To get the full list of phenotypic variables, please check the menu below. Please click on the scatter plot to access the network view page.
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.
BONOBO is a single-sample network inference method, which can be used to estimate patient-specific co-expression matrices, which are then fed as input for PANDA to build patient-specific GRNs. To adapt BONOBO-PANDA networks for patient's sex, and in addition to sample-specific co-expression, PANDA's motif prior networks are constructed for each sex (accounting for sex chromosomes), while the third input (PPI networks) are generic for all patients. 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.
Variable description
PANDA-LIONESS networks are single-sample networks generated by first estimating an aggregate PANDA network then deriving patient-specific LIONESS networks. 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 miRNA/TFs * number of genes) (~ 106). Otherwise, you can specify the sample network to download and you will get a miRNA/TF-by-gene matrix named after the GTEx sample reference.
Sample | Subject | Gender | Age | DTH-HRDY | SMAT-SSCR | SMRIN | SMTS | SMUBRID | Isch. time | Time point | Net. |
---|---|---|---|---|---|---|---|---|---|---|---|
All | All | - | - | - | - | - | - | - | - | - | Edg119 GB |
GTEX-11UD2-0726-SM-5EQ69 | GTEX-11UD2 | 1 | 50-59 | 2 | 2 | 6.9 | Lung | 8952 | 889 | Actual Death | |
GTEX-11WQC-0626-SM-5EQMF | GTEX-11WQC | 1 | 60-69 | 2 | 1 | 6.5 | Lung | 8952 | 693 | Actual Death | |
GTEX-11WQK-1226-SM-5GU5Z | GTEX-11WQK | 1 | 50-59 | 2 | 2 | 7.5 | Lung | 8952 | 776 | Actual Death | |
GTEX-11ZTS-1226-SM-5EQMQ | GTEX-11ZTS | 2 | 60-69 | 2 | 1 | 7.5 | Lung | 8952 | 650 | Actual Death | |
GTEX-11ZTT-0626-SM-5EQLM | GTEX-11ZTT | 2 | 60-69 | 0 | 0 | 6.3 | Lung | 8952 | 172 | Actual Death | |
GTEX-11ZUS-0126-SM-5EQM5 | GTEX-11ZUS | 1 | 30-39 | 1 | 1 | 6.5 | Lung | 8952 | 1345 | Actual Death | |
GTEX-1211K-0826-SM-5FQUP | GTEX-1211K | 2 | 60-69 | 0 | 1 | 8.2 | Lung | 8952 | 92 | Actual Death | |
GTEX-1212Z-1026-SM-5EGJ8 | GTEX-1212Z | 1 | 60-69 | 2 | 1 | 6.2 | Lung | 8952 | 636 | Actual Death | |
GTEX-12584-1426-SM-5EGJ9 | GTEX-12584 | 1 | 40-49 | 3 | 1 | 7.1 | Lung | 8952 | 1006 | Actual Death |