Computational protocol: Microarray Based Gene Expression Analysis of Murine Brown and Subcutaneous Adipose Tissue: Significance with Human

Similar protocols

Protocol publication

[…] DNA microarray data was analyzed using GeneSpring GX 12.1 software (Agilent Technologies) with the raw data files (.cel) of the Affymetrix Mouse chip imported into the software. RAM (Robust Multichip Averaging) algorithm was used to normalize the data where it was subjected to quantile normalization with median of all samples taken for baseline transformation. Gene expression profiles of murine WAT and BAT were studied by generating a differential expression list. The two parameters were subjected to paired student's T test statistical analysis where the false-positive event (p-value cut-off = 0.05) calculation done using asymptotic method on the normalized data assuming equal variances, incorporating Benjamini and Hochberg false discovery rate multiple-testing correction set at a rate of 0.05. The resultant list of genes differentially expressed between the two parameters were filtered to include only those that expressed absolute fold change by greater than two-fold, five-fold and ten-fold change. [...] Genes expressed in LACA mouse were investigated for their expression pattern across various publically available mouse microarray data using Genevestigator online tool using respective Affymetrix platforms (Mouse 430 2.0 Array, Human 133 Plus 2.0 Array)[]. Genevestigator uses RMA for normalization with P≤0.1. Genes that were common to LACA mouse and Human data were first investigated for comparing similarities and differences between LACA and other mice studied upon from an obesity oriented perspective. The BAT or WAT specific list was input in Genevestigator, and the expression of these genes in known mouse models were looked into. Using linear and log2 normalized expression, heatmaps and BAT/WAT relative fold expression in the data sets were analyzed and compared with LACA mouse data.To study the expression pattern of transcription factors in adipose tissue, probesets expressed ≥2 fold were compared with the factors listed in the MTFDB (http://genome.gsc.riken.jp/TFdb/). Transcri≥tion factors in LACA mouse data was identified and compared using Genevestigator online tool. Heatmap was made using MeV software tool. […]

Pipeline specifications

Software tools GeneSpring GX, Genevestigator
Applications Gene expression microarray analysis, Transcription analysis
Organisms Mus musculus, Homo sapiens