Module: quantitative PCR (reduced set)

Change module

This suplementary software allows you to use our neural network to predict diagnosis of invasive epithelial ovarian cancer (vs. controls or borderline) depending on the levels of miRNAs.

In order to use this software please set up the values in the panel on your left hand side. The calculations will be performed automatically as the values change.

Module description:

As qPCR has a lower sensitivity than sequencing, miRNAs values were undetectable for some miRNAs in some samples using this technique. We considered whether this might account for the lower AUC seen on the testing set using qPCR inputs rather than sequencing data. To minimize missing datapoints, we performed a global sensitivity analysis on the best neural network for qPCR data and iteratively removed the variables which did the least in terms of improving the classifier’s performance. Ultimately, we were able to reduce the neural network number of miRNAs down to 7 miRNAs (miR-92a, miR-450b, miR-335, miR-29a, miR-1307, miR-320c and miR-200c) and 4 normalizers.

The probability of cancer was estimated as: 

      

      

      Advanced details and features:
      
 

      

        
        

          

            
 

            
This tab allows you to evaluate several instances at once. Please upload CSV file and await the table with results. More details about CSV file format can be found in the other tab. 

            

              
              

                
                
              

              

                

              

            

            

              
              

                

                  
                

                

                  
                

                

                  
                

              

            

            
 

            

          

          

            
 

            
 Comma-separated values (CSV) file stores tabular data (numbers and text) in plain text. Each line of the file is a data record. Each record consists of one or more fields, separated by commas. The use of the comma as a field separator is the source of the name for this file format.
                 The first row should contain column "Id" and the miRNA names complient with the names on your left hand side. Column "Id" is important and should contain identifiers of patients, so you can recoginze and assing results to them.
Please remember that this format may be dependent on regional settings. You can use Microsft Excel, but we strongly encourage you to check in notepad whether comma is used as column delimiter and not as the decimal mark. Please see the example in the Keller-like data module.
                 

          

          

            
 

            

          

        

      

      

      This software is a part of paper entitled 'Diagnostic potential for a serum miRNA neural network for detection of ovarian cancer' and authored by Kevin M. Elias, Wojciech Fendler, Konrad Stawiski, Stephen J. Fiascone, Allison F. Vitonis, Ross S. Berkowitz, Gyorgy Frendl, Panagiotis A. Konstantinopoulos, Christopher P. Crum, Magdalena Kedzierska, Daniel W. Cramer, and Dipanjan Chowdhury.
      

      

      Corresponding author: Dipanjan Chowdhury, PhD, Department of Radiation Oncology, Dana-Farber Cancer Institute, dipanjan_chowdhury@dfci.harvard.edu.
      

      Software author, technical issues: Konrad Stawiski, MD (contact: konrad.stawiski@umed.lodz.pl; Department of Biostatistics and Translational Medicine, Medical University of Lodz, Poland).