PUMA

PANDA Using MicroRNA Associations

PUMA, or PANDA Using MicroRNA Associations, is an extension of the gene regulatory network reconstruction algorithm PANDA, which was published in "Passing messages between biological networks to refine predicted interactions" by Glass K, Huttenhower C, Quackenbush J, Yuan GC. PLoS One. 2013 May 31l8(5):e64983, doi: 10.1371/journal.pone.0064832, PMID: 23741402

PUMA can reconstruct gene regulatory networks using both transcription factors and microRNAs as regulators of mRNA expression levels. This Github repository contains both a C++ version and a MATLAB version of PUMA. The C++ version is based on PANDA version 2. The original PANDA C++ code is available at: http://sourceforge.net/projects/panda-net/. The MATLAB script to run PUMA has fewer options than the C++ code, but runs faster.

C++ code

The C++ code of PUMA and example files to run PUMA can be found in folder PUMAc. The code can be compiled using:

g++ PUMA.c -O3 -o PUMA

To run PUMA with the assumption that all regulators can form complexes (estimate responsibility for all regulators, eg a gene regulatory prior with transcription factors only):

./PUMA -e ToyExpressionData.txt -m ToyMotifData.txt -o ToyOutput

To tell PUMA to discriminate between regulators that can, and regulators that cannot cannot form complexes (for example a list of microRNAs in miRlist.txt), run:

./PUMA -e ToyExpressionData.txt -m ToyMotifData.txt -u miRlist.txt -o ToyOutput

MATLAB code

Condition-specific PUMA networks

The MATLAB code of PUMA and example files to run PUMA in MATLAB can be found in folder PUMAm. The main script to run PUMA is RunPUMA.m. This script is set-up to run PUMA on example data from folder ToyData. The script must be run with a regulatory prior (variable motif_file in the RunPUMA script) and expression data (variable exp_file). Please note that, in principle, PUMA can be run on an identity matrix of expression data as well, but this is not implemented. Protein-protein interaction data (variable ppi_file) and a list of microRNAs (variable mir_file) are optional parameters. If no mir_file is listed, the script will run PANDA to estimate regulatory edges. If a mir_file is listed, the script will run PUMA to estimate regulatory edges. In particular, regulators listed in that file will be treated as regulators that cannot form complexes with other regulators, such as microRNAs, while regulators not listed will be treated as regulators that can form complexes, such as transcription factors.

To run PUMA on your own data, change the paths and filenames under "Set Program Parameters". MATLAB functions NormalizeNetwork.m, PANDA.m, PUMA.m, Tfunction.m, and UpdateDiagonal.m will be called from the main script.

Some important notes of this script compared to the PUMA C++ code:

• The target genes in the regulatory prior (motif_file) should match the target genes in the expression data (exp_file).
• The regulators in mir_list should match symbols in the regulatory prior (motif_file).
• Self-interactions in the protein-protein interaction data will be set to 1. The algorithm converges around these edges. Protein-protein interaction "prior" edges therefore should have weights between 0-1.
• In the protein-protein interaction prior, edges between microRNAs from the mir_file (see RunPUMA.m script) and other regulators can have values, but these will automatically be set to 0, as the algorithm assumes that any regulator listed in mir_file will not be able to form edges with other regulators.

Resampling PUMA networks

RunPUMAresample.m runs PUMA as described above, but resamples the data multiple times (variable nrboots under "Set Program Parameters") by removing a certain percentage (variable perc under "Set Program Parameters") of samples to obtain a collection of networks.

Single-sample PUMA networks

LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to estimate single-sample networks using aggregate networks made with any network reconstruction algorithm (http://arxiv.org/pdf/1505.06440.pdf).

The main script to run PUMA+LIONESS is RunPUMALIONESS.m. For instructions to run this script, see instructions under "Condition-specific PUMA networks".

Other scripts

Some useful scripts can be found in the folder OtherScripts:

• bash scripts RunPUMA.sh and RunPUMALIONESS.sh can be used to remotely run RunPUMA.m and RunPUMALIONESS.m, respectively.
• getCompleteEdgelist.R is an R script that can convert an unweighted regulatory prior in a complete edgelist. This can be useful when preparing the regulatory prior and expression data.