PPICompare

Condition-specific networks interaction data
The mandatory input consists of two groups of networks constructed with PPIXpress in zipped format (.zip/.gz/.gzip). The PPIXpress output data needs to comprise the according protein-protein interaction networks, domain-domain interaction networks, and the major transcript files with the file suffixes as predefined by PPIXpress webserver or PPIXpress standalone tool.

Example: HSC.zip and MPP.zip are two groups of networks constructed with PPIXpress in zipped format.

• HSC.zip contains 5 samples (Cord_blood-M-C002UU, Cord_blood-U-C07002, Cord_blood-U-C12001_ddin, Cord_blood-U-S001FX, Cord_blood-U-S001QB and Cord_blood-U-S0025C). The names of those samples are used as the suffix of the PPIN, DDIN and major transcripts list files.
• Similarly, MPP.zip contains 3 samples (Cord_blood-M-C002UU, Cord_blood-U-C07015 and Cord_blood-U-S001FX). Their PPINs, DDINs and major transcripts list are named accordingly.
• *_ppin.txt, *_ddin.txt and *_major-transcripts.txt are the condition-specific protein interaction network, domain-domain interaction network and list of major transcript per protein built using the listed samples.

Note:
If the inputs are forwarded from PPIXpress Webserver, by default, the asterisk (*) is a number (1, 2, 3,...) indicating the expression data which the reference network uses to prune.
This number corresponds to the Sample and Matched output field in Sample summary file.
Read more about PPIXpress output here.

Protein-protein interaction network
Condition-specific protein interaction network file must be named *_ppin.txt(.gz) and contain the tab-separated information as below:

Protein 1	Protein 2	weight
Q9NUQ3	Q9UNE7	1.0
Q9NXF1	Q9UL18	1.0
...	...	...

Domain-domain interaction network
Condition-specific domain interaction network file must be named *_ddin.txt(.gz) and contain the tab-separated information as below:

Protein/Domain1	Domain2	IAType	Weight
Q9UKT9	0|FB|Q9UKT9	pd	10
Q9UKT9	1|PF00096|Q9UKT9	pd	10
...	...	...	...

Major transcript file
The list of major transcript per protein in the condition-specific protein interaction network must be named *_major-transcripts.txt(.gz) and contain the tab-separated information as below:

Protein	EnsemblID	Expression
Q9UKT9	ENST00000346872	8.425746
Q9UKT8	ENST00000608872	13.324804
P54852	ENST00000597279	6.8656335
...	...	...

Examples for run set-up

Pipeline log file
Once the PPICompare run is finished, select Download Log File to download the log containing run configurations.

Main output file
Select Download Result Files to download main output files, including:

• differential network.txt: List of all significantly rewired interactions between the groups.
• min_reasons.txt.txt: A minimal set of transcriptomic alterations that explain all the significant rewiring and is most likely given the data is determined.
• protein_attributes.txt: Protein attributes retrieved from Ensembl database, including:
  • UniProt ACC: UniProt accession of the protein.
  • Gene name: Gene name associated with the protein.
  • Part of min reasons: Is a transcriptomic alteration of this protein part of the min. reasons set (yes/no).
  • Alteration type: The type of the most relevant transcriptomic alteration (DE/AS, if any).
  • Transcriptomic alteration: Exact transcriptomic alteration as loss/gain (DE) between groups or exact transcript switch (AS).
  • Score: Internally used importance-score defined by the number of occurrences of the alteration above across all comparisons and all rewiring events.

Network visualization
Select Visualize Condition-Specific Networks to open Network Visualization tab and click Show to display the differential PPI network that distinguish two samples or conditions.