Performance of SVD on the GO prediction test with varying number of removed PCs (i.e., setting of ) on (left) Pickrell and (right) Montgomery data.

<p>The red star marks the optimal setting of for the cis-eQTL task.</p

Fraction of shared cis-eQTLs at 10% FDR between pairs of various versions of normalized Pickrell RNA-seq data.

<p>Each row depicts the fraction of cis-eQTLs discovered using a particular normalization method that are also discovered in another normalized version. For example, the element at row <i>i</i> and column <i>j</i> (the element) depicts the proportion of cis-eQTLs discovered using normalization method <i>i</i> that are also discovered in normalization method <i>j</i>.</p

Heatmap of RNA-seq data from (a) Pickrell data and (b) Montgomery data.

<p>Rows represent subjects (or individuals) and columns represent genes. Using k-means clustering on corresponding RPKM normalized data, subjects are grouped in three clusters and genes are also grouped into three clusters. As observed later, these broad clustering patterns are primarily driven by confounding factors such as sequencing depth.</p

Mean average precision (AUP) in predicting gene function from co-expression networks constructed from various normalization methods, on (a) Pickrell, and (b) Montgomery data.

<p>The figure shows the performance of SVD at two different parameter settings (SVD (10) with , and SVD (2) with ). Error bars show the standard errors. Figure shows the cumulative performance for (c) Pickrell, (d) and Montgomery, datasets for the top 50 best predicted GO categories for each method.</p

Results of the sensitivity analyses: a comparison of different nominal p-values.

<p><i>Note</i>. Results for variations of the method for the 32 Mbp width region on chromosome 5, 128–160 bp. Nom 0.01: the analysis was performed using p = 0.01 as the cutoff for nominal SNP-wise significance. Nom 0.11: the analysis was performed using p = 0.1 as the cutoff for nominal SNP-wise significance. EIGENSTRAT: the analysis was performed on data corrected for population stratification using the EIGENSTRAT procedure.</p

“Manhattan plot of the 22 autosomal chromosomes”.

<p>This figure shows at the y–axis the p-values of the SNPs in a GWA analysis. The chromosomes are shown at the x-axis. The red line indicates a p-value of 10-7, the blue line indicates a p-value of 10-5 and the green line indicates a p-value of .05.</p

Overview of disease associated genes located within the significantly associated region at chromosome 5 (128–136 Mbp).

<p>Note: The table shows genes that have previously reported to be associated with disease based on the UCSC Genome Bioinformatics site (NCBI36/hg18) (<a href="http://genome.ucsc.edu/" target="_blank">http://genome.ucsc.edu/</a>) and genes previously found to be associated with schizophrenia based on the Schizophrenia Research Forum (<a href="http://www.schizophreniaresearchforum.org" target="_blank">www.schizophreniaresearchforum.org</a>). The final column represents the phenotype and disease associations according to the UCSC Genome Bioinformatics site.</p><p>Set-based tests were performed in Plink to assess the association between SNPs within a particular gene and case-control status. This test uses permutation to determine the significance. The default values were used (r-squared = .5; p-value = .05; maximum number of SNPs within a gene = 5); more details can be found at <a href="http://pngu.mgh.harvard.edu/~purcell/plink" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink</a>.</p

Metasignificance of segments located in chromosome 5 (128–160 Mbp).

<p><i>Note</i>. Segment width refers to the width of regions over which tests of the number of nominally significant SNPs were tested. The replicable region indicates the location of the segment. The p-values provide the results of permutation based tests.</p

“Manhattan plot of the top segment located at chromosome 5 (128–136

<p> <b>Mbp)”.</b> This figure shows at the y–axis the p-values of the SNPs located at chromosome 5 (128–136 Mbp). The chromosomes are shown at the x-axis. The red line indicates a p-value of 10-7, the blue line indicates a p-value of 10-5 and the green line indicates a p-value of .05.</p