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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.

SampleSubjectGender
AgeDTH-HRDY
SMAT-SSCR
SMRIN
SMTS
SMUBRID
Isch. time
Time point
GTEX-1117F-2226-SM-5N9CH GTEX-1117F 2 60-69 4 1 6.6 Ovary 2119 1326 Actual Death
GTEX-11DXX-1426-SM-5GIDU GTEX-11DXX 2 60-69 0 1 7.3 Ovary 2119 117 Actual Death
GTEX-11EM3-1726-SM-5N9D1 GTEX-11EM3 2 20-29 0 0 8.8 Ovary 2119 194 Actual Death
GTEX-11EMC-1726-SM-5H11P GTEX-11EMC 2 60-69 2 1 7.6 Ovary 2119 731 Actual Death
GTEX-11GSP-0226-SM-5A5KV GTEX-11GSP 2 60-69 2 0 7.5 Ovary 2119 764 Actual Death
GTEX-11I78-1926-SM-59878 GTEX-11I78 2 50-59 0 1 8.6 Ovary 2119 130 Actual Death
GTEX-11P81-1526-SM-5P9GS GTEX-11P81 2 30-39 0 0 8.5 Ovary 2119 282 Actual Death
GTEX-11VI4-1026-SM-5EQM1 GTEX-11VI4 2 40-49 0 0 8.3 Ovary 2119 143 Actual Death
GTEX-11XUK-1626-SM-5GU5O GTEX-11XUK 2 40-49 0 0 7.6 Ovary 2119 167 Actual Death
GTEX-11ZTS-1926-SM-5CVLA GTEX-11ZTS 2 60-69 2 1 6.4 Ovary 2119 683 Actual Death
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