Additional file 9 of Aberrant expression of collagen type X in solid tumor stroma is associated with EMT, immunosuppressive and pro-metastatic pathways, bone marrow stromal cell signatures, and poor survival prognosis

Supplementary Material 9. Table S1: Overview of cancer datasets used in this study. (A) Breast and pancreatic cancer datasets used in this study. (B) Citations of breast cancer GEO accessions used in this study. Table S2: Gene modules characterized in this study. (A) WGCNA-generated COL10A1 (ColX) modules from TCGA breast and pancreatic cancer datasets, as well as gender-specific pancreatic cancer datasets. (B) WGCNA module assignments for all expressed genes in each dataset. Modules are numbered in descending order of size, beginning with module 1. “-” indicates genes which were filtered out based on low expression; genes labeled with a 0 were not assigned to any module by WGCNA. Table S3: Gene ontology and Reactome pathway enrichment analysis of ColX modules. (A–E) Gene ontology pathway enrichment for (A) breast cancer, (B) pancreatic cancer, (C) overlap between breast and pancreatic cancer, (D) male pancreatic cancer, and (E) female pancreatic cancer ColX modules. (F–J) Reactome pathway enrichment for (F) breast cancer, (G) pancreatic cancer, (H) overlap between breast and pancreatic cancer, (I) male pancreatic cancer, and (J) female pancreatic cancer ColX modules. All significantly enriched Reactome pathways/GO terms (q < 0.05) are shown. Table S4: Hallmark pathway enrichment analysis of WGCNA modules. (A–D) Hallmark pathway enrichment for (A) breast cancer, (B) pancreatic cancer, (C) male pancreatic cancer, and (D) female pancreatic cancer ColX modules. All p-values shown were BH-corrected across all 50 hallmark pathways for each module. ColX modules for each dataset (#8, #13, #7, and #23, respectively) are shown in the first column for clarity. Related to Figure S2A–D. Table S5: TFs implicated in ColX modules. (A) GTRD TFTs enriched in BRCA and PAAD ColX modules. Cancer-relevant TF functions and overlapping targets are shown where applicable. (Related to Figure 2E) (B) Selected QuSAGE-significant transcription factors whose targets are differentially activated/inactivated between tumors with high and low ColX module expression. Cancer/OA-relevant TF functions are shown where applicable. (Related to Figure 3C). Table S6: Differential expression of bone marrow and cartilage cell type-specific genes. List of all genes defined as specific to normal cartilage stromal cells/NCSCs, OA mesenchymal stromal cells/OA-MSCs, OA chondrocytes/OACs, and bone marrow stromal cells/BMSCs, based on OA RNA-Seq data. Differential expression results were computed across all cells and statistics were extracted for each pairwise comparison. See Methods section for definition of “cell type-specific” genes.