General description
This document describes how to use the MACCU, which was originally designed for clustering based on array data, to do PPI clustering based on PPI (protein-protein interaction) relationships.
Data file correspondence
When using the MACCU, you shall need at least the following files as input:
- -I: a tab-delimited table file contains (a) slide names in the first row, (b) probe names in the first column, and (c) (normalized) expression levels.
- (optional) -C: pre-computed probe-to-probe correlation values.
- -assign: a mapping file that maps probe names (in above two files) to accessions like Gene IDs.
- -P: gene list, or probe list
When doing PPI clustering, all things are so similar, and there should be the following things:
- a computed/curated protein-protein interaction datafile, maybe with a confidence value for each PPI.
- a gene/protein list that you want to do PPI clustering.
For example, to do PPI clustering based on Interactome2.0 using MACCU, we need the following two files:
- DummyExp.txt: which contains dummy expression information because the expression file (assigned by -I option) will no longer be useful if there is a pre-computed correlation file (assigned by -C option)
- DummyMapping.txt: which contains dummy Gene-ID-to-Gene-ID mapping because there is no probe in PPI clustering analysis
So for doing PPI clustering using MACCU, just remember to use options as follows:
- -I DummyExp.txt
- -C Interactome.correl
- -assign DummyMapping.txt
- -P: your gene list
Also note that, in the Interactome2.0, the confidence values of PPIs are all above or equal to 1. Just remember to set the -CF (correlation filter) to be 1, 2, or 11 for low-, medium-, or high-confidence, respectively.