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 - - - - - - - - -
Edg58 GB
GTEX-111CU-1226-SM-5EGIN GTEX-111CU 1 50-59 0 1 7.3 Colon 1159 91 Actual Death
Adj369 MBVis
GTEX-111YS-1826-SM-5GIEP GTEX-111YS 1 60-69 0 0 7.8 Colon 1159 182 Actual Death
Adj369 MBVis
GTEX-1122O-1426-SM-5H11R GTEX-1122O 2 60-69 0 0 7.2 Colon 1159 106 Actual Death
Adj369 MBVis
GTEX-117XS-2226-SM-5GIE1 GTEX-117XS 1 60-69 2 2 6.2 Colon 1159 907 Actual Death
Adj369 MBVis
GTEX-117YX-0526-SM-5EGJH GTEX-117YX 1 50-59 0 1 7.3 Colon 1159 88 Actual Death
Adj369 MBVis
GTEX-11DXX-1926-SM-5EGJK GTEX-11DXX 2 60-69 0 1 7.4 Colon 1159 131 Actual Death
Adj369 MBVis
GTEX-11DXY-2026-SM-5N9CZ GTEX-11DXY 1 60-69 2 1 5.8 Colon 1159 939 Presumed Death
Adj369 MBVis
GTEX-11DXZ-1626-SM-5GIDI GTEX-11DXZ 1 50-59 0 1 6.5 Colon 1159 306 Actual Death
Adj369 MBVis
GTEX-11EI6-2626-SM-5PNVT GTEX-11EI6 1 60-69 4 1 6.4 Colon 1159 1024 Actual Death
Adj369 MBVis
Showing 1 to 10 of 174 entries