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 - - - - - - - - -
Edg47 GB
GTEX-1117F-0626-SM-5N9CS GTEX-1117F 2 60-69 4 1 6.9 Blood Vessel 1621 1243 Actual Death
Adj369 MBVis
GTEX-1122O-0426-SM-5H12G GTEX-1122O 2 60-69 0 0 7.7 Blood Vessel 1621 63 Actual Death
Adj369 MBVis
GTEX-117YX-1726-SM-5GZZS GTEX-117YX 1 50-59 0 0 7.9 Blood Vessel 1621 115 Actual Death
Adj369 MBVis
GTEX-11DXX-0826-SM-5GZZP GTEX-11DXX 2 60-69 0 0 7.3 Blood Vessel 1621 98 Actual Death
Adj369 MBVis
GTEX-11DXY-1126-SM-5987W GTEX-11DXY 1 60-69 2 1 6.5 Blood Vessel 1621 908 Presumed Death
Adj369 MBVis
GTEX-11DXZ-0526-SM-5GU7J GTEX-11DXZ 1 50-59 0 1 6.4 Blood Vessel 1621 276 Actual Death
Adj369 MBVis
GTEX-11DYG-0926-SM-5EGGW GTEX-11DYG 1 60-69 2 1 5.8 Blood Vessel 1621 853 Actual Death
Adj369 MBVis
GTEX-11EM3-0526-SM-5H12N GTEX-11EM3 2 20-29 0 1 7.1 Blood Vessel 1621 138 Actual Death
Adj369 MBVis
GTEX-11GS4-0626-SM-5A5LC GTEX-11GS4 1 60-69 2 1 6 Blood Vessel 1621 803 Actual Death
Adj369 MBVis
Showing 1 to 10 of 141 entries