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 | - | - | - | - | - | - | - | - | - | Edg84 GB |
GTEX-111FC-3326-SM-5GZYV | GTEX-111FC | 1 | 60-69 | 1 | 2 | 7.1 | Brain | 2037 | 1221 | Presumed Death | |
GTEX-1128S-2826-SM-5N9DI | GTEX-1128S | 2 | 60-69 | 2 | 1 | 6.3 | Brain | 2037 | 1036 | Actual Death | |
GTEX-117XS-3126-SM-5GIDP | GTEX-117XS | 1 | 60-69 | 2 | 1 | 7.2 | Brain | 2037 | 1018 | Actual Death | |
GTEX-1192X-3226-SM-5987D | GTEX-1192X | 1 | 50-59 | 4 | 1 | 5.9 | Brain | 2037 | 989 | Actual Death | |
GTEX-11DXW-1026-SM-5H11K | GTEX-11DXW | 1 | 40-49 | 2 | 1 | 6 | Brain | 2037 | 1135 | Actual Death | |
GTEX-11DXY-3126-SM-5N9BT | GTEX-11DXY | 1 | 60-69 | 2 | 1 | 7.3 | Brain | 2037 | 1016 | Presumed Death | |
GTEX-11DYG-2926-SM-5H132 | GTEX-11DYG | 1 | 60-69 | 2 | 1 | 7 | Brain | 2037 | 915 | Actual Death | |
GTEX-11DZ1-2926-SM-5A5KI | GTEX-11DZ1 | 1 | 50-59 | 4 | 1 | 6.3 | Brain | 2037 | 1314 | Actual Death | |
GTEX-11EI6-2926-SM-5985U | GTEX-11EI6 | 1 | 60-69 | 4 | 1 | 6.2 | Brain | 2037 | 1045 | Actual Death |