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QuanTP (version 1.1.2)
Protein abundance input file
Transcript abundance input file
If the input files already have fold-change values, select Log fold-change. Else, select abundances and the tool will perform the fold-change analysis
Please check the format of the experiment design file
Perform T-Test on selecting Mean; Wilcoxon Ranksum Test on selecting Median

What it does

QuanTP correlates transcript abundance and protein abundance to examine the association between them.

It either takes in the log fold-change of abundances as input or raw abundances from different conditions where it calculates the log ratios of abundances between two conditions.

Transcript input file can be generated from the quantitative RNA-Seq study whereas Protein input file can be generated from quantitative analysis of mass-spectrometry-based protein data.


Input file formats

Protein data file

First column - Gene

Following columns - Abundance values (or log fold-change values)

Example of Protein input file

Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
GeneX value value value value value value value value
GeneY value value value value value value value value
GeneZ value value value value value value value value

Transcript data file

First column - Gene

Following columns - Abundance values (or log fold-change values)

Example of Transcript input file

Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
GeneX value value value value value value value value
GeneY value value value value value value value value
GeneZ value value value value value value value value

Data input type

If data input type is abundance, experiment design file is required.

Example of experiment design file

case groupA
control groupB
sample1 groupA
sample2 groupA
sample3 groupA
sample4 groupA
sample5 groupB
sample6 groupB
sample7 groupB
sample8 groupB

Note: No title/header in experiment design file and the first two lines of the experiment design must have keyword "case" and "control"