Additional file 2: of Identification of new biomarkers for Acute Respiratory Distress Syndrome by expression-based genome-wide association study

Table S2. Chi-square values of cross-referenced genes. Given that different microarray platforms have multiple probes for a single gene, the cross-referencing of such platforms generates numerous combinations of expression values for a given gene (32160 in this study). Chi-square value was calculated for each of these combinations and combination with the best chi-square value for a given gene was retained, which resulted in 3152 unique gene entries. These genes were linked to human genome and plotted against their location (Fig. 1). (XLS 185 kb

Additional file 1: of Identification of new biomarkers for Acute Respiratory Distress Syndrome by expression-based genome-wide association study

Table S1. Detailed representation of data obtained from GEO. ARDS gene expression submissions were retrieved from GEO using two terms “Acute lung injury” and “Lung injury”, which resulted in 23 and 25 data sets, respectively. These 48 entries were filtered down to 31 entries according to conditions described in Methods. The reason for filtering out an experiment is provided. (XLSX 16 kb

A transcription profile of HMVEC cells (Control A) for chromosome 1.

<p>The RNASeq read density plotted along chromosome 1 is shown. Average alignment was computed by igvtools. The coverage values were measured along intervals of the genome. These intervals vary in size depending on how variable the read density is for a particular genomic location. Each bar represents the log₂ frequency of reads plotted against chromosome coordinates.</p

Top networks affected by down-regulated genes/isoforms after thrombin treatment of HMVEC cells.

<p>Networks significantly down-regulated by thrombin treatment as determined by Ingenuity Pathway Analysis. The score is based on the p-value calculation. Networks with a score of 15 or greater were defined as significant.</p

Networks affected by up-regulated genes/isoforms after thrombin treatment of HMVEC cells.

<p>Networks significantly down-regulated by thrombin treatment as determined by Ingenuity Pathway Analysis. The score is based on the p-value calculation. Networks with a score of 15 or greater were defined as significant.</p

qRT-PCR validation of three differentially expressed genes from thrombin-treated HMVEC RNA-Seq data. qRT-PCR was carried out as described in the Method.

<p>Fold changes determined from the relative Ct values of TaqMan Gene Expression assay for CUGBP, Elav-like family member 1 (CELF1), Fanconi anemia, complementation group D2 (FANCD2) and TNF receptor-associated factor 1 (TRAF1) were compared to those detected by RNA-seq. Replicates (n = 4) of each sample were run and the Ct values averaged. All Ct values were normalized to beta-actin. The error bars represent the range of the fold change as determined by the Data Assist software.</p

Top 10 up-/down-regulated gene isoforms in thrombin treated HMVEC.

<p>The differentially expressed gene isoforms in thrombin treated HMVEC vs those in control cells were determined by CuffDiff, after Benjamini-Hochberg correction. The fold change is the ratio of FPKM of those gene isoforms in thrombin treated HMVEC to FPKM of those in control cells. The differentially expressed gene isoforms were ranked on their fold change and the 10 with the highest or lowest fold changes are shown here. The full name of each gene isoform symbol is provided in text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031229#pone.0031229.s002" target="_blank">Table S2</a>.</p

Top canonical pathways affected by up-regulated genes/isoforms after thrombin treatment of HMVEC cells.

<p>Top canonical pathways significantly up-regulated by thrombin treatment as determined by Ingenuity Pathway Analysis. Pathways with a p-value less than 0.05 defined as significant.</p

Top ten up- and down- regulated novel isoforms in thrombin treated HMVEC Cells.

<p>Novel Isoforms significantly differentially expressed as determined by CuffDiff, after Benjamini-Hochberg correction. The fold change is the ratio of thrombin FPKM to control FPKM. The novel isoforms were ranked on their fold change and the 10 with the highest or lowest fold changes are listed here.</p

Gene/Isoform expression summary.

<p>Genes, known isoforms and novel isoforms expressed in control and thrombin-treated HMVEC cells. Expression determined by CuffDiff, after Benjamini-Hochberg correction. The fold change is the ratio of thrombin FPKM to control FPKM.</p