Additional file 3 of Coordinated regulation of WNT/β-catenin, c-Met, and integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits

Additional file 3 Supplementary Table 1. List of target proteins assayed by RPPA, together with identifiers for the protein (UniProtKB), protein names abbreviations, and identifiers of the cognate transcript genes (HUGO Gene ID, Entrez Gene ID, ENSEMBL Gene ID), as well as information regarding the antibodies used in RPPA (Company, Antibody ID, experimental notes). Supplementary Table 2. Results of the limma test on RPPA HTS data. Columns B to BK display corrected p-values and columns BN to DW display log2 fold changes computed comparing the effect of miRNAs to the negative controls of the same transfection round. Data is displayed for all the 62 proteins investigated by RPPA. Supplementary Table 3. Results of enrichment analysis of predicted interactions in experimental results of RPPA HTS. P-values are marked in green when statistically significant < 0.05. Enrichment is divided into TargetScan conserved (TS Cons), TargetScan non-conserved (TS NC), and microCosm Target (MCT). Supplementary Table 4. List of target proteins and respective associated pathway(s). Literature review was done to define the putative effect of the target on the associated pathway(s). Supplementary Table 5. After bootstrapping test, miRNAs are considered as repressors of the pathway(s) (− 1, green field) or activators of the pathway(s) (1, red field). The table lists all 722 miRNAs that had at least one statistically significant interaction with one target protein. Supplementary Table 6. Gene sets used for GSEA investigating the relationship of miR-193b and the WNT pathway. The positive and negative geneset were generated as subset of the KEGG_WNT_SIGNALING_PATHWAY geneset based on the established function of the encoded proteins within the pathway. Supplementary Table 7. Refering to reveiwer 1 concerns: ENCORI database (previously known as StarBase, http://starbase.sysu.edu.cn/index.php) results for miR-193b-3p for targets probed in the RPPA HTS. Narrow and broad sites of binding from the experimental data are shown, together with the number of CLIP experiments reporting the binding (ClipExpNum). RBP column indicates which Argonaute protein have been immunoprecipitated in the experiments listed. The columns of prediction algorithm show whether the discovered binding site is also predicted. The column of pathways associated to our network analysis was added to indicate, of the targets selected, to which pathway they were assigned.Supplementary Table 7 - refering to reveiwer 1 concerns: ENCORI database (previously known as StarBase, http://starbase.sysu.edu.cn/index.php) results for miR-193b-3p for targets probed in the RPPA HTS. Narrow and broad sites of binding from the experimental data are shown, together with the number of CLIP experiments reporting the binding (ClipExpNum). RBP column indicates which Argonaute protein have been immunoprecipitated in the experiments listed. The columns of prediction algorithm show whether the discovered binding site is also predicted. The column of pathways associated to our network analysis was added to indicate, of the targets selected, to which pathway they were assigned.