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 - - - - - - - - -
Edg72 GB
GTEX-1117F-2826-SM-5GZXL GTEX-1117F 2 60-69 4 1 5.8 Breast 8367 1340 Actual Death
Adj369 MBVis
GTEX-111YS-1926-SM-5GICC GTEX-111YS 1 60-69 0 0 7.2 Breast 8367 188 Actual Death
Adj369 MBVis
GTEX-1122O-1226-SM-5H113 GTEX-1122O 2 60-69 0 0 6.7 Breast 8367 93 Actual Death
Adj369 MBVis
GTEX-117XS-1926-SM-5GICO GTEX-117XS 1 60-69 2 1 6 Breast 8367 894 Actual Death
Adj369 MBVis
GTEX-117YX-1426-SM-5H12H GTEX-117YX 1 50-59 0 1 7.7 Breast 8367 107 Actual Death
Adj369 MBVis
GTEX-1192X-2326-SM-5987X GTEX-1192X 1 50-59 4 1 6.2 Breast 8367 940 Actual Death
Adj369 MBVis
GTEX-11DXW-0626-SM-5N9ER GTEX-11DXW 1 40-49 2 1 5.7 Breast 8367 1102 Actual Death
Adj369 MBVis
GTEX-11DXY-2326-SM-5GICW GTEX-11DXY 1 60-69 2 1 7 Breast 8367 948 Presumed Death
Adj369 MBVis
GTEX-11DXZ-1926-SM-5GZZL GTEX-11DXZ 1 50-59 0 0 7.7 Breast 8367 318 Actual Death
Adj369 MBVis
Showing 1 to 10 of 218 entries