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.

SampleSubjectGender
AgeDTH-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
Adj369 MBVis
GTEX-1128S-2826-SM-5N9DI GTEX-1128S 2 60-69 2 1 6.3 Brain 2037 1036 Actual Death
Adj369 MBVis
GTEX-117XS-3126-SM-5GIDP GTEX-117XS 1 60-69 2 1 7.2 Brain 2037 1018 Actual Death
Adj369 MBVis
GTEX-1192X-3226-SM-5987D GTEX-1192X 1 50-59 4 1 5.9 Brain 2037 989 Actual Death
Adj369 MBVis
GTEX-11DXW-1026-SM-5H11K GTEX-11DXW 1 40-49 2 1 6 Brain 2037 1135 Actual Death
Adj369 MBVis
GTEX-11DXY-3126-SM-5N9BT GTEX-11DXY 1 60-69 2 1 7.3 Brain 2037 1016 Presumed Death
Adj369 MBVis
GTEX-11DYG-2926-SM-5H132 GTEX-11DYG 1 60-69 2 1 7 Brain 2037 915 Actual Death
Adj369 MBVis
GTEX-11DZ1-2926-SM-5A5KI GTEX-11DZ1 1 50-59 4 1 6.3 Brain 2037 1314 Actual Death
Adj369 MBVis
GTEX-11EI6-2926-SM-5985U GTEX-11EI6 1 60-69 4 1 6.2 Brain 2037 1045 Actual Death
Adj369 MBVis
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