Inter Disease Relations Based on Human Biomarkers by Network Analysis

A biomarker (short for biological marker) is a medical sign of a disease or condition which indicates a normal or abnormal state of a body. The biomarker is a key factor in the analysis of diseases and also for analyzing inter disease relations. In the previous study, we designed and developed a human biomarker (metabolites and proteins) database and the database is currently available online. This work was supported by the Ministry of Education, Japan and NAIST Big Data Project. We have used our previously developed database and collected 486 human biomarkers and their respective diseases. We determined the similarity among NCBI disease classes based on associated biomarker fingerprints. For this purpose, we collected biomarker PubChem IDs and using them downloaded the SDF files in a batch, then with those molecular description files determined their atom pair fingerprints using ChemmineR package. We constructed a network of biomarkers based on Tanimoto similarity between their fingerprints and applied DPclusO algorithm to find clusters consisting of biomarkers with similar chemical structures. We also conducted hierarchical clustering of the biomarkers. We categorized all the diseases in our data into 18 NCBI disease classes. Combining all information, we finally determined inter disease relations based on structural similarity between biomarkers.