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Pipeline publication

[…] ators. Complmentarity between CDK1 and three drugs, Aminophenazone, Pomalidomide and the Rosoxacin, implies novel pharmacological value of those drugs in breast cancer., The microarray data GSE21422 was collected from Gene Expression Omnibus(GEO) which was built upon GPL570 platform. This platform was stored by Schaefer C et al [] and houses 19 microarray data of nine DCIS, 5 invasive ductal carcinoma(IDC) and 5 healthy control samples obtained from patients with breast reduction surgery., The original CEL data were imported into R and affy package was implemented for background correction and normalization. The expression of genes corresponding to multi probes were summarized. mas5calls in Affy was run to filter out samples with no gene expression., DEGs between 5 healthy samples and 9 DCIS samples were identified using Limma package []. The FDR was set to 0.01 and those genes with |log2 fold change | > =2 were regarded as differentially expression genes (DEGs)., Database for Annotation, Visualization, and Integrated Discovery (DAVID) is a web-server that combines functional genomic annotations with intuitive graphical summaries []. Gene lists or protein identifiers were rapidly annotated and categorized using comprehensive categorical data from Gene Ontology (GO), protein domain, and biochemical pathway membership. To investigate the inter-connection between pathways involved in pathogical mechanism of DCIS, GO and Pathway enrichment analysis on DEGs were performed with the DAVID analysis system, significance level p<= 0.05., Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) [] database (http://string-db.org/) was used to analyze protein interactions. STRING has advantages in that it aggregat […]

Pipeline specifications

Software tools affy, limma, DAVID
Databases GEO