Computational protocol: Prokineticin receptor-1-dependent paracrine and autocrine pathways control cardiac tcf21+ fibroblast progenitor cell transformation into adipocytes and vascular cells

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Protocol publication

[…] RNA from a total of six animals (3xWTn = 3 wild-type (WT); n = 3 3xTG-PKR1) was hybridized to Agilent Mouse Gene Expression Microarrays. Fluorescence values corresponding to raw expression data were extracted. The values for the positive- and negative negative-control probes were removed. Non-linear effects, such as background or saturation, were corrected by with the Locally-Weighted regression Scatterplot Smoother (LOWESS) method against a median profile of all samples. The values of replicate probes were averaged, and the data matrix was filtered to 20,000 probes based on the highest median expression values. Clusters of co-expressed genes were identified using K-means clustering (k = 10) on log2-transformed and gene-median-centered data with un-centered correlation as a similarity metric in Gene Cluster 3.0 . Hierarchical clustering was performed using Gene Cluster 3.0, and heat maps were displayed using Java Treeview. Gene Ontology enrichment analysis was performed using GoMiner. Functional annotation was further analyzed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) v6.7 . Transcripts that were significantly associated with the PKR1 phenotype were identified using two-class unpaired Significance Analysis of Microarrays (SAM). The GEO data link is https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94603. […]

Pipeline specifications

Software tools TreeView, GoMiner
Application Gene expression microarray analysis
Organisms Mus musculus