COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression

<p dir="ltr"><u>Supplementary Information</u> to accompany the manuscript, <i>"</i><b>COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression</b><i>"</i> The files are:</p><p dir="ltr">S1 -- dataset</p><p dir="ltr">S2 -- Sorted linear model - full information</p><p dir="ltr">S3 -- stage-specific DEGs</p><p dir="ltr">S4 -- Clustering of stage-salient genes</p><p dir="ltr">S5 -- Sorted numeric model - full information</p><p dir="ltr">S6 -- significant MEGs</p><p dir="ltr">S7 -- Expression visualization of MEGs</p><p dir="ltr">S8 -- MEGs significant in Linear Model and Numeric Model (adj. p-val < 1E-05)</p><p dir="ltr">S9 -- MEGs that are in the Linear Model top200</p><p dir="ltr">S10 -- MEGs in the Numeric Model top200</p><p dir="ltr">S11 -- Overlap between the Top 200 of Linear & Numeric Models</p><p dir="ltr">S12 - Stage-salient genes identified in the normals-augmented RNAseqDB COADREAD data</p><p dir="ltr">S13 - Stage-salient genes identified in an external cohort (GSE39582) for benchmarking</p><p dir="ltr">S14 - Univariate Cox survival analysis of all the 157 stage-salient genes</p><p dir="ltr">S15 - Expression trends of APC and MSH2, involved in Familial CRC</p><p dir="ltr">S16 - Consensus between the stage-salient genes and the stage-specific DMGs identified using ChAMP software</p><p dir="ltr">S17 - Summary of the stage-salient genes documented in the Network of Cancer Genes</p><p dir="ltr">S18 - Summary of the stage-salient genes that have been used as targets or endpoints in clinical trials, as documented in ClinicalTrials.gov</p><p dir="ltr">S19 - Monotonically expressed genes (MEG) identified in the external dataset GSE39582, and STRINGdb network reconstruction using the overlap between MEGs and stage-4 salient DEGs</p><p dir="ltr">S20 - Deconvolution results from Cibersort immuno-cyte profiling analysis, yielding significant samples, as well as the raw data used in the related figures</p><p dir="ltr">S21 - Figures A, B, C, D: Analysis of immune cell-type infiltration between tumor and normals, with visualization of immune ecotypes and differential distribution of immune cell-type populations.</p>