Additional file 1 of TOP2A and CENPF are synergistic master regulators activated in cervical cancer

Additional file 1: Supplementary Table 1: MR DA and DE signatures for the 10 datasets. “MR_set”, categories of functions of MRs (TF, transcriptional factor; TFcoFac, transcriptional co-factors; SigPathway, signal pathway); “regulon_size”, number of regulons for a MR; “rank_cat”, category of ranking. For example, 100 indicates that the MR is a common MR of the top 100 activated MRs in the 5 discovery datasets. -100 indicates that the MR is a common MR of the top 100 suppressed MRs in the 5 discovery datasets. 0 indicates the MR is not the common top MRs in the 5 discovery datasets. “nes.”, the NES score of a MR in a dataset calculated using VIPER, representing the DA signature. “pval.”, the P-value of the NES from the VIPER analysis. “t.”, the value representing the DE signature (e.g. the t-statistics for microarray). “DiscoverySet_DA-DE_consistent”, whether the DA and DE are consistent. The DA-DE Consistency set was selected using |DE| value> 3 and same sign as DA in all the five discovery datasets. Supplementary Table 2: DE signatures of the common regulons of TOP2A and CENPF for the 10 datasets. “MOR_sign”, sign of MOR (positive (1) or negative (− 1) MOR for both TOP2A-regulons and CENPF-regulons). “DE.average”, the average values of the DE values for the 10 datasets. Supplementary Table 3: Network of TOP2A, CENPF and their regulons. “Regulator” is the gene ID of a MR (here CENPF or TOP2A). “interaction” is always “regulate”. “Target” is the regulon of a regulator. “MOR”, mode of regulation, ranges between − 1 and + 1. “likelihood”, range from 0 to 1, an edge weight that indicates how strong the mutual information for an edge is. All information was extracted from the aracne.networks R package. Supplementary Table 4: “Functional Annotation Clustering” analysis of the 34 TOP2A-CENPF common regulons on DAVID 6.8 website. See DAVID website for details of methods used and interpretation of header names. “Category”, the gene annotation category. UP_KEYWORDS, UniProt Keywords annotation of genes; UP_SEQ_FEATURE, UniProt sequence feature annotation of genes; GOTERM_BP_DIRECT, Gene ontology biological process annotation; GOTERM_CC_DIRECT, Gene ontology cellular component annotation. Supplementary Table 5: CENPF and TOP2A expression in dataset Biewenga_2008 (GSE7410). The expression data were extracted from GEO database using GEO2R tool. The probe ID is indicated after the gene symbol. “Avg_Gex”, the average expression value of CENPF and TOP2A. “sample_type”, sam