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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

    Liver cancer networks

    Data sets 1 Networks Single-sample 24

    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 Liver Cancer LIONESS netZooPy 0.8
    AdjCodeVis
    TF 1132 18560 CCLE 24 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-000217 JHH6 1240159.0 Female asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000221 SNU398 1240217.0 Male asian Mixed adherent and suspension liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000316 SNU886 - Male asian - liver - Liver Cancer LIHC
    Adj359 MBVis
    ACH-000361 SKHEP1 909719.0 Male caucasian Adherent ascites Metastasis Liver Cancer LIHC
    Adj359 MBVis
    ACH-000393 HLF - Male asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000420 SNU449 909738.0 Male asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000422 SNU475 909739.0 Male asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000471 LI7 - Male - - liver - Liver Cancer LIHC
    Adj359 MBVis
    ACH-000475 HUH1 1298146.0 Male asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000476 JHH4 1240158.0 Male asian - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000478 SNU387 909736.0 Female asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000480 HUH7 907071.0 Male asian - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000483 SNU182 1240216.0 Male asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000493 SNU423 909737.0 Male asian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000537 SNU761 - Male asian - liver - Liver Cancer LIHC
    Adj359 MBVis
    ACH-000577 JHH2 1240157.0 Male asian Adherent ascites Metastasis Liver Cancer LIHC
    Adj359 MBVis
    ACH-000620 JHH1 1298151.0 Male asian - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000625 HEP3B217 1240147.0 Male african_american - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000671 HUH6 - Male asian - liver - Liver Cancer LIHC
    Adj359 MBVis
    ACH-000686 SNU878 - Female asian - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000734 JHH5 - Male asian - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000739 HEPG2 - Male caucasian Adherent liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-000848 JHH7 1240160.0 Male asian - liver Primary Liver Cancer LIHC
    Adj359 MBVis
    ACH-001318 PLCPRF5 - Male - Adherent liver Primary Liver Cancer LIHC
    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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