BRCA cancer networks

Data sets 1 Networks Aggregate 2 Single-sample 1182

To get the full list of phenotypic variables, please check the menu below.

Tool description

Like PANDA, OTTER reconstructs a gene regulatory network from the TF PPI, TF DNA binding motif, and gene expression samples. OTTER formulates network inference as a well-defined objective function that optimizes the graph matching of the three network priors. Check the phenotypic information for the clinical variables of the samples that were used to reconstruct the network.
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
GenderRaceEthnicityWeight
Height
Anatomic location
Stage
DiagnosisVital statusTime
Age
Network
Network format
TCGA-3C-AAAU-01A-11R-A41B-07 female white not hispanic or latino NA NA Breast stage x c50.9 alive NA 55
Adj84.0 MBVis
TCGA-3C-AALI-01A-11R-A41B-07 female black or african american not hispanic or latino NA NA Breast stage iib c50.9 alive NA 50
Adj84.0 MBVis
TCGA-3C-AALJ-01A-31R-A41B-07 female black or african american not hispanic or latino NA NA Breast stage iib c50.9 alive NA 62
Adj84.0 MBVis
TCGA-3C-AALK-01A-11R-A41B-07 female black or african american not hispanic or latino NA NA Breast stage ia c50.9 alive NA 52
Adj84.0 MBVis
TCGA-4H-AAAK-01A-12R-A41B-07 female white not hispanic or latino NA NA Breast stage iiia c50.9 alive NA 50
Adj84.0 MBVis
TCGA-5L-AAT0-01A-12R-A41B-07 female white hispanic or latino NA NA Breast stage iia c50.9 alive NA 42
Adj84.0 MBVis
TCGA-5L-AAT1-01A-12R-A41B-07 female white hispanic or latino NA NA Breast stage iv c50.9 alive NA 63
Adj84.0 MBVis
TCGA-5T-A9QA-01A-11R-A41B-07 female black or african american not hispanic or latino NA NA Breast stage iia c50.9 alive NA 52
Adj84.0 MBVis
TCGA-A1-A0SB-01A-11R-A144-07 female white not hispanic or latino NA NA Breast stage i c50.9 alive NA 70
Adj84.0 MBVis
TCGA-A1-A0SD-01A-11R-A115-07 female white not hispanic or latino NA NA Breast stage iia c50.9 alive NA 59
Adj84.0 MBVis
Showing 1 to 10 of 1,165 entries

Variable description

BONOBO estimates single-sample co-expression networks for each individual patient. Networks for each individual sample can be downloaded as a miRNA-by-gene adjacency matrix named after the GEO sample reference.

SampleGenderSubtypeMutationHER2 statusEstrogen receptor statusAnatomic locationTimeVital statusNetwork
GSM496794 Female - tp53 mutation status: Mut - Negative Breast Primary Tumor 105.625 Dead of other disease than BC
Adj152.3 MBVis
GSM496795 Female breast cancer subtype: Lum A tp53 mutation status: WT Negative Positive Breast Primary Tumor 127.4013158 Alive
Adj152.3 MBVis
GSM496796 Female breast cancer subtype: Lum A tp53 mutation status: WT Negative Positive Breast Primary Tumor 126.6118421 Alive
Adj152.3 MBVis
GSM496797 Female breast cancer subtype: Lum A tp53 mutation status: WT Negative Positive Breast Primary Tumor 126.5131579 Alive
Adj152.3 MBVis
GSM496798 Female breast cancer subtype: Lum A tp53 mutation status: WT Negative Positive Breast Primary Tumor 80.98684211 Dead of other disease than BC
Adj152.3 MBVis
GSM496799 Female breast cancer subtype: Basal tp53 mutation status: Mut Negative Negative Breast Primary Tumor - -
Adj152.3 MBVis
GSM496800 Female breast cancer subtype: Lum A tp53 mutation status: WT Negative Positive Breast Primary Tumor 52.56578947 Dead of BC
Adj152.3 MBVis
GSM496801 Female breast cancer subtype: Normal-like tp53 mutation status: WT Negative Negative Breast Primary Tumor 81.67763158 Dead of other disease than BC
Adj152.3 MBVis
GSM496802 Female breast cancer subtype: Lum B tp53 mutation status: Mut Negative Positive Breast Primary Tumor 126.25 Alive
Adj152.3 MBVis
GSM496803 Female breast cancer subtype: Normal-like tp53 mutation status: WT Positive Positive Breast Primary Tumor 32.59868421 Dead of BC
Adj152.3 MBVis
Showing 1 to 10 of 101 entries

Benchmarking OTTER networks

The accuracy of OTTER cancer networks were benchmarked for their accuracy to predict ChIP-seq binding in comparison to other methods. The ground truth data can be found here.

*refers to a modified input PPI and motif networks. For more details, please check this page.