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 | - | - | - | - | - | - | - | - | - | Edg142 GB |
GTEX-111YS-0006-SM-5NQBE | GTEX-111YS | 1 | 60-69 | 0 | - | 8.2 | Blood | 13756 | -121 | Actual Death | |
GTEX-1122O-0005-SM-5O99J | GTEX-1122O | 2 | 60-69 | 0 | - | 7.6 | Blood | 13756 | 1363 | Actual Death | |
GTEX-1128S-0005-SM-5P9HI | GTEX-1128S | 2 | 60-69 | 2 | - | 6.7 | Blood | 13756 | 783 | Actual Death | |
GTEX-113IC-0006-SM-5NQ9C | GTEX-113IC | 1 | 60-69 | - | - | 8.6 | Blood | 13756 | -351 | Cross Clamp Applied | |
GTEX-113JC-0006-SM-5O997 | GTEX-113JC | 2 | 50-59 | 2 | - | 7.6 | Blood | 13756 | 587 | Actual Death | |
GTEX-117XS-0005-SM-5PNU6 | GTEX-117XS | 1 | 60-69 | 2 | - | 6.4 | Blood | 13756 | 802 | Actual Death | |
GTEX-117YW-0005-SM-5NQ8Z | GTEX-117YW | 1 | 50-59 | 3 | - | 8.5 | Blood | 13756 | 771 | Actual Death | |
GTEX-1192W-0005-SM-5NQBQ | GTEX-1192W | 1 | 60-69 | 2 | - | 8 | Blood | 13756 | 645 | Actual Death | |
GTEX-1192X-0005-SM-5NQC3 | GTEX-1192X | 1 | 50-59 | 4 | - | 8.3 | Blood | 13756 | 757 | Actual Death |