Additional file 4 of An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes

Additional file 4: Table S1. List of HCT116 TFs and their corresponding files obtained from ENCODE portal ( https://www.encodeproject.org/ ). Table S2. Interpretations of the different combinations of signs of TF and histone mark change weights. Table S3. Expression changes in AP1-complex components upon JunD Knockdown. Table S4. Survival analysis on TCGA COAD cohort. Survival analysis of 374 patients was performed using different gene sets for clustering of omics profiles. Each row indicates the criterion used to pick the gene set (gene set type) and the setting used in the best clustering of patients in terms of survival analysis p-value (pval). The gene set was chosen to be of one of the following: 1. Using the data of all genes provided (Unfiltered). 2. Genes with the highest RPOR value in down-analysis (RPOR_down). 3. Genes with the highest RPOR value in up-analysis (RPOR_up). 4. Significantly differentially expressed genes (DE Genes). For all types of gene sets except “Unfiltered” sizes of 50, 70, and 100 were tested. To find the best clustering for the patients using each gene set, two types of networks, viz., protein-protein interaction network (PPI) and Enrichr pathway network were tested using the knowledge-guided clustering pipeline in KnowEnG; two different settings of smoothing (0.3 and 0.8), representing different levels of network-guidance, were explored. (Knowledge-guided clustering was applied only to the sparse somatic mutation data, while other types of omics profiles were clustered in the default mode.). Cluster sizes of 3 and 4 were tested. The total number of clusterings explored and followed by survival analysis, for RPOR-down and RPOR-up combined, DE Genes, and Unfiltered, are 48, 24, and 8 respectively, which were used to adjust the p-values by Bonferroni Correction (adj. p-val). Table S5. List of K562 TFs and their corresponding files obtained from ENCODE portal ( https://www.encodeproject.org/ ).