7 research outputs found
Samples description and microarray quality.
<p>Type of tumor and delay to tumor freezing are shown. RNA integrity is evaluated through the RIN number. The ratio of centiles P95/P05 reflects the overall strength of the signal compared to the background. The Pearson correlation coefficient (r<sup>2</sup>) shows the correlation between log-expression levels of the central and peripheral samples, for each tumor and each time to cryopreservation.</p><p>HCC: HepatoCellular Carcinoma.</p><p>LC: Lung Carcinoma.</p><p>ND: Not Determined.</p
List of 34 HCC specific genes: comparison of gene expression data from the Liverome database and experimental dataset.
<p>Expression trend of 34 HCC specific genes reported as deregulated in more than 4 studies in the public Liverome database was compared to experimental expression trend.</p>a<p>average rate of expression from different Illumina probes.</p>b<p>discrepancies between Liverome studies results.</p><p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079826#pone-0079826-t003" target="_blank">Table 3</a> References.</p><p>1) Chan, K.Y., Lai, P.B., Squire, J.A., Beheshti, B., Wong, N.L., Sy, S.M., Wong, N., 2006. Positional expression profiling indicates candidate genes in deletion hotspots of hepatocellular carcinoma. Mod Pathol 19, 1546–1554.</p><p>2) Chung, E.J., Sung, Y.K., Farooq, M., Kim, Y., Im, S., Tak, W.Y., Hwang, Y.J., Kim, Y.I., Han, H.S., Kim, J.C., Kim, M.K., 2002. Gene expression profile analysis in human hepatocellular carcinoma by cDNA microarray. 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Gene expression for all probes and for restricted sets of probes.
<p>Over-all rate of expression changes for all probes in all samples combined, in LC and HCC samples and in peripheral and central samples are estimated as percent-change per hour. Expression levels changes are also estimated for different sets of probes (lowest and highest 5% of geometric mean expression, probes in warm ischemia genes and probes in HCC genes).</p
Within- and between-sample variance box-plot of microarray non-normalized fluorescent signals.
<p>The non-normalized fluorescent signals (AVG_Signal) have been generated by the Illumina Genome Studio V2010.2 for the 3 HepatoCellular Carcinomas (HCC) and the 3 Lung Carcinomas (LC ) samples taken at the center and at the periphery of the tumors and maintained at room temperature and then frozen in liquid nitrogen at different times: 5 minutes (t5, reference time), 15 minutes (t15), 30 minutes (t30) and 120 minutes (t120).</p
Average log-expression profiles of the 12 genes with significant up- or down-regulation over harvesting time (FDR<0.05) in HCC.
<p>The BRB-ArrayTools v4.2 time course analysis model was applied to whole-genome expression microarray data (HCC and LC samples) to identify significant individual deregulated genes over harvesting time. No significant deregulated genes in LC were observed. Individual log-expression profiles () and average log-expression line plots (3 HCC samples taken at the center and at the periphery) in relation to delay to tumor cryopreservation are displayed.</p
Hierarchical cluster analysis of all samples following log-transformation and quantile normalization of the microarray data.
<p>Dendrogram for clustering experiments was created using centred correlation and average linkage method. Length of nodes corresponds to correlation between samples. HCC4_5P: HCC from patient 4 taken at the periphery of the tumor and maintained at room temperature and then frozen in liquid nitrogen at t5 (min).</p
Time-course scatter-plots of HCC and LC genome-wide expression profiling quantile normalized data.
<p>Scatter plots for each tumor pair at t5 (HCC_5_AVG_Signal and LC_5_AVG_Signal on the X Axis) versus harvested tumor pairs at t15, t30 and t120 (on the Y Axis) were generated on a logarithmic scale. Genes showing greater than 2-fold change relative to the t5 sample from the same tumor were highlighted.</p