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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.
| # | Tissue | Tool | netZoo release | Network |
PPI |
Regulation prior | Expression |
Regulator |
nReg |
Genes | Samples | Precision |
Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Kidney cortex | PANDA | netZooM 0.1 | Motif | TF | 644 | 30243 | 36 | D | ||||
| 2 | Kidney cortex | PUMA | netZooM 0.3 | - | miRanda | miRNA | 643 | 16161 | 36 | D | |||
| 3 | Kidney cortex | PUMA | netZooM 0.3 | - | TargetScan | miRNA | 643 | 16161 | 36 | D |
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-11GS4-2326-SM-5A5KS | GTEX-11GS4 | 1 | 60-69 | 2 | 2 | 6.1 | Kidney | 1225 | 910 | Actual Death |
| GTEX-11OF3-1326-SM-5N9FJ | GTEX-11OF3 | 1 | 60-69 | 2 | 2 | 5.7 | Kidney | 1225 | 800 | Presumed Death |
| GTEX-11PRG-2226-SM-5GU5R | GTEX-11PRG | 1 | 50-59 | 2 | 3 | 6 | Kidney | 1225 | 931 | Actual Death |
| GTEX-11TTK-1926-SM-5PNW8 | GTEX-11TTK | 2 | 60-69 | 4 | 2 | 6.2 | Kidney | 1225 | 1154 | Actual Death |
| GTEX-12696-0926-SM-5FQTV | GTEX-12696 | 1 | 60-69 | 3 | 1 | 7.8 | Kidney | 1225 | 521 | Actual Death |
| GTEX-12WSG-0826-SM-5EQ5A | GTEX-12WSG | 2 | 50-59 | 0 | 2 | 7.3 | Kidney | 1225 | 341 | Actual Death |
| GTEX-13112-2126-SM-5GCO4 | GTEX-13112 | 1 | 50-59 | 2 | 2 | 6.2 | Kidney | 1225 | 1261 | Actual Death |
| GTEX-1399S-0526-SM-5IJG8 | GTEX-1399S | 2 | 30-39 | 0 | 1 | 5.9 | Kidney | 1225 | 75 | Actual Death |
| GTEX-13NYB-1726-SM-5N9G2 | GTEX-13NYB | 1 | 40-49 | 2 | 2 | 5.7 | Kidney | 1225 | 1056 | Presumed Death |
| GTEX-13O1R-2526-SM-5N9FW | GTEX-13O1R | 1 | 60-69 | 2 | 2 | 5.7 | Kidney | 1225 | 864 | Actual Death |
| GTEX-13OVI-1126-SM-5KLZF | GTEX-13OVI | 2 | 60-69 | 0 | 1 | 8.8 | Kidney | 1225 | 177 | Actual Death |
| GTEX-13OVL-1826-SM-5KLZR | GTEX-13OVL | 1 | 50-59 | 2 | 2 | 6 | Kidney | 1225 | 958 | Actual Death |
| GTEX-13OW6-1826-SM-5N9F9 | GTEX-13OW6 | 1 | 50-59 | 2 | 1 | 5.7 | Kidney | 1225 | 629 | Actual Death |
| GTEX-13RTJ-2226-SM-5S2Q1 | GTEX-13RTJ | 1 | 60-69 | 4 | 3 | 5.9 | Kidney | 1225 | 922 | Actual Death |
| GTEX-145MN-0326-SM-5QGQI | GTEX-145MN | 1 | 30-39 | 0 | 1 | 7.5 | Kidney | 1225 | 112 | Actual Death |
