Gene set collections used in the study.

<p>Gene set collections used in the study.</p

Prediction performance of various gene set collections and single genes.

<p>Shown are the prediction performance with TR, C1-4, and IS gene set collections as well as with only single genes (SG). Subplots are for <b>(A)</b> likelihood ratio of Cox proportional hazard model fitting, <b>(B)</b> Harrell’s C index, <b>(C)</b> R², and <b>(D)</b> the log-rank test p-value when stratified in the median. Dashed lines represent the median statistics of single gene predictions.</p

Prediction performance for the trauma benchmark data set.

<p>The Kaplan-Meier curves for the recovery of high-risk (solid) and low-risk (dashed) patients according to the recovery risk predicted <b>(A)</b> by the conventional method with only single genes and <b>(B)</b> by the proposed hybrid method using both single genes and gene sets.</p

Benchmark data sets used in the study.

<p>Benchmark data sets used in the study.</p

Chromatograms comparing purity and yield of final product before and after purification.

<p>A = unincorporated common and variable strands, B = FLP, C = S1–S6 after size-exclusion purification, and D = S1–S6 after gel extraction.</p

Prediction performance of the proposed hybrid method.

<p>Shown are the prediction performance of the proposed hybrid method using both gene sets and single genes for various gene set collections (TR, C1-4, and IS). The prediction performance with only single genes are also shown as a reference (SG). Subplots are for <b>(A)</b> likelihood ratio of Cox proportional hazard model fitting, <b>(B)</b> Harrell’s C index, <b>(C)</b> R², and <b>(D)</b> the log-rank test p-value when stratified in the median. Dashed lines represent the median statistics of single gene predictions.</p

Agarose gel images showing the effects of DMSO and betaine during the PCA assembly (A and C) and amplification (B and D) of IGF2R and BRAF gene fragments.

<p>Based on a 20 µl reaction volume, both additives were introduced with increasing percentage (%) for DMSO, and molarity (M) for betaine; ‘No Additive’ lanes correspond to the control samples. A 1 kb DNA ladder in the outermost lanes marked at 400, 500 and 700 bp indicates the area of highest product band population. IGF2R and BRAF full-length gene fragments are shown at 517 bp and 512 bp, respectively.</p

Figure shows the general process of probe ligation followed by FLP size-exclusion purification.

<p> To make each probe, the variable, bridge and common strands are first combined in the presence of a ligase mix (e.g. Fast-Link or Quick Ligase); the reaction is then carried out at RT for 10 min. Afterward, the sample is passed through P-10 polymeric resin where unincorporated species are thus retained, and FLP eluted. The final purified, desalted product of pooled ODN probes is now ready for downstream application.</p

Agarose gel images showing the effects of DMSO and betaine during LCR assembly (A and C) and amplification (B and D) of IGF2R and BRAF gene fragments.

<p>Based on a 20 µl reaction volume, both additives were introduced with increasing percentage (%) for DMSO, and molarity (M) for betaine; ‘No Additive’ lanes correspond to the control samples. A 1 kb DNA ladder in the outermost lanes marked at 400, 500 and 700 bp indicates the area of highest product band population. IGF2R and BRAF full-length gene fragments are shown at 517 bp and 512 bp, respectively.</p

Sequences used for generating 101 bp probes (variables, S1–S6, were pooled with the complimentary bridge and common strand in the presence of Fast-Link/Quick Ligase).

<p>Sequences used for generating 101 bp probes (variables, S1–S6, were pooled with the complimentary bridge and common strand in the presence of Fast-Link/Quick Ligase).</p