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 | Expr. |
Reg. |
nReg |
Genes | Samples | Precision |
Reference |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Skeletal muscle | PANDA | netZooM 0.1 | Motif | TF | 644 | 30243 | 469 | D | ||||
2 | Skeletal muscle | PANDA-LIONESS | netZooM 0.1 | Motif | TF | 644 | 30243 | 469 | D | ||||
3 | Skeletal muscle | PUMA | netZooM 0.3 | - | miRanda | miRNA | 643 | 16161 | 119 | D | |||
4 | Skeletal muscle | PUMA | netZooM 0.3 | - | 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 |
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