Microarray Analysis of Lung Granulomas

The CEL files obtained from microarrays was processed as reported previously [7 (link),24 (link)]. Briefly, probe level analysis of CEL files was performed using R and Bioconductor and a list of gene expressions in various granulomas was obtained. Raw intensities of perfectly matching (PM) probes expressed in each array were subjected to local background correction using Microarray Suite Version 5.0 software (MAS5; Affymetrix, Santa Clara, CA). The values from each sample (in triplicate) were log₂-transformed and median-centered. A family-wise p-value of ≤ 0.05 was applied to select the list of significantly differentially expressed genes (SDEG) between lung granulomatous lesion and uninvolved (control) parenchyma from raw CHP files using Partek Genomics Suite Version 6.7 software (Partek, St. Louis, MO). The expression levels in various granulomas were normalized with the corresponding gene expression in the uninvolved parenchyma. Gene ontology analysis and intensity plots of SDEG expressed exclusively or commonly between different types of lung granulomas were generated using Partek Genomics Suite Version 6.7 software (Partek, St. Louis, MO) as described previously [25 (link)]. The SDEG were further analyzed to determine pathway/network significantly affected by SDEG using Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems, Redwood City, CA).