecular function term GO:0004365: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity. Genes ADH1, ADH2, ADH3, and ADH5 are annotated by only one molecular function term GO:0004022: alcohol dehydrogenase activity. Genes PDC1, PDC5, and PDC6 are annotated by the same molecular function term GO:0004737: pyruvate decarboxylase activity. Genes ENO1 and ENO2 are annotated by the same molecular function term GO:0004634: phosphopyruvate hydratase activity. Genes HXK1 and HXK2 are annotated by the same molecular function term GO:0004396: hexokinase activity. Genes PFK1 and PFK2 are annotated by the same molecular function term GO:0003872: 6-phosphofructokinase activity.

Thus, ALD5 and ALD6 have the same molecular function. TDH1, TDH2, and TDH3 have the same molecular function. ADH1, ADH2, ADH3, and ADH5 have the same molecular function. PDC1, PDC5, and PDC6 have the same molecular function. ENO1 and ENO2 have the same molecular function. HXK1 and HXK2 have the same molecular function. PFK1 and PFK2 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 ALD5 and ALD6. The similarity between ALD5 and ALD6 is greater than the similarity among PDC1, PDC5, and PDC6. The similarity among PDC1, PDC5, and PDC6 is greater than the similarity among ADH1, ADH2, ADH3, and ADH5. The similarity among ADH1, ADH2, ADH3, and ADH5 is greater than the similarity between ENO1 and ENO2. The similarity between ENO1 and ENO2 is greater than the similarity between HXK1 and HXK2. These results are inconsistent with the human perception.

Furthermore, there are many 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 HXK1 and HXK2. However, based on Resnik's method, the similarity value between TPI1 and PGI1 is greater than the similarity between HXK1 and HXK2, two genes annotated by the same term.

conclusion: