Additional file 2: of Landscape of transcriptional deregulation in lung cancer

Table S1. TFs deregulated in each lung cancer dataset. Columns are: DS (dataset), DIR (direction of regulation), TF, lfc (log2 fold change), p (differential t test p value), ntargs (number of targets deregulated) and targs (targets deregulated). Table S2. GO terms enriched in targets of each TF. Columns are: DS (dataset), DIR (direction of regulation), TF, GO, Term, Annotated (Number of genes annotated and recognized in GO term), GOI (Number of deregulated targets for each TF), Hits (TF targets annotated in the GO term), OR (odds ratio), pFisher (Fisherâ s Exact Test p value) and Genes (Gene Hits). Table S3. Evaluation of SVM parameters. Different parameter combinations were used to set up the OC-SVM model for training. Each model was used to predict a TF network, which was then applied to the LUSC dataset to see if the two positive control TFs (TP63 and SOX2) can be recalled. Table S4. Evaluation of differential analysis parameters. Several combinations of log2fc and q value thresholds were applied to determine up- and down-regulated genes in the LUSC dataset, which are further used for TF identification. The identified TFs are compared with each other to evaluate the procedural robustness upon the various parameter choices. Top left and right: summarizing tables; Bottom: detailed tables of TFs identified in each parameter combination. (XLS 3594 kb)