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 - - - - - - - - -
Edg119 GB
GTEX-11UD2-0726-SM-5EQ69 GTEX-11UD2 1 50-59 2 2 6.9 Lung 8952 889 Actual Death
Adj369 MBVis
GTEX-11WQC-0626-SM-5EQMF GTEX-11WQC 1 60-69 2 1 6.5 Lung 8952 693 Actual Death
Adj369 MBVis
GTEX-11WQK-1226-SM-5GU5Z GTEX-11WQK 1 50-59 2 2 7.5 Lung 8952 776 Actual Death
Adj369 MBVis
GTEX-11ZTS-1226-SM-5EQMQ GTEX-11ZTS 2 60-69 2 1 7.5 Lung 8952 650 Actual Death
Adj369 MBVis
GTEX-11ZTT-0626-SM-5EQLM GTEX-11ZTT 2 60-69 0 0 6.3 Lung 8952 172 Actual Death
Adj369 MBVis
GTEX-11ZUS-0126-SM-5EQM5 GTEX-11ZUS 1 30-39 1 1 6.5 Lung 8952 1345 Actual Death
Adj369 MBVis
GTEX-1211K-0826-SM-5FQUP GTEX-1211K 2 60-69 0 1 8.2 Lung 8952 92 Actual Death
Adj369 MBVis
GTEX-1212Z-1026-SM-5EGJ8 GTEX-1212Z 1 60-69 2 1 6.2 Lung 8952 636 Actual Death
Adj369 MBVis
GTEX-12584-1426-SM-5EGJ9 GTEX-12584 1 40-49 3 1 7.1 Lung 8952 1006 Actual Death
Adj369 MBVis
Showing 1 to 10 of 334 entries