Supplementary Figure 2 from Archetype Analysis of Lung Adenocarcinoma Premalignancy Links Heterogeneity in Premalignant Lesions to Diverging Features of Invasive Disease
Year: 2026
Type: supplementary-materials
Abstract: Optimization of archetype analysis (A) Line graph of explained variance versus number of potential archetypes (k = 2 to k = 10), with red dashed line showing suggested number of archetypes based on elbow. Elbow computed by finding the most distant point from the line that passes through k = 2 to kmax = 10 (B) Line graph of t-ratio versus number of potential archetypes (k = 3 to k = 6) to confirm that k = 4 is the optimal number of archetypes. We computed empirical p-values by using randomized gene modules to calculate GSVA scores. We performed this randomization 5000 times and recomputed the t-ratio for k = 3, k = 4, k = 5, and k = 6 for each iteration. Using these t-ratios as a test statistic, we determined how often the t-ratio in the randomized data was greater than the t-ratio of the PML data, and the p-value from the permutation test for each value of k is annotated, with a red dashed line showing the first value for k with a significant p-value at k = 4.
Authors: Kelley E. Anderson, Linh M. Tran, Kostyantyn Krysan, Yohana Kefella, Lingge Yu, Gregory A. Fishbein, Erika F. Rodriguez, Maryam Shabihkhani, Daniel P. Stefanko, Emily Green, Gang Liu, Hanqiao Liu, Sherry Zhang, Erin Kane, Mitra Mehrad, Avrum E. Spira, Steven M. Dubinett, Eric J. Burks, Sarah A. Mazzilli, Marc E. Lenburg, Jennifer E. Beane
Topic: Lung Cancer Research Studies
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Open Access status: gold
OpenAlex ID: W7204995813
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