Computational protocol: Ror2, a developmentally regulated kinase, promotes tumor growth potential in renal cell carcinoma

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Protocol publication

[…] Fresh frozen tumors from the UNC Tissue Procurement Facility tumor bank (1994-2007) were used for these studies. Total mRNA was prepared as described above, incorporating a Rotor-Stator for tissue homogenization. Quantitation was performed by NanoDrop (NanoDrop Technologies, Wilmington, DE). RNA quality check, amplification, labeling, and hybridization was performed by the UNC Genomics Core Facility. Two-color hybridization was performed, with a modified reference human mRNA derived from the Stratagene Universal Human Tumor Reference RNA (kindly provided by Dr. C. Perou, Chapel Hill, NC).Raw data was derived using Agilent feature extraction software, and results were expressed as a Log (2)-transformed ratio between tumor and control mRNA. Three-way comparison was performed using Significance Analysis of Microarrays (SAM) version 3.01 () for . Duplicate genes were removed, targets were median centered and complete linkage analysis was performed with Pearson’s Correlation with Cluster 3.0. For , quantitative analysis of data according to Ror2 gene expression was performed using SAM. Genes with a false discovery rate <5% were then used for average linkage analysis with Cluster 3.0. Gene set analysis was also performed in SAM according to Ror2 gene expression values, using a cutoff of FDR=0. Gene sets analyzed were from Erin Segal or the MSigDB collection at the Broad Institute. […]

Pipeline specifications

Software tools Agilent Feature Extraction, SAM
Databases MSigDB
Application Gene expression microarray analysis
Diseases Brain Neoplasms, Carcinoma, Renal Cell, Neoplasms