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 - - - - - - - - -
Edg68 GB
GTEX-111CU-0926-SM-5EGIK GTEX-111CU 1 50-59 0 0 7.8 Stomach 945 83 Actual Death
Adj369 MBVis
GTEX-111YS-1126-SM-5GZYQ GTEX-111YS 1 60-69 0 1 6.4 Stomach 945 151 Actual Death
Adj369 MBVis
GTEX-1122O-1926-SM-5EGIQ GTEX-1122O 2 60-69 0 1 6.5 Stomach 945 123 Actual Death
Adj369 MBVis
GTEX-117YW-2226-SM-5N9DB GTEX-117YW 1 50-59 3 2 7.3 Stomach 945 910 Actual Death
Adj369 MBVis
GTEX-117YX-1026-SM-5H11V GTEX-117YX 1 50-59 0 1 7 Stomach 945 101 Actual Death
Adj369 MBVis
GTEX-11DXX-1326-SM-5GIDZ GTEX-11DXX 2 60-69 0 1 6.2 Stomach 945 112 Actual Death
Adj369 MBVis
GTEX-11EI6-2426-SM-5PNVS GTEX-11EI6 1 60-69 4 2 5.8 Stomach 945 1018 Actual Death
Adj369 MBVis
GTEX-11EM3-1026-SM-5A5KL GTEX-11EM3 2 20-29 0 1 7.4 Stomach 945 156 Actual Death
Adj369 MBVis
GTEX-11EQ9-1226-SM-5987E GTEX-11EQ9 1 30-39 2 1 7.4 Stomach 945 108 Actual Death
Adj369 MBVis
Showing 1 to 10 of 205 entries