Predictors of Outcome in Aneurysmal Subarachnoid Hemorrhage Patients:Observations From a Multicenter Data Set

A table containing information on the qRT-PCR performed with seven novel miRNAs and two known miRNAs. Per miRNA, this information includes mean CT, range of CT, cDNA dilution, the number of samples (of 12) with CT < 40, the average read depth, and primer used. (XLSX 8 kb

Additional file 1: of Novel microRNA discovery using small RNA sequencing in post-mortem human brain

Provides information on each of the 93 samples used in this study. This information includes ID, type (Control/HD/PD), PMI (Post-mortem-interval), age at death, sex, batch, brain bank, and cause of death. (XLSX 13 kb

DE statistics.

<p>A) Histogram of log2 fold changes for DE genes showing that 54.8% of the DE genes are overexpressed in HD cases. B) Fraction of up vs down regulated genes across the gene list ranked by significance. Top and bottom plots are top 500 and remaining genes, respectively. Sliding windows lines plot the fraction up vs down in the 100 gene window of greater rank than the x coordinate. This plot shows that the most highly differentially expressed genes are predominantly over-expressed in HD relative to control BA9. C) Pie chart shows proportions of biotypes for DE genes according to Ensembl. Protein coding genes are over-represented among the DE genes. D) Normalized counts for all samples in HD and control for top ten significant genes. Rows are normalized for visualization such that the highest count is equal to 1. These genes are almost exclusively expressed in HD cases.</p

Clustergram of Top Enriched Pathway, TF, and GO terms.

<p>Concatenated enrichment profiles for GO, C2, and TF gene set collections, similar to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143563#pone.0143563.g003" target="_blank">Fig 3</a>, ordered by hierarchical clustering of Euclidean distance between rows. Rows have been normalized by dividing by the row sum for visualization, intensity is proportional to normalized enrichment. Heatmap is partitioned into groups A-E based on hierarchical clustering. Clusters A, B, and C are primarily involved in the immune response and are enriched in gene subsets that include more genes. Clusters D and E are predominantly related to developmental and transcriptional regulation processes.</p

DE genes by significance.

<p>DE genes by significance.</p

HD sample statistics.

<p>HD sample statistics.</p

Control sample statistics.

<p>Control sample statistics.</p

Protein coding genes associated with clinical covariates.

<p>P-values are nominal.</p

DAVID functional clustering network.

<p>Network representation of the DAVID clusters from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143563#pone.0143563.t005" target="_blank">Table 5</a>. Nodes represent clusters, the size of the node is proportional to the number of unique genes that make up the cluster and numbers within nodes are the number of unique genes mapped to terms in the cluster. Edges between nodes indicate the existence of overlapping genes, where the width is proportional to the percent overlap of genes in the smaller of two connected nodes. The color of nodes and edges is proportional to the average fold change of the genes in the node or edge.</p

Detailed GO enrichment.

<p>Top 25 enriched GO categories across all three GO namespaces identified by topGO for different numbers of DE genes. X-axis indicates the number of top genes used for the enrichment in each GO category, e.g. the first column uses the top 25 genes, the second column uses the top 50, and so on. The intensity is proportional to–log10(p-value) from topGO. White dots indicate the gene set with the most significant p-value, concordant with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143563#pone.0143563.t005" target="_blank">Table 5</a>. This figure shows that the first three GO Categories are defined by genes that are among the top 25 to 150 DE genes in the dataset. GO Categories further down the list are defined by genes whose differential expression is less pronounced between HD and controls.</p