Additional file 2: of Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Hierarchical clustering, expression plots and top 10 tissues, primary cells and cell lines of RFX TSS locations. Hierarchical clustering of 30 RFX TSS locations (with shorthand p for promoter) based on expression values (TPM) across 135 human tissue samples, using a 1-Pearson correlation distance measure and average linkage method, as computed by the pvclust R package with nboot = 1000 with the numbers representing approximately unbiased (au) p-values (Suzuki and Shimodaira, 2006). Tissue clusters are color-coded and represent the groups of tissues with the highest overall expression values: immune system (teal), gastrointestinal tract (purple), testis (green), brain and spinal cord (red), and two minor clusters, uterus and lung (black). RFX TSS locations without color code have low expression values (TPM < 5). This is followed by the expression profiles of 30 RFX TSS locations in human tissues, primary cells and cell lines, whereby for every one of the eight human RFX genes (1–8), summarized TSS profile data are presented vertically (“top-down”), starting with the a tissue plot, followed by a table of the top 10 tissues, a table of the top 10 primary cells and a table of the top 10 cell lines (highest expression levels are listed first, respectively). The tissue plot is the expression level in log (base 10) TPM against tissues that are sorted from the highest to the lowest expressed from 135 tissues, whereby the plot only includes the first 100 tissues. The arbitrary unit for detection of expression is tags per million (TPM) as defined by FANTOM5. We consider TPM < 5 to be lowly expressed and TPM < 1 to be background noise. (PDF 3276 kb

Additional file 4: of Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Detailed candidate RFX regulator oPOSSUM3 scanning results using JASPAR 2016 core vertebrate TF binding profiles. Transcription factor binding sites (TFBS) scanning results from oPOSSUM3 within the promoter and enhancer regions of RFX1–8 using the CORE vertebrate TF binding profiles in JASPAR 2016. Included are the DNA regions that were considered as foreground and the following TF binding site details: SP2 (specificity protein 2) (JASPAR profile MA0516.1) and ESR1 (estrogen receptor alpha) (MA0112.3). (XLSX 50 kb

Additional file 5: of Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Ct levels of qRT-PCR, used for validation of candidate RFX regulators by siRNA knockdown. Individual Ct levels with automatic threshold obtained on an AB7500 Fast machine for SP2 and ESR1 as candidate RFX regulators and their respective test siRNA and scrambled (Scr) control siRNA knockdown data on RFX genes (RFX1, RFX2, RFX3, RFX5, RFX7) and the two reference genes (HPRT1, HSPCB). (XLSX 33 kb

Additional file 1: of Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Detailed expression values (TPM) for RFX TSS locations. Expression values in tags per million (TPM) for all 30 RFX TSS locations in all 889 biological samples and their categorization into tissues (135), primary cells (473 donor replicates and 170 merged replicates from the average TPM value of the donor replicates), cell lines (255) and time courses (26). (XLSX 355 kb