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 - - - - - - - - -
Edg256 GB
GTEX-1117F-3226-SM-5N9CT GTEX-1117F 2 60-69 4 1 6.2 Brain 1870 1418 Actual Death
Adj369 MBVis
GTEX-111FC-3126-SM-5GZZ2 GTEX-111FC 1 60-69 1 1 6.1 Brain 1870 1221 Presumed Death
Adj369 MBVis
GTEX-1128S-2726-SM-5H12C GTEX-1128S 2 60-69 2 1 6.3 Brain 1870 1034 Actual Death
Adj369 MBVis
GTEX-117XS-3026-SM-5N9CA GTEX-117XS 1 60-69 2 1 6.4 Brain 1870 1017 Actual Death
Adj369 MBVis
GTEX-117YW-2926-SM-5GIEQ GTEX-117YW 1 50-59 3 1 5.9 Brain 1870 1045 Actual Death
Adj369 MBVis
GTEX-1192X-3126-SM-5N9BY GTEX-1192X 1 50-59 4 1 7.1 Brain 1870 989 Actual Death
Adj369 MBVis
GTEX-11DXW-1126-SM-5H12Q GTEX-11DXW 1 40-49 2 1 6.6 Brain 1870 1137 Actual Death
Adj369 MBVis
GTEX-11DXY-3226-SM-5GIDE GTEX-11DXY 1 60-69 2 1 7.7 Brain 1870 1016 Presumed Death
Adj369 MBVis
GTEX-11EI6-3026-SM-5GZZO GTEX-11EI6 1 60-69 4 1 6.4 Brain 1870 1048 Actual Death
Adj369 MBVis
Showing 1 to 10 of 780 entries