Additional file 1 of Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts

Supplementary Figures. A PDF file that contains eight supplementary figures. (PDF 22937 kb

Heat map showing relative chemokine and chemokine receptor expression aligned with the same dendrogram shown in Fig 3.

<p>Heat map showing relative chemokine and chemokine receptor expression aligned with the same dendrogram shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137654#pone.0137654.g003" target="_blank">Fig 3</a>.</p

Principal component analysis based on significantly up-regulated and significantly down-regulated probe sets in TED orbital adipose (T) against uninflamed controls (C).

<p>The discovery set (Set 1) had 36 significantly up-regulated and 254 significantly down-regulated probe sets. The validation set (Set 2) had 66 significantly up-regulated and 604 significantly down-regulated probe sets. At least 1.5-fold change with FDR adjusted p-value < 0.05 is considered statistically significant.</p

Ages for each experimental group.

<p>*one repeated from set 1;</p><p>**two repeated from set 1</p><p>Ages for each experimental group.</p

Probe sets with a significantly lower signal in orbital tissue from TED subjects compared to uninflamed controls.

<p>Probe sets with a significantly lower signal in orbital tissue from TED subjects compared to uninflamed controls.</p

Principal component analysis reveals that gene expression in TED orbital adipose is more similar to uninflamed controls than to tissues from subjects with sarcoidosis, GPA, or NSOI.

<p>C = control. T = TED. N = NSOI. S = Sarcoidosis. G = GPA. Set 1 is based on the discovery set and Set2 is based on the validation set.</p

A dendrogram produced by hierarchical cluster analysis and an independently created heat map of signals for immunoglobulin, cytokine, and cytokine receptor transcripts compares the expression profiles of subjects within each disease group in array dataset 2.

<p>The heat maps were created with the GSEA program comparing probe set signal levels for subjects in branches A and B versus branches C and D. Genes with the highest signals in branches A and B are at the top of each section. The end branch labels are N—NSOI, S—sarcoidosis, G—GPA, T—TED, C—control.</p