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 - - - - - - - - -
Edg41 GB
GTEX-111FC-3026-SM-5GZYJ GTEX-111FC 1 60-69 1 3 6.4 Pituitary 7 1221 Presumed Death
Adj369 MBVis
GTEX-1128S-2626-SM-5H11Z GTEX-1128S 2 60-69 2 1 6.7 Pituitary 7 1030 Actual Death
Adj369 MBVis
GTEX-113JC-2826-SM-5EGIT GTEX-113JC 2 50-59 2 2 6.1 Pituitary 7 818 Actual Death
Adj369 MBVis
GTEX-117XS-2926-SM-5N9BX GTEX-117XS 1 60-69 2 1 7.5 Pituitary 7 1016 Actual Death
Adj369 MBVis
GTEX-117YW-2826-SM-5H116 GTEX-117YW 1 50-59 3 1 6 Pituitary 7 1042 Actual Death
Adj369 MBVis
GTEX-1192W-3026-SM-5GZZV GTEX-1192W 1 60-69 2 1 5.9 Pituitary 7 857 Actual Death
Adj369 MBVis
GTEX-1192X-3026-SM-5N9BM GTEX-1192X 1 50-59 4 2 7 Pituitary 7 987 Actual Death
Adj369 MBVis
GTEX-11DXW-1226-SM-5H133 GTEX-11DXW 1 40-49 2 1 7 Pituitary 7 1138 Actual Death
Adj369 MBVis
GTEX-11DXY-3026-SM-5N9CB GTEX-11DXY 1 60-69 2 1 7.5 Pituitary 7 1019 Presumed Death
Adj369 MBVis
Showing 1 to 10 of 125 entries