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Table 3 GeneTopics results for GAD gene sets with GAD genes as background

From: GeneTopics - interpretation of gene sets via literature-driven topic models

GAD gene set LDA model # Relevant number of topics Best Topic
esophageal cancer 20 7 polymorphism, genotype, risk, associated, 95, cancer, or, gene, ci, allelic, studies, gstm1, patients, controls, p, gstt1, frequency, genetic, population, variants
kidney cancer 15 2 cyclin, d1, expressed, cancer, tumor, cells, carcinomas, breast, cases, cycle, correlated, survival, invasive, cdk4, patients, gastric, proteins, oncogene, overexpression, associated
Alzheimer's disease 15 10 diseases, alzheimers, ad, amyloid, abeta, app, tau, brain, ide, platelets, gammasecretase, parkinsons, ps1, pd, protein, fe65, precursor, lrrk2, titin, beta
blood pressure, arterial 20 11 renal, hypertension, ace, kidney, pressure, aldosterone, angiotensin, uroguanylin, ace2, blood, cyp11b2, sodium, enzyme, intestinal, excretion, urinary, guanylin, ae1, kae1, peptides
hepatitis c, chronic 10 7 chemokin,cell,t,ccr5,express,rant,mcp1,cytokin,macrophag,il10,il8,cxcr1,monocyt,receptor,infect,immun,hiv1,virus,secret,neutrophil
longevity 15 7 patients, il6, diseases, ad, clinical, therapy, serum, level, p, values, group, outcome, survival, healthy, cytokines, predicted, prognostic, stages, correlate, transplantation
diabetes, type 2 20 14 insulin, glucose, diabetes, leptin, adipose, muscle, obese, expression, metabolism, adiponectin, fat, fatty, mice, islets, increase, mrna, tissues, adipocytes, skeletal, levels
  1. This table shows the best topics found by GeneTopics using the GAD genes as the background. Comparing to results in table 2, the best topics are much more consistent with the expected disease terms.