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  • Changelog
    v0.1 cell line networks
    v0.2 aggregate tissue networks
    v0.3 TF enrichement tool
    v0.4 single-sample tissue networks
    v0.5 CLUEreg tool
    v0.6 colon cancer networks
    v0.7 drug networks
    v0.7.1 API v1
    v0.8 liver, cervix, and breast cancer networks
    v0.9 miRNA tissue networks
    v0.9.1 bootstrap 5
    v1.0 glioblastoma networks
    v1.0.1 drug combinations
    v1.1 Cell line networks
    v1.2 User upload network
    v1.2.1 Gene targeting table
    v1.2.2 DRAGON miRNA network
    v1.3 Network comparison
    v1.3.1 Guided tours
    v1.4.0 CCLE multi-omic map
    v1.5.0 EGRET networks

    Breast cancer networks

    Data sets 1 Networks Single-sample 61

    To get the full list of phenotypic variables, please check the menu below. Click on the bar 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. LIONESS reconstructs sample-specific PANDA networks for each gene expression sample. To download sample-specific networks, you can check the phenotypic information and select the networks by variables of interest.

    Publication
    The reference for this network is Ben Guebila et al. (in preparation) at the following link.
    # Tissue Tool netZoo release Network
    PPI
    Motif Expression
    Regulator
    nReg
    Genes Data Samples Precision
    Reference
    1 Breast Cancer LIONESS netZooPy 0.8
    AdjCodeVis
    TF 1132 18560 CCLE 61 D

    Variable description

    You can specify the sample network to download by phenotypic variable and you will get a TF/miRNA-by-gene matrix named after the CCLE sample reference. The number of edges is the number of TFs/miRNA * number of genes (~ 106).

    DepMap ID
    Cell name COSMIC ID
    Sex Race Culture Collection site
    Type
    Cancer
    TCGA code
    Network
    ACH-000017 SKBR3 - Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000019 MCF7 905946.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000028 KPL1 - Female asian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000044 MDAMB134VI - Female caucasian - pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000097 ZR751 - Female caucasian Adherent ascites Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000111 HCC1187 749711.0 Female caucasian Mixed adherent and suspension breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000117 EFM192A 1290798.0 Female caucasian - pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000147 T47D 905945.0 Female - Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000148 HS578T 905957.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000196 HCC1599 749713.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000212 CAL120 906826.0 Female - Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000223 HCC1937 749714.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000248 AU565 910704.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000258 DU4475 906844.0 Female caucasian Suspension skin Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000276 HCC38 749717.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000277 HCC1419 907045.0 Female - - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000288 BT549 905951.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000330 EFM19 906851.0 Female caucasian - pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000349 HCC1500 1303900.0 Female african_american - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000352 HCC1428 1290905.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000374 HCC1143 749710.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000536 BT20 906801.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000554 UACC893 909778.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000568 UACC812 910910.0 Female - Suspension breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000573 MDAMB436 1240172.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000621 MDAMB157 925338.0 Female african_american Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000624 HCC1806 907047.0 Female african_american Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000643 HDQP1 1290922.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000668 HCC70 907048.0 Female african_american - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000691 HCC2157 749715.0 Female african_american - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000699 HCC1395 749712.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000711 JIMT1 1298157.0 Female - - pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000721 HMC18 - Female asian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000725 HCC202 1290906.0 Female caucasian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000755 HCC2218 749716.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000759 MDAMB175VII 908120.0 Female african_american - pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000768 MDAMB231 905960.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000783 CAMA1 946382.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000818 BT483 949093.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000828 ZR7530 909907.0 Female african_american - ascites Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000849 MDAMB468 908123.0 Female african_american Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000856 CAL51 910927.0 Female - Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000857 CAL851 910852.0 Female - - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000859 HCC1954 749709.0 Female east_indian Adherent breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000876 MDAMB415 924240.0 Female caucasian Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000902 CAL148 924106.0 Female - - pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000910 MDAMB453 908122.0 Female caucasian Adherent pericardial_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-000927 BT474 946359.0 Female caucasian - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000930 HCC1569 907046.0 Female african_american - breast Primary Breast Cancer BRCA
    Adj359 MBVis
    ACH-000934 MDAMB361 908121.0 Female caucasian - central_nervous_system Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-001388 SUM102PT - Female - - breast Primary Breast Cancer -
    Adj359 MBVis
    ACH-001389 SUM1315MO2 - Female - Adherent skin Metastasis Breast Cancer -
    Adj359 MBVis
    ACH-001390 SUM149PT - Female - Adherent breast Primary Breast Cancer -
    Adj359 MBVis
    ACH-001391 SUM159PT - Female - Adherent breast Primary Breast Cancer -
    Adj359 MBVis
    ACH-001392 SUM185PE - Female - Adherent pleural_effusion Metastasis Breast Cancer -
    Adj359 MBVis
    ACH-001394 SUM229PE - Female - Adherent pleural_effusion Metastasis Breast Cancer -
    Adj359 MBVis
    ACH-001395 SUM44PE - Female - - pleural_effusion Metastasis Breast Cancer -
    Adj359 MBVis
    ACH-001396 SUM52PE - Female - Adherent pleural_effusion Metastasis Breast Cancer -
    Adj359 MBVis
    ACH-001419 VP229 - Female - Adherent breast Primary Breast Cancer -
    Adj359 MBVis
    ACH-001819 MFM223 - Female - Adherent pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    ACH-001820 COLO824 - Female - Mix (loosely adherent with floating clumps) pleural_effusion Metastasis Breast Cancer BRCA
    Adj359 MBVis
    DepMap ID CCLE Name COSMIC ID Sex Race Culture Collection site Type Cancer TCGA code Network
    Contact

    Department of Biostatistics
    Harvard T.H. Chan School of Public Health

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