Demographic, clinical and pathologic characteristics.

<p>Demographic, clinical and pathologic characteristics.</p

Kaplan-Meier survival curve comparing overall survival estimation between low- and high-expressing E-cadherin groups.

<p>a) Patients with high tumor E-cadherin expression exhibit a higher probability of OS (69.6% vs. 44.3%, p = 0.05). b) There was no association between beta-catenin and OS (p = 0.16). c) Patients with high tumor EGFR expression had inferior 5-year overall survival compared with those with low tumor EGFR expression (27.7% vs. 54%, p = 0.029).</p

Multivariable 5-year overall survival (OS) analysis, by Cox regression.

<p>Multivariable 5-year overall survival (OS) analysis, by Cox regression.</p

Kaplan-Meier survival curve comparing progression-free survival estimation between low- and high-expressing E-cadherin, beta-catenin and EGFR groups.

<p>a) Patients with high tumor E-cadherin expression exhibit a higher probability of PFS (59.7% vs. 40.6%, p = 0.04). b) Patients with low expression of beta-catenin trended towards worse PFS (p = 0.057). c) There was no association between EGFR expression and PFS (p = 0.49).</p

Histograms showing heterogeneity of distributions of individuals shown in the CTLA-4 genotype landscape, defined by the inter-personal differences in <i>prp</i>'s for the five most discriminating <i>RRP</i> combinations.

<p>Two selected combination of distance differences are plotted on <b><i>x</i></b> and <b><i>y</i></b> axes, on the <b><i>z</i></b> axis are numbers of subjects having a given combination of the distance differences. Blue-controls, red-cases.</p

Selection of maximally case-control survival discriminating combination of distances from all <i>RRP</i>'s.

<p>Points are defined by the coordinates (see text) computed by averaging the distance differences over all patients separately in case and control sub-cohorts for all 190 possible <b><i>RRP</i></b> pairs. In the neighborhood of diagonal line are non-discriminatory combinations. The two lines are used to identify the combinations, with maximal case – control and control-case bias in <b><i>PRP</i></b>-<b><i>RRP</i></b> distances. The optimal selection is shown by boxes.</p

Example how experimentally determined CTLA-4 genotype (top panel) for a patient (id = 55) is transformed into a) <i>prp</i> graph and b) <i>PRP</i> graph.

<p><b>a</b>-major allele, <b>b</b>-minor allele, <b>ab</b>-heterozygous allele status vertices. Each SNP is represented by a graph partition (rectangles), identified by the SNP code. Lines – graph edges, representing the co-occurrences of all alleles in the patient's CTLA-4 genotype.</p

Case-control discrimination by “missing” CTLA-4 genotype reference profile <i>rrp₈</i> (dashed lines in all figures).

<p>Solid lines in schemes <b>a</b>) – <b>e</b>) show five <b><i>prp</i></b> CTLA-4 genotype profiles, found exclusively for 219 (77%) patients identified from the complete case cohort by condition that their <b><i>prp</i></b> have maximal possible distance from the <b><i>rrp₈</i></b>. Symbols as in Fig. 1.</p

Study graphs <i>g</i>(a) and <i>G</i> (b) constructed as union of all <i>prp</i>'s (<i>g</i>) or <i>PRP</i>'s (<i>G</i>).

<p>Symbols as in Fig. 1, thickness of edges in <b><i>g</i></b> and <b><i>G</i></b> are proportional to co-occurrence frequencies of respective SNP pairs, connected by the edge.</p