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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. Check the phenotypic information for the clinical variables of the samples that were used to reconstruct the network.
Variable description
PANDA-LIONESS networks are single-sample networks generated by first estimating an aggregate PANDA network then deriving patient-specific LIONESS networks. This is a description of the primary clinical variables of the gene expression samples that were used to generate the gene regulatory network.
| Sample | Subject | Gender | Age | DTH-HRDY | SMAT-SSCR | SMRIN | SMTS | SMUBRID | Isch. time | Time point |
|---|---|---|---|---|---|---|---|---|---|---|
| GTEX-111CU-1526-SM-5N9FS | GTEX-111CU | 1 | 50-59 | 0 | 1 | 5.7 | Prostate | 2367 | 103 | Actual Death |
| GTEX-111FC-2026-SM-5GZYO | GTEX-111FC | 1 | 60-69 | 1 | 2 | 5.8 | Prostate | 2367 | 1121 | Presumed Death |
| GTEX-111YS-1726-SM-5GIED | GTEX-111YS | 1 | 60-69 | 0 | 1 | 6.3 | Prostate | 2367 | 179 | Actual Death |
| GTEX-117YW-1426-SM-5EGGO | GTEX-117YW | 1 | 50-59 | 3 | 1 | 5.9 | Prostate | 2367 | 884 | Actual Death |
| GTEX-117YX-1526-SM-5H12T | GTEX-117YX | 1 | 50-59 | 0 | 1 | 6.1 | Prostate | 2367 | 110 | Actual Death |
| GTEX-11DXZ-1826-SM-5H12Y | GTEX-11DXZ | 1 | 50-59 | 0 | 0 | 7.5 | Prostate | 2367 | 316 | Actual Death |
| GTEX-11DYG-2526-SM-5N9BB | GTEX-11DYG | 1 | 60-69 | 2 | 3 | 5.7 | Prostate | 2367 | 886 | Actual Death |
| GTEX-11EQ9-1726-SM-5HL6U | GTEX-11EQ9 | 1 | 30-39 | 2 | 1 | 7.6 | Prostate | 2367 | 130 | Actual Death |
| GTEX-11NSD-0826-SM-5986S | GTEX-11NSD | 1 | 20-29 | 0 | 1 | 7.5 | Prostate | 2367 | 91 | Actual Death |
| GTEX-11O72-2726-SM-5HL6K | GTEX-11O72 | 1 | 40-49 | 2 | 3 | 6.1 | Prostate | 2367 | 1012 | Actual Death |