Hover over the bar plot to get the GO term. Differentially targeted genes and TFs were computed by comparing a cancer network to all other cancers.

Tool description

PANDA reconstructs a gene regulatory network using TF PPI, TF DNA binding motif, and gene expression samples. LIONESS reconstructs patient-specific PANDA networks for each gene expression sample. To download patient-specific networks, you can check the phenotypic information of the TCGA dataset. You can also select the networks by clinical variables or download all the samples in a single file.
The variable Samples indicates the number of samples used for network reconstruction. For single-sample networks, clicking the number of samples links to the phenotypic variable table and the individual networks. The number in the Sample variable and the phenotypic variable table may be different because the table can include samples from other studies. For example, in colon cancer, 444 TCGA samples were used to build LIONESS networks in a first study and 445 samples were used for a more recent study. The superset of both TCGA samples is comprised of 487 samples, which is the size of the pheotypic variables table. This discrepancy is due to different pre-processinng techniques, inclusion/exclusion criteria, and sample quality-control.

Variable description

This is a description of the primary clinical variables of the gene expression samples that were used to generate the gene regulatory network.

Sample
GenderRaceStage
Vital statusAge
Days to last follow upTumor ID
Network
Network format
TCGA-BR-4371-01A FEMALE WHITE [Not Available] Alive 71 0 STAD
Adj83.9 MBVis
TCGA-D7-6815-01A FEMALE WHITE Stage IIB Alive 70 111 STAD
Adj83.9 MBVis
TCGA-IN-A7NT-01A FEMALE WHITE Stage IIB Alive 73 169 STAD
Adj83.9 MBVis
TCGA-SW-A7EA-01A FEMALE WHITE Stage IB Alive 61 13 STAD
Adj83.9 MBVis
TCGA-BR-8588-01A FEMALE WHITE Stage IIB Alive 55 23 STAD
Adj83.9 MBVis
TCGA-BR-4201-01A FEMALE WHITE [Not Available] Alive 66 0 STAD
Adj83.9 MBVis
TCGA-CD-8524-01A FEMALE ASIAN Stage II Alive 61 2 STAD
Adj83.9 MBVis
TCGA-D7-6526-01A FEMALE WHITE Stage IIIA Alive 67 201 STAD
Adj83.9 MBVis
TCGA-VQ-A8PU-01A FEMALE WHITE Stage IIIA Alive 72 717 STAD
Adj83.9 MBVis
TCGA-BR-6709-01A FEMALE WHITE Stage IIIB Alive 57 38 STAD
Adj83.9 MBVis
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