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 - - - - - - - - -
Edg142 GB
GTEX-111YS-0006-SM-5NQBE GTEX-111YS 1 60-69 0 - 8.2 Blood 13756 -121 Actual Death
Adj369 MBVis
GTEX-1122O-0005-SM-5O99J GTEX-1122O 2 60-69 0 - 7.6 Blood 13756 1363 Actual Death
Adj369 MBVis
GTEX-1128S-0005-SM-5P9HI GTEX-1128S 2 60-69 2 - 6.7 Blood 13756 783 Actual Death
Adj369 MBVis
GTEX-113IC-0006-SM-5NQ9C GTEX-113IC 1 60-69 - - 8.6 Blood 13756 -351 Cross Clamp Applied
Adj369 MBVis
GTEX-113JC-0006-SM-5O997 GTEX-113JC 2 50-59 2 - 7.6 Blood 13756 587 Actual Death
Adj369 MBVis
GTEX-117XS-0005-SM-5PNU6 GTEX-117XS 1 60-69 2 - 6.4 Blood 13756 802 Actual Death
Adj369 MBVis
GTEX-117YW-0005-SM-5NQ8Z GTEX-117YW 1 50-59 3 - 8.5 Blood 13756 771 Actual Death
Adj369 MBVis
GTEX-1192W-0005-SM-5NQBQ GTEX-1192W 1 60-69 2 - 8 Blood 13756 645 Actual Death
Adj369 MBVis
GTEX-1192X-0005-SM-5NQC3 GTEX-1192X 1 50-59 4 - 8.3 Blood 13756 757 Actual Death
Adj369 MBVis
Showing 1 to 10 of 445 entries