Computational protocol: Epithelial and Stromal MicroRNA Signatures of Columnar Cell Hyperplasia Linking Let-7c to Precancerous and Cancerous Breast Cancer Cell Proliferation

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Protocol publication

[…] CGH analysis was performed on the Agilent G3 Human 1×1 m CGH Microarray by ATLAS Biolabs GmbH in Berlin, Germany. The list of potentially significantly altered miRNAs in the epithelial cells and statistical significance to all in vitro experiments were calculated using two-sided Student’s T-tests. The R package qvalue was used to compute the false discovery rate . The Affymetrix GeneChip Human Gene 1.0 ST Arrays were performed by AROS Applied Biotechnology A/S (Aarhus, Denmark) and analysed with R, Bioconductor and Ingenuity Systems (Redwood City, CA). The RMA was used to normalise and summarise the expression values at the probeset level . Probesets were mapped to genes using the Bioconductor package annmap to position probesets relative to Ensembl version 60 annotations . The R package Limma was used to find differentially expressed genes and Ingenuity to find the enriched pathways from the differentially expressed gene lists. The raw array data is located at the GEO database with the accession number: GSE46199. […]

Pipeline specifications

Software tools Annmap, limma
Application Gene expression microarray analysis
Diseases Brain Diseases, Breast Diseases, Breast Neoplasms, Neoplasms