Directed annotations parially explain gene expression variance in GTEx. The BAGEA model was fit using various GTEx eQTL data (supplemented with GEAU-VADIS eQTL data) and with Expecto-derived directed annotations on genes in the trainig set (chr1,..,chr15) with a top nominal p-value< 10 −7 . Expecto includes 2002 total annotations, of which histone and DNase1 annotations from Roadmap were used (1187 annotations in total). For each gene j in the test set (chr16,..,chr22 and top nominal p-value< 10 −7 ), we calculated an approximate version of S j , the squared magnitude of the directed predictorˆµpredictorˆ predictorˆµ j , where the approximation uses external LD information. Further, we calculated an approximate version of M SE dir j , the mean squared error (M SE) when predicting gene expression y j fromˆµfromˆ fromˆµ j . a) Displayed is the average (approximated) M SE dir

Contexts in source publication

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... again split genes into training and test set, fitting BAGEA on the training set and building directed expression predictorsˆµpredictorsˆ predictorsˆµ j for all genes in the test set. We observed that the average M SE dir per data set was variable across GTEx data sets ranging from 100% to below 98.5% (Figure 5a). ...

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... again saw that increased directed predictor magnitude tended to decrease M SE dir . For instance in fibroblast, the quarter of the genes with the highest directed predictor magnitude had an average M SE dir of 97.2%, whereas the quarter with the lowest directed predictor magnitude had an average M SE dir close to 100% (Figure 5b). ...

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... accommodate the wide range of tissues explored in GTEx, we expanded the number of directed annotations used in the fitting process to over a thousand. While for some tissues, the analysis strategy was underpowered to derive a predictive model of gene expression from directed annotations, others had a significant fraction of gene expression explained by directed annotations ( Figure 5). Many of the directed annotations BAGEA selected, were derived from tissues that were biologically related to the original tissue of the eQTL studies (Figure 6a). ...