GRAND

Tool description

PANDA reconstructs a gene regulatory network using TF PPI, TF DNA binding motif as regulation prior, and gene expression samples. PUMA reconstructs a gene regulatory network with miRNA as regulators using gene expression samples and miRNA predicted targets by miRanda or TargetScan as regulation priors. The Regulator-regulator interaction matrix is set to the identity matrix in the algorithm. LIONESS reconstructs patient-specific PANDA networks for each gene expression sample. To download sample-specific networks, you can check the phenotypic information and select the networks by clinical variables or download all the samples in a single file.

#	Tissue	Tool	netZoo release	Network	PPI	Reg. prior	Reg.	nReg	Genes	Samples	Precision
1	Skeletal muscle	PANDA	netZooM 0.1	co R		Motif	TF	644	30243	469	D
2	Skeletal muscle	PANDA-LIONESS	netZooM 0.1	co R		Motif	TF	644	30243	469	D
3	Skeletal muscle	PUMA	netZooM 0.3	co R	-	miRanda	miRNA	643	16161	119	D
4	Skeletal muscle	PUMA	netZooM 0.3	co R	-	TargetScan	miRNA	643	16161	119	D

Variable description

You can either download all the networks to get a matrix of size the number of samples by the number of edges. The number of edges is 644 * 30243 (number of TFs * number of genes) (~ 10⁶). Otherwise, you can specify the sample network to download and you will get a TF-by-gene matrix named after the GTEx sample reference.

Sample	Subject	Gender	Age	DTH-HRDY	SMAT-SSCR	SMRIN	SMTS	SMTSD	SMUBRID	SMTSISCH	Network

Networks

Tool description

Phenotypic information GTEx

Variable description