MCPNet : A parallel maximum capacity-based genome-scale gene network construction framework

This deposit contains the gene expression profile datasets used for the paper titled "MCPNet : A parallel maximum capacity-based genome-scale gene network construction framework". 

There are three sets of data:

Simulated yeast data from NetBenchmark, with random noise injected, as well as the ground truth network matrix.  In "SimulatedYeast.zip".

Real Yeast dataset and the ground truth network as an adjacency list file.  in "yeast_data.exp" and "yeast_gs1_list_filtered.tsv".  Data acquired from "Castro DM, de Veaux NR, Miraldi ER, Bonneau R (2019) Multi-study inference of regulatory networks for more accurate models of gene regulation. PLoS Comput Biol 15(1): e1006591. https://doi.org/10.1371/journal.pcbi.1006591", https://github.com/simonsfoundation/multitask_inferelator/tree/AMuSR.

Real Arabidopsis athaliana datasets for 5 tissues and 1 environmental challenge. 

athaliana_gs_probes.tsv : ground truth as an adjacency list

microarray gene expression profiles for "development", "leaf", "seed", "flower", "seedling1week", "hormone-aba-iaa-ga-br".

Aathaliana.Datasets-CEL-File-URLs.xlsx: list of SRA accession numbers for the A. athaliana datasets