Colorectal cancer is the third most commonly diagnosed cancer in the world. Microarray-based colorectal cancer diagnosis is increasingly paid more and more attentions. In view of a number of pathway information available in the KEGG database, this paper proposes to model pathways for colorectal cancer diagnosis, and as a result, a pathway-based classification method is developed. The proposed m...

KEGG database The KEGG [1, 2] is a suite of databases and associated software that integrates current knowledge on molecular interaction networks in biological processes (PATHWAY database), the information about the universe of genes and proteins (GENES/SSDB/KO databases), and the information about the universe of chemical compounds, drugs and their biochemical reactions (COMPOUND/DRUG/GLYCAN/R...

Identifying disease genes is one of the most important topics in biomedicine and may facilitate studies on the mechanisms underlying disease. Age-related macular degeneration (AMD) is a serious eye disease; it typically affects older adults and results in a loss of vision due to retina damage. In this study, we attempt to develop an effective method for distinguishing AMD-related genes. Gene on...

A routine approach to inferring functions for a gene set is by using function enrichment analysis based on GO, KEGG or other curated terms and pathways. However, such analysis requires the existence of overlapping genes between the query gene set and those annotated by GO/KEGG. Furthermore, GO/KEGG databases only maintain a very restricted vocabulary. Here, we have developed a tool called "CoCi...

understanding cattle metabolism and its relationship with milk products is important in bovine breeding. a systemic view could lead to consequences that will result in a better understanding of existing concepts. topological indices and quantitative characterizations mostly result from the application of graph theory on biological data. in the present work, the enzyme network involved in cattle...