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.
Sample | Subject | Gender | Age | DTH-HRDY | SMAT-SSCR | SMRIN | SMTS | SMUBRID | Isch. time | Time point | Net. |
---|---|---|---|---|---|---|---|---|---|---|---|
All | All | - | - | - | - | - | - | - | - | - | Edg119 GB |
GTEX-11GSP-0011-R5a-SM-57WBE | GTEX-11GSP | 2 | 60-69 | 2 | - | 8.4 | Brain | 1873 | - | Actual Death | |
GTEX-11GSP-0011-R6b-SM-57WBQ | GTEX-11GSP | 2 | 60-69 | 2 | - | 5.9 | Brain | 1882 | - | Actual Death | |
GTEX-11GSP-0011-R7b-SM-57WC3 | GTEX-11GSP | 2 | 60-69 | 2 | - | 7.8 | Brain | 1874 | - | Actual Death | |
GTEX-11H98-0011-R5b-SM-57WCF | GTEX-11H98 | 1 | 50-59 | 2 | - | 7.4 | Brain | 1873 | - | Actual Death | |
GTEX-11NV4-0011-R5a-SM-5NQ88 | GTEX-11NV4 | 1 | 60-69 | 2 | - | 8.5 | Brain | 1873 | - | Presumed Death | |
GTEX-11NV4-0011-R6a-SM-57WD5 | GTEX-11NV4 | 1 | 60-69 | 2 | - | 6.9 | Brain | 1882 | - | Presumed Death | |
GTEX-11NV4-0011-R7a-SM-57WDH | GTEX-11NV4 | 1 | 60-69 | 2 | - | 7.5 | Brain | 1874 | - | Presumed Death | |
GTEX-11OF3-0011-R5a-SM-57WB4 | GTEX-11OF3 | 1 | 60-69 | 2 | - | 7.7 | Brain | 1873 | - | Presumed Death | |
GTEX-11OF3-0011-R6b-SM-57WBG | GTEX-11OF3 | 1 | 60-69 | 2 | - | 7 | Brain | 1882 | - | Presumed Death |