Computational protocol: Comprehensive establishment and characterization of orthoxenograft mouse models of malignant peripheral nerve sheath tumors for personalized medicine

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Protocol publication

[…] Gene expression profiles were determined using Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA) following standard protocols. Expression data were analyzed using R version 3.0.2 (Dean & Nielsen, ) and the Bioconductor (Gentleman et al, ) package Affy (Gautier et al, ). Raw CEL files were normalized with RMA, and the normalized expression values were extracted. Samples were compared at the level of normalized expression values using the Pearson correlation coefficient to quantify the changes between primary tumors and the derived orthoxenografts. Expression profiles were classified using a hierarchical clustering approach with Euclidean distance and average as agglomeration method. Heatmaps represent the Pearson correlation between pairs of samples and were drawn using the gplots library. […]

Pipeline specifications

Software tools affy, gplots
Application Gene expression microarray analysis
Organisms Mus musculus, Homo sapiens
Diseases Neoplasms, Neurilemmoma, Neurofibromatosis 1, Sarcoma
Chemicals Doxorubicin, Sirolimus