Computational protocol: Beta-Carotene Reduces Body Adiposity of Mice via BCMO1

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Protocol publication

[…] Signal intensities for each microarray spot were quantified using Feature Extraction 9.1 (Agilent Technologies). Median density values and background values of each spot were extracted for both the experimental samples (Cy5) and the reference samples (Cy3). Quality control was performed visually, by using Quality control graphs from Feature extraction and M-A plots and boxplots were made using limmaGUI in R (Bioconductor) for every microarray. Data were imported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium). Spots with a Cy5 and Cy3 signal twice above background were selected and log transformed. 31295 spots had at least a 2-fold signal to noise ratio. The Cy5 signal was normalized against the Cy3 intensity as described before . P-values for differential expressions were calculated between 2 groups using t-test statistics on log intensity values. Changes were considered statistically different at p<0.05. Vulcano plots were made using Graphpad Prism 5.0.2 (La Jolla, CA) with all spots or a selection of spots. Heatmapping and hierarchical clustering was performed in GeneMathsXT (Applied Maths, St.Martens Lathem, Belgium). Pathway analysis was performed using MetaCore (GeneGo Inc, St. Joseph, MI, USA). Promoter analysis and the literature based network were performed with the Genomatix suite (Genomatix Software GmbH, Germany). Biochemical and biometric parameters in , , and are presented as means ± SEM. Statistical significance of effects on these parameters was assessed by two-way ANOVA and two-tailed Student's t test using SPSS 14.0 for windows (SPSS, Chicago, IL, USA), with threshold of significance set at p<0.05. Microarray data has been submitted in a MIAME compliant form to Gene Expression Omnibus (GEO) data base of the National Center of Biotechnology Information (NCBI),, and is accessible through GEO series accession number GSE27271 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27271). […]

Pipeline specifications

Software tools limmaGUI, MetaCore
Application Gene expression microarray analysis
Organisms Mus musculus
Chemicals Retinaldehyde, Retinoids, beta Carotene