The number of genes in top 20 gene sets for group discrimination (PROG) and top 20 gene sets for prediction accuracy (PRED) is box plotted

P-value was inferred from an unpaired -test.<p><b>Copyright information:</b></p><p>Taken from "A gene sets approach for identifying prognostic gene signatures for outcome prediction"</p><p>http://www.biomedcentral.com/1471-2164/9/177</p><p>BMC Genomics 2008;9():177-177.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2364634.</p><p></p

In each dataset, patients were divided into two groups (poor and good prognostic groups) based on the gene expression pattern in the 11823860 ST2 gene set, and their survival or recurrence proportions were then plotted

The log-rank test was used to infer the statistical significance of survival or recurrence differences between the two groups. In each graph, the x-axis represents overall or relapse-free survival years and the y-axis represents the proportion of overall survival (A, B, C, D, E, F, I, and K) or relapse-free survival (G, H, J, and L). Black indicates poor prognosis and red indicates good prognosis.<p><b>Copyright information:</b></p><p>Taken from "A gene sets approach for identifying prognostic gene signatures for outcome prediction"</p><p>http://www.biomedcentral.com/1471-2164/9/177</p><p>BMC Genomics 2008;9():177-177.</p><p>Published online 16 Apr 2008</p><p>PMCID:PMC2364634.</p><p></p

The relationship between the mixing coefficient (alpha) and the average inter-gene correlation.

<p>The relationship between the mixing coefficient (alpha) and the average inter-gene correlation.</p

Significant gene-sets detected by the absolute GSEA-GP filtering (FDR<0.1) with the mod-<i>t</i> score (DHT-treated and control LNCaP cell line).

<p>Significant gene-sets detected by the absolute GSEA-GP filtering (FDR<0.1) with the mod-<i>t</i> score (DHT-treated and control LNCaP cell line).</p

Performance comparison of gene-permuting GSEA methods for simulated read counts.

<p>GSEA-GP methods combined with eight gene statistics, (moderated <i>t</i>-statistic, SNR, Ranksum, logFC and their absolute versions), Camera combined with voom normalization, RNA-Enrich and two preranked GSEA methods for edgeR <i>p</i>-values and FCs were compared for false positive rate, true positive rate and area under the receiver operating curve using simulated read count data with three (A-C) and five replicates (D-F).</p

Average receiver operating characteristic (ROC) curves.

<p>The average ROC curves (20 repetitions) of the twelve gene-permuting GSEA methods applied to simulation data with the inter-gene correlation of 0.3 for (A) three and (B) five replicate cases.</p

Expression of <i>PDGFR</i> isoforms in bladder cancer (NMIBC and MIBC) patients.

<p>FDR, false discovery rate; NMIBC, non-muscle invasive bladder cancer; MIBC, muscle invasive bladder cancer; BT, bladder tumor</p><p>Expression of <i>PDGFR</i> isoforms in bladder cancer (NMIBC and MIBC) patients.</p

MMP2 and MMP9 may be downstream effectors of <i>c-MET</i> knockdown, leading to suppression of migration in T24 bladder cancer cells.

<p>(A) Wound-healing assay showing that knockdown of c-MET inhibitsthe migration of T24 cells. (B) Loss of <i>c-MET</i> downregulated the expression of matrix metalloproteinases (MMP)-2 and MMP-9. All experiments were performed using two <i>c-MET</i> knockdown cell lines (si<i>c-MET</i>-1 and si<i>c-MET</i>-2) transfected with different MET siRNAs, and two control cell lines (Ctrl and NT). Ctrl, control; NT, non-transfected.</p

<i>AXL</i> mRNA expression in bladder cancer (NMIBC and MIBC) patients and normal controls.

<p>FDR, false discovery rate; NMIBC, non-muscle invasive bladder cancer; MIBC, muscle invasive bladder cancer; BT, bladder tumor</p><p><i>AXL</i> mRNA expression in bladder cancer (NMIBC and MIBC) patients and normal controls.</p

Overexpression of DPY30 in gastric cancers.

<p>(A-D) Immunohistochemical staining demonstrated the overexpression of DPY30 in gastric cancer tissues. Notably its overexpression was obviously greater in invading cancer cells (B-D) than in normal gastric mucosa (A). (E) The mRNA level of DPY30 in gastric cancer cells (SNU1, SNU16, SNU216, SNU620, SNU638 and NCI-N87) and normal gastric epithelial cell (HFE145) was determined by real-time PCR using specific primers for DPY30. GAPDH was used to normalize data. Values shown are the means ± SDs of the three independent experiments performed in triplicate. *, <i>p</i> < 0.01 (Student’s <i>t</i> test, versus HFE145). (F) The expression of DPY30 in gastric cancer tissues was examined by real-time PCR using specific primers for DPY30. GAPDH was used to normalize data. Values are the means ± SDs of three independent experiments performed in triplicate. *, <i>p</i> < 0.01; **, <i>p</i> < 0.05 (Student’s <i>t</i> test, versus normal).</p