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Fig. 1 | BMC Research Notes

Fig. 1

From: miRCancerdb: a database for correlation analysis between microRNA and gene expression in cancer

Fig. 1

A workflow of the analysis pipeline and miRCancerdb application control panel. a The diagram represents the data sources, the analysis pipeline and the representation views. Briefly, expression profiles of three assays; miRNASeq, RNAseq and RPPA from TCGA were obtained using RTCGA package. miRNA gene targets were obtained using the targetscan.Hs.eg.db package. After tidying and filtering the data, Pearsons correlations for each miRNA to features (mRNA/protein) in each of the TCGA studies were calculated. Target features were then identified. Different types of views are available on the web interface to visualize different aspects of queries results. miRNASeq, miRNA sequencing; RNAseq, RNA sequencing; and RPPA, Reverse Phase Protein Array. b The panel contains two main areas to enter and customize the query. Query options: to choose the kind of feature expression to base the calculation on, the TCGA study/ies identifier and the miRNAs miRBase IDs. Subset options: to customize the query and limit the results. Options include using feature targets only, limit the results to the top n features for each miRNA in each TCGA study, choosing a direction of correlation; positive, negative or both and indicating an absolute minimum correlation to show

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