Gene Expression Omnibus (GEO) datasets and data preprocessing

Two genome wide expression datasets of accession {"type":"entrez-geo","attrs":{"text":"GSE27276","term_id":"27276"}}GSE27276 and {"type":"entrez-geo","attrs":{"text":"GSE4316","term_id":"4316"}}GSE4316 were obtained from Gene Expression Omnibus (GEO) repository of NCBI. The dataset {"type":"entrez-geo","attrs":{"text":"GSE27276","term_id":"27276"}}GSE27276 was an expression profiling by array which compared genome wide expression in the trabecular meshwork tissues of 15 POAG patients with that of 13 controls using Sentrix Human-6 Expression BeadChip platform. The dataset {"type":"entrez-geo","attrs":{"text":"GSE4316","term_id":"4316"}}GSE4316 was an expression profiling by array which compared genome wide expression in the trabecular meshwork tissues of 2 POAG patients with that of 3 controls using Affymetrix Human Genome U133 Plus 2.0 Array platform.

The GEO2R tool was used to perform differential expression analyses and statistical tests. The GEO2R tool uses GEOquery R package to parse GEO data into R data structures and the limma (Linear Models for Microarray Analysis) R package to carry out statistical tests for identifying differentially expressed genes. Significant differentially expressed genes were filtered based on adjusted P. Value ≤ 0.05 which is adjusted based on the Benjamini and Hochberg false discovery rate method. For dataset {"type":"entrez-geo","attrs":{"text":"GSE27276","term_id":"27276"}}GSE27276, significant differentially expressed genes were filtered using P. Value ≤ 0.05 and having at least twofold change expression, since filtering using the adjusted P. Value gave very few entries which would not fit into the criteria to perform downstream pathway enrichment analyses.