Additional file 1: of Using OWL reasoning to support the generation of novel gene sets for enrichment analysis

A complete over-representation analysis for RCV gene sets against GTEx tissue type transcriptomes. The analysis is displayed as a heat map with RCV on the Y-axis, GTEx on the X-axis, over-respresentation in blue and under-respresentation in red. Both axes are clustered for similarity (see Methods for details). (PDF 91 kb

Additional file 4 of Detect tissue heterogeneity in gene expression data with BioQC

Supplementary Document 3. This document can also be assessed on the BioQC website under [29] respectively. (ZIP 325 kb

Potential miR-223 targets are repressed in a miR-223 −/− system.

<p>A) miR-223 expression across the profiled cell types (bars) is plotted against the relative expression profile (lines) of 82 genes identified as potential miR-223 targets (TargetScan, significant negative correlation). Red line represent mean expression profile of target genes, dotted line represents mean expression across cell types. B) 82 genes were identified in our study as being significant miR-223 targets. We used the data from a previously published miR-223 −/− system <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029979#pone.0029979-Baek1" target="_blank">[25]</a> to see if those targets would correspondingly be de-repressed when miR-223 is knocked-out. 62 of these 82 genes had matching mouse homologs (in red). The change in expression of these genes was compared against all TargetScan predicted miRNA target genes, which included predicted targets not negatively correlated with miRNA expression in our dataset (234 genes, in blue). Fold-change for all probe sets is also plotted in this figure as a null distribution (black).</p

696 transcripts are uniquely expressed by 1, 2 or 3 blood cell subsets.

<p>696 transcripts are uniquely expressed by 1, 2 or 3 blood cell subsets.</p

Significant overlap observed between Roche and HUG datasets.

<p>A) Excluding mDCs and pDCs, 749 genes were identified as cell-type specific in the Roche dataset, compared to 672 in HUG dataset. 416 genes were common to both (<i>p</i><2.2e-16). The Jaccard coefficient (i.e. the intersection to union ratio), which measures sample set similarity, is 0.41. B) Excluding mDCs and pDCs, 35 miRNAs were identified as cell-type specific in the Roche dataset, compared to 54 in HUG dataset. 24 miRNAs were common to both (<i>p</i><2.2e-16) with a Jaccard coefficient of 0.37. C) 6 miRNAs were significantly negatively correlated with their TargetScan predicted target genes in the Roche dataset, compared to 21 in the HUG dataset. 4 miRNAs were common to both datasets with a Jaccard coefficient of 0.17.</p

Cell type specific expression of miRNAs.

<p>miRNAs were grouped based on specificity to one, two or three cell types. <b>A</b>) miR-143 and miR-31 were specific to neutrophils and T cells respectively, while <b>B</b>) miR-362 and miR-125 were specific to monocytes, pDCs and T cells, neutrophils. <b>C</b>) miR-223 was specific to myeloid lineage cells (neutrophils, eosinophils and monocytes), whereas miR-155 was specific to lymphoid lineage cells (pDCs, T cells, B cells and NK cells).</p

6 cell-type specific miRNAs are negatively correlated with significant numbers of target mRNAs as predicted by TargetScan.

<p>6 cell-type specific miRNAs are negatively correlated with significant numbers of target mRNAs as predicted by TargetScan.</p

MOESM2 of Selective pharmacological inhibition of DDR1 prevents experimentally-induced glomerulonephritis in prevention and therapeutic regime

Additional file 2. Additional tables

Additional file 2: Table S2. of Functional analysis and transcriptional output of the GĂśttingen minipig genome

Contig assembly statistics. Roche-454 reads that were not incorporated into the minipig genome were assembled de-novo with Roche-Newbler software. (DOCX 13 kb

MOESM1 of Selective pharmacological inhibition of DDR1 prevents experimentally-induced glomerulonephritis in prevention and therapeutic regime

Additional file 1. Additional figures