CancerTSP

Predicting Cancer Stage from RNA Expression Data of Protein coding transcripts

This tool allows the users to submit FPKM values of protein coding RNA transcripts and predict if the cancer patient has Early Stage cancer or Late Stage cancer using RNA expression data of 37 protein coding RNA transcripts, resulting from classification analysis of RNA-seq data of Papillary Thyroid Carcinoma (PTC) from TCGA data. This method requires FPKM values of 37 protein coding RNA transcripts in each patient to predict whether it’s in early or late stage of cancer. The first column is RNA and in second column expression of corresponding RNA in a particular number of patients. For more information please click Help.

Submit csv file in which each number represents the FPKM value derived from genomics value of each patient derived from RNAseq data of the cancer patient. User can provide expression data for required 37 signature protein coding genes or complete genes containing them. Here is a list of 37 protein coding RNA transcripts.



   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