Additional file 2: of Integrating heterogeneous genomic data to accurately identify disease subtypes

Heatmaps of patient similarity for kidney cancer. The similarity scores were measured by the Pearson correlation coefficients based on single data types (DNA methylation, mRNA expression and miRNA expression) and the integrated scores (integrated by direct concatenation, SNF and iBFE). (DOCX 875 kb

GBF1 interacts with viral 3A protein.

<p>(A) Immunoprecipitation was conducted with Protein G agarose plus anti-FLAG antibody. Western blots were probed with specific antibodies, as indicated. (B) Immunoprecipitation was conducted with Protein G agarose plus anti-GFP antibody. Western blots were probed with specific antibodies, as indicated.</p

Quantitative real-time PCR primers.

<p>Quantitative real-time PCR primers.</p

GBF1 is required for EV71 replication.

<p>(A) Targeted siRNAs could effectively knockdown the expression of each GEF (<i>P</i><0.05). (B) Knockdown of GBF1, but not BIG1 or BIG2, inhibited EV71 replication in cells (<i>P</i><0.05). (C) GBF1-EGFP is overexpressed in RD cells by transfection. (D) Overexpression of GBF1 rescued viral replication from BFA exposure (<i>P</i><0.05).</p

COPI is required for EV71 production.

<p>(A) αCOP, (B) ζ1COP silencing with two individual siRNA duplexes blocked EV71 viral protein VP1 expression by Western blotting with the indicated antibodies (<i>P</i><0.05). Quantification analysis of EV71 VP1 synthesis was performed by Image J. Standard deviations of three independent experiments are shown. (C) αCOP and ζ1COP depletion by siRNA inhibited EV71 virions production (<i>P</i><0.05). Values were obtained from triplicate wells and are mean ± SD.</p

COPI but not COPII is essential for EV71 replication.

<p>COPI subunits (A) αCOP and (B) ζ1COP silencing with two individual siRNA duplexes blocked replication of EV71 (<i>P</i><0.05). COPII subunits (C) Sec13p and (D) Sec23p depletion by siRNA was dispensable to EV71 replication (<i>P</i>>0.05). Values were obtained from triplicate wells and are mean ± SD.</p

COPI is required downstream of viral entry.

<p>(<b>A</b>) Cells were pretreated with siRNA, infected at 4°C to allow surface binding, followed by 3 hr at 25°C to resume endocytosis. Viral entry was measured by determining viral genome copies, which was almost unchanged between COPI knocked down group and control group (<i>P</i>>0.05). (<b>B</b>) BFA and GCA inhibited EV71 replication (<i>P</i><0.05), when added up to 6 hpi. RD cells were infected with at 0.1 MOI and harvested at 24 hpi. The experiment was performed in triplicate, and the bars represent means ± SD.</p

Additional file 1: of Integrating heterogeneous genomic data to accurately identify disease subtypes

Heatmaps of patient similarity for lung cancer. The similarity scores were measured by the Pearson correlation coefficients based on single data types (DNA methylation, mRNA expression and miRNA expression) and the integrated scores (integrated by direct concatenation, SNF and iBFE). (DOCX 802 kb

siRNA sequences used in this study.

*<p>Stealth-990 corresponds to the siRNA against EV71 VP2.</p

Overexpression of Arf proteins could not rescue EV71 replication from BFA exposure.

<p>(A) All the Arf proteins tested are expressed at high levels in RD cells. (B) Overexpression of Arf proteins did not rescue viral replication under BFA exposure (<i>P</i>>0.05).</p