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 - - - - - - - - -
Edg219 GB
GTEX-1117F-2926-SM-5GZYI GTEX-1117F 2 60-69 4 0 7.7 Skin 1416 1341 Actual Death
Adj369 MBVis
GTEX-111CU-1126-SM-5EGIM GTEX-111CU 1 50-59 0 1 6.5 Skin 1416 86 Actual Death
Adj369 MBVis
GTEX-111CU-1926-SM-5GZYZ GTEX-111CU 1 50-59 0 1 5.9 Skin 1511 141 Actual Death
Adj369 MBVis
GTEX-111FC-0126-SM-5N9DL GTEX-111FC 1 60-69 1 1 7.2 Skin 1511 1036 Presumed Death
Adj369 MBVis
GTEX-111FC-2526-SM-5GZXU GTEX-111FC 1 60-69 1 1 7 Skin 1416 1135 Presumed Death
Adj369 MBVis
GTEX-111VG-1626-SM-5EGIO GTEX-111VG 1 60-69 3 1 6.8 Skin 1416 1046 Actual Death
Adj369 MBVis
GTEX-111VG-2426-SM-5GZXD GTEX-111VG 1 60-69 3 1 7.4 Skin 1511 1084 Actual Death
Adj369 MBVis
GTEX-111YS-1526-SM-5GZYW GTEX-111YS 1 60-69 0 0 7.5 Skin 1416 163 Actual Death
Adj369 MBVis
GTEX-1122O-2126-SM-5EGIR GTEX-1122O 2 60-69 0 0 7.1 Skin 1511 128 Actual Death
Adj369 MBVis
Showing 1 to 10 of 662 entries