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 - - - - - - - - -
Edg45 GB
GTEX-1192X-1026-SM-5H12P GTEX-1192X 1 50-59 4 1 6 Liver 1114 889 Actual Death
Adj369 MBVis
GTEX-11DXY-0526-SM-5EGGQ GTEX-11DXY 1 60-69 2 1 6.8 Liver 1114 891 Presumed Death
Adj369 MBVis
GTEX-11DXZ-0126-SM-5EGGY GTEX-11DXZ 1 50-59 0 1 7.9 Liver 1114 250 Actual Death
Adj369 MBVis
GTEX-11EQ9-0526-SM-5A5JZ GTEX-11EQ9 1 30-39 2 1 8.1 Liver 1114 82 Actual Death
Adj369 MBVis
GTEX-11GSP-0626-SM-5986T GTEX-11GSP 2 60-69 2 1 6.2 Liver 1114 771 Actual Death
Adj369 MBVis
GTEX-11NUK-1226-SM-5P9GM GTEX-11NUK 1 50-59 2 1 6.1 Liver 1114 956 Actual Death
Adj369 MBVis
GTEX-11NV4-1326-SM-5HL6V GTEX-11NV4 1 60-69 2 1 5.9 Liver 1114 1152 Presumed Death
Adj369 MBVis
GTEX-11OF3-0726-SM-5BC4Z GTEX-11OF3 1 60-69 2 2 6 Liver 1114 790 Presumed Death
Adj369 MBVis
GTEX-11TT1-1726-SM-5EQLJ GTEX-11TT1 1 20-29 0 1 9.1 Liver 1114 98 Actual Death
Adj369 MBVis
Showing 1 to 10 of 138 entries