Computational protocol: Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury

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Protocol publication

[…] RNA extraction was performed using RNeasy kits (Qiagen); Affymetrix Mouse Genome 430 2.0 and Mouse Gene 2.0 ST arrays used to detect genome-wide expression levels summarized by the gcrma package in Bioconductor with GC robust multichip average (GCRMA) normalization. The expression level of each transcript in Mouse Gene 2.0 ST arrays was summarized by the RMA method in “oligo” package in Bioconductor. SAM (Significance Analysis of Microarrays), implemented in the samr library of the R Statistical Package, for comparing log2-transformed gene expression levels between groups. Enriched BIOCARTA pathways were searched among differentially- expressed genes using NIH/DAVID. […]

Pipeline specifications

Software tools GC–RMA, Oligo package, SAM, DAVID
Databases BioCarta
Application Gene expression microarray analysis
Diseases Neural Tube Defects, Pneumonia, Lung Injury
Chemicals Niacinamide