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README.md

Data Sources

Protein-Protein Interaction Networks

Bossi & Lehner composite PPI network

From the supplementary section of the paper "Tissue specificity and the human protein interaction network".

This can be automatically downloaded via the download_data.sh script.

Dana Farber CCSB PPI network

The Human Interactome 2012 is still in preliminary form, thus you have to sign up at the CCSB and to download the Human interactome database here.

Download the HI_2012_PRE.tsv file and save it into the ppis/ folder.

Havugimana et al. protein complexes PPI network

This is the protein complex network from the paper "A Census of Human Soluble Protein Complexes" by Havugimana et al.

Download the network from the supplemental information Table S2 here

The protein-protein interactions are in the Excel sheet "14K Denoised PPI". Copy the first two columns into a tab-separated text file with headers "Gene1" and "Gene2".

Note:

Right now this network is already part of the repository. This might complicate giving free access to the repo, as I am currently unsure about the licencing of the PPI network from Havugimana et al.

string-db

The protein interaction data can be loaded from string-db automatically with the download_data.sh shell script.

If you already downloaded the string-db file or import it manually for other reasons, do the following:

Go to string-db to the Download section and download the protein.links.vX.XX.txt.gz file. This file contains all protein protein interactions using Ensembl IDs and a reliability score per interaction.

Direct download link (for version 9.05): here

Save this file into the data/download folder, and then run the download_data.sh script, which will pre-filter the string-db interactions for human interactions with score >= 0.7

Protein Expression data sets

These are all downloaded and unpacked automatically via the download_data.sh script. The following just describes the data sources.

Human Protein Atlas (HPA)

From the Human Protein Atlas version 11 the normal_tissue.csv and subcellular_location.csv files are used.

Manual download here

GeneAtlas (now BioGPS)

This is RNA micro-array data from Su Al et al. 2009. It can be downloaded from BioGPS here.

The files gnf1h-gcrma.zip and gnf1h-anntable.zip are needed, where the first is the actual expression data while the second holds the annotation for the genes.

Illumina Body Map RNAseq

The RNAseq data from Illumina Body Map can be downloaded from EBI here.

The automatic script removes all filters (no gene selection, especially not only protein coding genes; and a cutoff of 0).