Characteristics of the selected datasets.

<p>The number of excluded arrays for each dataset using the standardized QC procedure is indicated in brackets. Abbreviations: NP: normal prostate, pPC: primary prostate cancer, mPC: metastatic prostate cancer, AI: androgen independent, AD: androgen dependent.</p

Overview of the QC results of two selected datasets.

<p>Several QC results of the dataset by Varambally <i>et al.</i> comparing arrays of benign prostate tissue (maroon), primary prostate cancer (blue) and metastatic prostate cancer samples (green) are shown in panel a-d. Several QC results of the dataset by Gregg <i>et al.</i> comparing arrays of prostatic epithelial (maroon) with interstitial stromal cell samples (teal) are depicted in panel e-h. a) Boxplot of raw intensities; b) density histogram of log intensities before normalization; c) density histogram of log intensities after normalization; d) MA-plot before (upper panel) and after normalization (lower panel) of one example array of the dataset by Varambally <i>et al.</i>; e) boxplot of raw intensities; f) density histogram of log intensities before normalization; g) density histogram of log intensities after normalization; h) MA-plot before (upper panel) and after normalization (lower panel) of one example array of the dataset by Gregg <i>et al.</i></p

PathVisio results of significant pathways found in the dataset by Best <i>et al.</i> comparing processed data provided by ArrayExpress with the reprocessed data after quality control.

<p>Pathway analysis is based on a comparison between androgen-dependent and androgen-independent prostate cancer. Only significant pathways with a Z-score >1.9 in at least one of the two analyses are included. Significant Z-scores are depicted in bold; matches between the analyses are in italics.</p

PathVisio results of significant pathways found in the dataset by Varambally <i>et al.</i> comparing processed data provided by ArrayExpress with the reprocessed data.

<p>Pathway analysis is based on a comparison between primary prostate cancer and metastatic prostate cancer. Only significant pathways with a Z-score >1.9 in at least one of the two analyses are included. Significant Z-scores are depicted in bold; matches in pathways between the analyses are in italics.</p

PathVisio results of significant pathways found in the dataset by Varambally <i>et al.</i> comparing processed data provided by ArrayExpress with the reprocessed data.

<p>Pathway analysis is based on a comparison between benign prostate tissue and primary prostate cancer. Only significant pathways with a Z-score >1.9 in at least one of the two analyses are included. Significant Z-scores are depicted in bold; matches in pathways between the analyses are in italics.</p

PathVisio results of significant pathways found in the dataset by Sun <i>et al.</i> comparing processed data provided by ArrayExpress with the reprocessed data after quality control.

<p>Pathway analysis is based on a comparison between recurrent and non-recurrent prostate cancer. Only significant pathways with a Z-score >1.9 in at least one of the two analyses are included. Significant Z-scores are depicted in bold. A NaN value commonly occurs when none of the genes in the pathway is present in the dataset.</p

PathVisio results of significant pathways found in the dataset by Wallace <i>et al.</i> comparing processed data provided by ArrayExpress with the reprocessed data after quality control.

<p>Pathway analysis is based on a comparison between normal prostate tissue and prostatic adenocarcinoma. Only significant pathways with a Z-score >1.9 in at least one of the two analyses are included. Significant Z-scores are depicted in bold; matches between the analyses are in italics.</p

Standardized microarray data analysis workflow.

<p>Starting from the publicly available EMBL repository ArrayExpress: 1) Relevant prostate cancer studies were selected and downloaded; 2) Quality control and data pre-processing steps were performed in the R environment. Microarrays with insufficient sample quality, hybridization quality, signal comparability or array correlation were excluded; 3) For each included study, statistical analysis was performed and pathway analysis was run with PathVisio to identify the biological processes involved; 4) Results were then integrated and compared to literature findings.</p