| GTEX-147F4-2626-SM-5Q5CS | GTEX-147F4 | 1 | 50-59 | 2 | 2 | 6.8 | Kidney | 1225 | 1311 | Actual Death |
| GTEX-1497J-0826-SM-5NQAJ | GTEX-1497J | 1 | 60-69 | 0 | 1 | 6.3 | Kidney | 1225 | 240 | Actual Death |
| GTEX-N7MS-1626-SM-3LK5F | GTEX-N7MS | 1 | 60-69 | 2 | 2 | 6.8 | Kidney | 1225 | 1250 | Actual Death |
| GTEX-NPJ8-2226-SM-3TW8D | GTEX-NPJ8 | 1 | 40-49 | 4 | 1 | 7.2 | Kidney | 1225 | 342 | Presumed Death |
| GTEX-P4QS-1126-SM-3NMD5 | GTEX-P4QS | 1 | 60-69 | 0 | 1 | 6.4 | Kidney | 1225 | 157 | Actual Death |
| GTEX-QDVN-1626-SM-48TZC | GTEX-QDVN | 1 | 50-59 | 0 | 2 | 7.3 | Kidney | 1225 | 227 | Actual Death |
| GTEX-QLQW-1626-SM-4R1K1 | GTEX-QLQW | 1 | 30-39 | 0 | 1 | 8.4 | Kidney | 1225 | 812 | Actual Death |
| GTEX-RN64-1626-SM-48FD7 | GTEX-RN64 | 1 | 50-59 | 1 | 2 | 6.6 | Kidney | 1225 | 780 | Actual Death |
| GTEX-T5JC-1526-SM-4DM68 | GTEX-T5JC | 1 | 20-29 | 2 | 2 | 5.9 | Kidney | 1225 | 723 | Actual Death |
| GTEX-UPIC-1126-SM-4IHLO | GTEX-UPIC | 2 | 20-29 | 0 | 1 | 7.4 | Kidney | 1225 | 236 | Actual Death |
| GTEX-WI4N-2026-SM-4OOS7 | GTEX-WI4N | 2 | 40-49 | 0 | 2 | 5.9 | Kidney | 1225 | 751 | Actual Death |
| GTEX-XPVG-0526-SM-4B65N | GTEX-XPVG | 1 | 50-59 | 0 | 1 | 7.9 | Kidney | 1225 | 86 | Actual Death |
| GTEX-Y5V6-2026-SM-5IFHO | GTEX-Y5V6 | 1 | 60-69 | 0 | 1 | 6.5 | Kidney | 1225 | 191 | Actual Death |
| GTEX-ZC5H-1726-SM-5HL7X | GTEX-ZC5H | 2 | 40-49 | 0 | 2 | 6.1 | Kidney | 1225 | 288 | Actual Death |
| GTEX-ZDXO-0226-SM-4WKH7 | GTEX-ZDXO | 1 | 60-69 | 2 | 2 | 6.2 | Kidney | 1225 | 1167 | Actual Death |
| GTEX-ZE9C-1426-SM-4WKGM | GTEX-ZE9C | 1 | 60-69 | 2 | 2 | 6.1 | Kidney | 1225 | 650 | Actual Death |
| GTEX-ZLFU-0926-SM-5P9F8 | GTEX-ZLFU | 1 | 40-49 | 0 | 1 | 6.4 | Kidney | 1225 | 128 | Actual Death |
| GTEX-ZVZP-0926-SM-5GIDB | GTEX-ZVZP | 1 | 50-59 | 0 | 2 | 7.8 | Kidney | 1225 | 90 | Actual Death |
| GTEX-ZYFD-1526-SM-5NQ7T | GTEX-ZYFD | 1 | 50-59 | 3 | 2 | 5.8 | Kidney | 1225 | 629 | Actual Death |
| GTEX-ZYFG-1626-SM-5GZYY | GTEX-ZYFG | 2 | 60-69 | 0 | 1 | 8 | Kidney | 1225 | 106 | Actual Death |
| GTEX-ZYT6-2226-SM-5GIC9 | GTEX-ZYT6 | 1 | 30-39 | 1 | 3 | 6.8 | Kidney | 1225 | 1430 | Actual Death |
| Sample | Subject | Gender | Age | DTH-HRDY | SMAT-SSCR | SMRIN | SMTS | SMUBRID | SMTSISCH | SMTSTPTREF |