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 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

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

The time course of activation of enhancers and promoter at the <i>TNFAIP3</i> locus.

<p>The core panel shows a genome browser view of the TNFAIP3 locus with the locations of FANTOM5 enhancers. The lower right panel (p1@TNFAIP3) shows the time course of induction of <i>TNFAIP3</i> mRNA, detected by CAGE, which peaks around 2 hours and declines to a new, elevated steady state by 8 hours. Other panels show the transient activity of the enhancers indicated, the majority of which peak around 1–2 hours and decline rapidly. Panel at bottom right shows the activity of the enhancer containing the SNP originally associated with CD susceptibility, 185kb upstream of the <i>TNFAIP3</i> locus [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006641#pgen.1006641.ref002" target="_blank">2</a>]. Data are expressed as TPM, and are the average of the three replicates.</p

The time course of activation of enhancers and promoter at the IL6 locus.

<p>The core panel shows a genome browser view of the <i>IL6</i> locus with the locations of FANTOM5 enhancers. The upper right panel shows the time course of induction of <i>IL6</i> mRNA, detected by CAGE, which peaks around 3–4 hours and declines by 12 hours. The lower panels show the transient activity of the enhancers indicated, the majority of which peak around 1–2 hours and decline rapidly. Data are expressed at TPM, and are the average of the three replicates.</p

Enrichment of macrophage-expressed or regulated genes in genomic regions associated with IBD susceptibility

<p>Each panel shows the enrichment of GWAS-associated variants in vicinity of genes meeting the expression criteria (specifically inducible in monocytes AND down regulated during differentiation to macrophages) for each of the traits/diseases shown. For 1000 bins spanning a region of 1Mb above and below all TSS meeting expression criteria, observed:expected ratios were calculated as the ratio of the absolute count of variants with p<1e06 for association with each trait, to the absolute count of all SNPs genotyped in the same study. p-values for enrichment were calculated for the whole set using PASCAL (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006641#sec018" target="_blank">Methods</a>).</p

The time course of activation of enhancers and promoters at the <i>CCL3/CLL4/CCL18</i> locus.

<p>The core panel shows a genome browser view of the locus with the locations of FANTOM5 enhancers. The upper panel show the time course of induction of each of the mRNAs, detected by CAGE. Whereas <i>CCL3</i> and <i>CCL4</i> are coordinately-regulated, <i>CCL18</i> follows a much slower time course and is still rising at 48 hours. The lower panels show the activity of the enhancers indicated. The lowest track shows the histograms of CAGE tags mapped to the region, with colours indicating direction of transcription; green to the right and purple to the left. Note that the entire regions shows evidence of bidirectional transcription initiation. Data are expressed as TPM, and are the average of the three replicates.</p

Results of coexpression analysis for a range of human traits for which high-quality data are available: Crohn's disease, ulcerative colitis, high-density lipoprotein (HDL), low-density lipoprotein (LDL), total cholesterol, triglycerides, height, systolic blood pressure (SBP) and diastolic blood pressure (DBP).

<p>Results of coexpression analysis for a range of human traits for which high-quality data are available: Crohn's disease, ulcerative colitis, high-density lipoprotein (HDL), low-density lipoprotein (LDL), total cholesterol, triglycerides, height, systolic blood pressure (SBP) and diastolic blood pressure (DBP).</p

Examples of detail of chromosomal regions surrounding regulatory regions significantly coexpressed in ulcerative colitis (TSS+/-150Mb).

<p>(a) Region surrounding IL10 (b) Region surrounding C1orf106. Top panel: Coloured rectangles show genomic location of individual regulatory regions (promoters or enhancers). Height of regulatory regions on y-axis depicts the coexpression score assigned to this regulatory region; groups of regulatory regions considered as a single unit (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005934#sec002" target="_blank">Methods</a>) share the same colour. Black circles show GWAS p-values for individual SNPs. Red circles show causative probabilities estimated by Huang <i>et al</i> for specific variants, where available. Bottom panel: genomic locations of known protein coding transcripts in sense (green) and antisense (purple).</p