title: A NEW RELEVANCE ESTIMATOR FOR THE COMPILATION AND VISUALIZATION OF DISEASE PATTERNS AND POTENTIAL DRUG TARGETS.
abstract: A new computational method is presented to extract disease patterns from heterogeneous and text-based data. For this study, 22 million PubMed records were mined for co-occurrences of gene name synonyms and disease MeSH terms. The resulting publication counts were transferred into a matrix Mdata. In this matrix, a disease was represented by a row and a gene by a column. Each field in the matrix represented the publication count for a co-occurring disease-gene pair. A second matrix with identical dimensions Mrelevance was derived from Mdata. To create Mrelevance the values from Mdata were normalized. The normalized values were multiplied by the column-wise calculated Gini coefficient. This multiplication resulted in a relevance estimator for every gene in relation to a disease. From Mrelevance the similarities between all row vectors were calculated. The resulting similarity matrix Srelevance related 5,000 diseases by the relevance estimators calculated for 15,000 genes. Three diseases were analyzed in detail for the validation of the disease patterns and the relevant genes. Cytoscape was used to visualize and to analyze Mrelevance and Srelevance together with the genes and diseases. Summarizing the results, it can be stated that the relevance estimator introduced here was able to detect valid disease patterns and to identify genes that encoded key proteins and potential targets for drug discovery projects.
authors.affiliation: Research Information Management, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16 Allschwil, 4123, Switzerland, modest.korff@actelion.com.
authors.forename: Modest
authors.initials: M
authors.lastname: VON Korff
authors.forename: Tobias
authors.initials: T
authors.lastname: Fink
authors.forename: Thomas
authors.initials: T
authors.lastname: Sander
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods; D003924:Diabetes Mellitus, Type 2 / Q000188:drug therapy / Q000235:genetics; D004194:Disease / Q000235:genetics*; D055808:Drug Discovery; D004358:Drug Therapy; D053263:Gene Regulatory Networks; D006801:Humans; D008545:Melanoma / Q000188:drug therapy / Q000235:genetics; D039781:PubMed; D012878:Skin Neoplasms / Q000188:drug therapy / Q000235:genetics; D014820:Vitiligo / Q000188:drug therapy / Q000235:genetics