Brain basal ganglia networks

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 - - - - - - - - -
Edg119 GB
GTEX-11GSP-0011-R5a-SM-57WBE GTEX-11GSP 2 60-69 2 - 8.4 Brain 1873 - Actual Death
Adj369 MBVis
GTEX-11GSP-0011-R6b-SM-57WBQ GTEX-11GSP 2 60-69 2 - 5.9 Brain 1882 - Actual Death
Adj369 MBVis
GTEX-11GSP-0011-R7b-SM-57WC3 GTEX-11GSP 2 60-69 2 - 7.8 Brain 1874 - Actual Death
Adj369 MBVis
GTEX-11H98-0011-R5b-SM-57WCF GTEX-11H98 1 50-59 2 - 7.4 Brain 1873 - Actual Death
Adj369 MBVis
GTEX-11NV4-0011-R5a-SM-5NQ88 GTEX-11NV4 1 60-69 2 - 8.5 Brain 1873 - Presumed Death
Adj369 MBVis
GTEX-11NV4-0011-R6a-SM-57WD5 GTEX-11NV4 1 60-69 2 - 6.9 Brain 1882 - Presumed Death
Adj369 MBVis
GTEX-11NV4-0011-R7a-SM-57WDH GTEX-11NV4 1 60-69 2 - 7.5 Brain 1874 - Presumed Death
Adj369 MBVis
GTEX-11OF3-0011-R5a-SM-57WB4 GTEX-11OF3 1 60-69 2 - 7.7 Brain 1873 - Presumed Death
Adj369 MBVis
GTEX-11OF3-0011-R6b-SM-57WBG GTEX-11OF3 1 60-69 2 - 7 Brain 1882 - Presumed Death
Adj369 MBVis
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