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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

    Prostate cancer networks

    Data sets 1 Networks Single-sample 11

    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 Prostate Cancer LIONESS netZooPy 0.8
    AdjCodeVis
    TF 1132 18560 CCLE 11 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-000090 PC3 905934.0 Male caucasian Adherent bone Metastasis Prostate Cancer PRAD
    Adj359 MBVis
    ACH-000115 VCAP 1299075.0 Male caucasian Adherent bone Metastasis Prostate Cancer PRAD
    Adj359 MBVis
    ACH-000177 NCIH660 1330975.0 Male caucasian - lymph_node Metastasis Prostate Cancer PRAD
    Adj359 MBVis
    ACH-000952 MDAPCA2B - Male african_american - bone Metastasis Prostate Cancer PRAD
    Adj359 MBVis
    ACH-000956 22RV1 924100.0 Male - - prostate Primary Prostate Cancer PRAD
    Adj359 MBVis
    ACH-000977 LNCAPCLONEFGC 907788.0 Male caucasian Mixed adherent and suspension lymph_node Metastasis Prostate Cancer PRAD
    Adj359 MBVis
    ACH-001422 WPE1NA22 - Male - Adherent prostate Primary Prostate Cancer -
    Adj359 MBVis
    ACH-001453 BPH1 924105.0 Male - Adherent prostate Primary Prostate Cancer PRAD
    Adj359 MBVis
    ACH-001627 P4E6 - Male - Adherent prostate Primary Prostate Cancer -
    Adj359 MBVis
    ACH-001648 SHMAC4 - Unknown - Adherent prostate Primary Prostate Cancer -
    Adj359 MBVis
    ACH-001649 SHMAC5 - Unknown - - prostate Primary Prostate Cancer -
    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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