Computational protocol: Dysplasia-Carcinoma Transition Specific Transcripts in Colonic Biopsy Samples

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Protocol publication

[…] Quality control analyses were performed according to the suggestions of the Tumour Analysis Best Practices Working Group . Scanned images were inspected for artifacts, percentage of present calls (>25%) and control of the RNA degradation were evaluated. Based on the evaluation criteria all biopsy measurements fulfilled the minimal quality requirements. The Affymetrix expression arrays were pre-processed by gcRMA with quantile normalization and median polish summarization. The datasets are available in the Gene Expression Omnibus databank for further analysis (, series accession numbers: GSE4183, GSE10714).Differentially expressed genes were identified by Significance Analysis of microarrays (SAM) method between different diagnostic groups. The nearest shrunken centroid method (Prediction Analysis for miroarrays – PAM) was applied for sample classification from gene expression data. The pre-processing, data mining and statistical steps were performed using R-environment with Bioconductor libraries. Hierarchical cluster analysis represents on each comparisons of correlation. Logistic regression was applied to analyze dependence of binary diagnostic variables (represented 0 as control, 1 as disease). Discriminant and principal component analysis were also performed. In the discriminant analysis, leave-one out classification was applied for cross-validation. […]

Pipeline specifications

Software tools GC–RMA, SAM
Databases GEO
Application Gene expression microarray analysis
Diseases Adenoma, Carcinoma, Colorectal Neoplasms