CancerTSP



Predicting Cancer status from RNA Expression Data of Protein coding transcripts

This tool allows the users to submit FPKM values of mRNA and predict the disease's condition using mRNA expression data of 5 signature mRNAs, resulting from analysis of mRNA-seq data of PTC (or THCA) from TCGA dataset from GDC Data portal . This method requires FPKM values of 5 mRNA in each patient to predict whether subject have normal or cancerous status. The first column is mRNA and in second column expression of corresponding mRNA in terms of FPKM value in a particular number of patients. For more information please click Help.

Submit csv file in which each number represents the FPKM value obtained from mRNA expression of each patient derived from RNAseq data of the subject. User can provide expression data for required 5 signature genes or complete genes containing them. Here is a list of 5 signature mRNAs.



   Example csv file   

Choose SVM threshold:                  SVM threshold is required for prediction. The user can change the threshold for less or more stringent results in terms of recall and specificity. The lower threshold will increase the recall but decrease the specificity and higher threshold will do the opposite to prediction outcomes. More Detail