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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

    Bone cancer networks

    Data sets 1 Networks Single-sample 39

    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 Bone Cancer LIONESS netZooPy 0.8
    AdjCodeVis
    TF 1132 18560 CCLE 39 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-000039 SKNMC - Female caucasian Adherent bone Metastasis Bone Cancer SARC
    Adj359 MBVis
    ACH-000041 RDES - Male caucasian Adherent bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000052 A673 684052.0 Female - Adherent soft_tissue Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000082 G292CLONEA141B1 1290807.0 Female caucasian Adherent bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000087 SKES1 684072.0 Male caucasian - bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000210 CADOES1 753539.0 Female asian Mixed adherent and suspension pleural_effusion Metastasis Bone Cancer SARC
    Adj359 MBVis
    ACH-000279 EWS502 - Unknown - not found bone - Bone Cancer -
    Adj359 MBVis
    ACH-000359 MG63 908131.0 Male caucasian - bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000364 U2OS 909776.0 Female caucasian Adherent bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000391 MHHES1 908134.0 Male turkish Adherent ascites Metastasis Bone Cancer SARC
    Adj359 MBVis
    ACH-000410 SAOS2 909707.0 Female caucasian Adherent bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000418 SW1353 - Female caucasian - bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000424 TC71 1240221.0 Male - - bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000499 EW8 - Male - not found bone - Bone Cancer -
    Adj359 MBVis
    ACH-000516 CAL78 1290765.0 Male - Adherent soft_tissue - Bone Cancer SARC
    Adj359 MBVis
    ACH-000613 HOS 907060.0 Female caucasian - bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-000748 SJSA1 909717.0 Male african_american Adherent bone Primary Bone Cancer SARC
    Adj359 MBVis
    ACH-001001 143B - Female caucasian not found bone Primary Bone Cancer -
    Adj359 MBVis
    ACH-001022 CBAGPN - Unknown - - bone - Bone Cancer -
    Adj359 MBVis
    ACH-001029 CHLA10 - Female - not found lymph_node - Bone Cancer -
    Adj359 MBVis
    ACH-001030 CHLA218 - Female - - bone - Bone Cancer -
    Adj359 MBVis
    ACH-001032 CHLA32 - Female - - bone - Bone Cancer -
    Adj359 MBVis
    ACH-001033 CHLA57 - Unknown - not found bone - Bone Cancer -
    Adj359 MBVis
    ACH-001034 CHLA9 - Female - - bone - Bone Cancer -
    Adj359 MBVis
    ACH-001035 CHLA99 - Male - - bone - Bone Cancer -
    Adj359 MBVis
    ACH-001038 COGE352 - Male - not found haematopoietic_and_lymphoid_tissue - Bone Cancer -
    Adj359 MBVis
    ACH-001192 SKNEP1 - Female - not found pleural_effusion Metastasis Bone Cancer KIRC
    Adj359 MBVis
    ACH-001193 SKPNDW 909731.0 Male - not found Embryonal - Bone Cancer -
    Adj359 MBVis
    ACH-001283 TC106 - Male - not found skin Metastasis Bone Cancer -
    Adj359 MBVis
    ACH-001430 TC138 - Male - not found bone - Bone Cancer -
    Adj359 MBVis
    ACH-001431 TC205 - Unknown - not found bone - Bone Cancer -
    Adj359 MBVis
    ACH-001519 HEMCSS 907290.0 Female - - soft_tissue Primary Bone Cancer -
    Adj359 MBVis
    ACH-001526 HUO9 907072.0 Female - Adherent bone Primary Bone Cancer -
    Adj359 MBVis
    ACH-001712 HS860T - Male - - bone - Bone Cancer -
    Adj359 MBVis
    ACH-001715 CAL72 906827.0 Male - Adherent bone - Bone Cancer -
    Adj359 MBVis
    ACH-001814 OS252 - Unknown - Adherent bone Primary Bone Cancer -
    Adj359 MBVis
    ACH-001818 C396 - Unknown - - bone Metastasis Bone Cancer -
    Adj359 MBVis
    ACH-002067 NOS1 - Male - Adherent bone Primary Bone Cancer -
    Adj359 MBVis
    ACH-002069 HSOS1 - Female - Adherent bone Primary Bone 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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