I want to understand my SWATH quantitation data in a more biological context. Do you have pathway mapping applications?
Yes, there is a powerful application called iPathwayGuide from Advaita. This is a web based pathway analysis tool that uses a unique Impact Analysis method to determine which pathways are perturbed, as well modeling SNPs, miRNA and drugs on the pathways. It has a modern, interactive user interface for easy data exploration and very nice visualizations. The software can analyse both transcriptomics and proteomics data and includes the ability to model multiple contrasts in a single report! Input data includes data from CuffDiff, DEseq, and SWATH data from the OneOmics™ or from SWATH® 2.0 / MarkerView™ Software pipelines.
The impact analysis provided by this tool is an extension of previous statistical approaches and takes a more biological approach by considering additional features such as magnitude of the gene/protein expression change, the position in the pathway, the signaling interactions and directionality of the pathway in additional to the classical enrichment analysis. The goal of the analysis is to develop an analysis model that would require both a statistically significant number of differentially expressed genes as well as a biologically meaningful changes on a given pathway. This provides fewer false positives in your data and more biologically meaningful results.
Check out the Advaita website (www.AdvaitaBio.com) for more information.
Download the FoldChange[XXX].csv file from either your folder in SCIEX Cloud or your BaseSpace Project. Login to your iPathwayGuide account then select Analyze a New Experiment. Using the Intake form, select the Organism, the file format (SCIEX SWATH Proteomics data), then browse for the fold change file with the correct control (experimental group used as the control/denominator is denoted in the square brackets). Select Upload to load in your data.
Next, your need to provide a title and a description for your report. Then select the contrasts you want to be analyzed. Provide the fold change and p-value filters that you want to use, then click View/Apply button to see what proteins will be used in the analysis. A volcano plot is generated to allow you to visualize the input data. Select Analyze Data once you are happy with your filters.
It's worth noting that currently to look at your OneOmics data in iPathwayGuide you need to change the p-value setting to equal "1-confidence value", i.e. if your confidence cut-off was 75% then your "p-value" in iPathwayGuide will be 0.25 in order to select the same differentially expressed proteins.
Yes that is exactly right! Thanks for pointing out that very important point!