Fig. 9

AMD association of pathways under collective inference. a AUC score versus pathway size (number of SNPs in each pathway). Symbols show collective and independent-SNP inference AUCs under 5-fold cross validation. Vertical lines are 95 % C.I. The horizontal line represents the Bonferroni-corrected nominal discovery threshold based on the p-value estimates. b Regression of AUC versus pathway p-values. The latter were obtained for a selection of pathways via phenotype-label reshuffling using AUC as the statistic. Dotted line is the linear fit for AUC>0.52. c–e Pathways with association strength AUC>0.55, grouped according to the top hierarchical classes they belong to. We excluded pathways in the Disease class. Dendrograms below the bars show their hierarchical relationships. Abl, Abl tyrosine kinase; activ., activation; assoc., association/associated; biosynth., biosynthesis; C3, complement component 3; C5, complement component 5; CCT, chaperonin-containing T-complex polypeptide 1; cell., cellular; ChREBP, carbohydrate response element-binding protein; ECM, extracellular matrix; EHMT2, euchromatic histone-lysine-methyltransferase 2; elong., elongation; ER, endoplasmic reticulum; ERCC6, excision repair cross-complementation group 6; expr., expression; form., formation; HSF, heat shock factor; IFN, interferon; indep., independent; Lys, lysine; MDA5, melanoma differentiation-associated gene 5; med., mediated; metab., metabolism; MYD88, myeloid differentiation primary response 88; NFKB, nuclear factor- κ B; PA, phosphatidic acid; PKMT, protein lysine methyltransferase; pol, polymerase; proc., processing; reg., regulate/regulation/regulated; RIG-I, retinoic acid-inducible gene-I; RIP, receptor-interaction protein; Robo, roundabout; SASP, senescence-associated secretory phenotype; sig., signaling; SMAC, second mitochondrial activator of caspases; synth., synthesis; sys., system; thru, through; TP53, tumor protein p53; transc., transcription/transcriptional; TriC, T-complex polypeptide 1 ring complex; ZBP1, Z-DNA-binding protein-1