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    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

    Gastric cancer networks

    Data sets 1 Networks Single-sample 40

    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 Gastric Cancer LIONESS netZooPy 0.8
    AdjCodeVis
    TF 1132 18560 CCLE 40 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-000110 NCCSTCK140 - Female - - stomach - Gastric Cancer STAD
    Adj359 MBVis
    ACH-000144 RERFGC1B 1240209.0 Male asian - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000225 ECC12 906849.0 Male - - stomach - Gastric Cancer STAD
    Adj359 MBVis
    ACH-000239 HUG1N - Male asian - stomach Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000247 OCUM1 1298358.0 Female asian - stomach Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000255 LMSU - Female - - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000303 SNU5 908445.0 Female asian - ascites Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000325 SNU620 - Female asian - ascites Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000344 SNU668 - Male asian - ascites Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000351 MKN1 908138.0 Male asian - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000356 MKN45 925340.0 Female asian - liver Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000427 NCIN87 908461.0 Male - Adherent liver Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000466 SNU216 - Female asian - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000485 GSU - Male - - ascites Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000507 KE39 - Male asian Adherent lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000538 HUTU80 907073.0 Male caucasian - small_intestine Primary Gastric Cancer -
    Adj359 MBVis
    ACH-000560 ECC10 906848.0 Male - - liver - Gastric Cancer STAD
    Adj359 MBVis
    ACH-000581 SNU16 908446.0 Female asian - ascites Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000616 HS746T 1240151.0 Male caucasian Adherent soft_tissue Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000633 FU97 1290806.0 Female asian - stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000674 NUGC4 1298357.0 Female asian - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000678 MKN7 924250.0 Male asian - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000736 SNU601 - Male asian - ascites Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000746 GSS - Male - - liver Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000758 MKN74 - Male asian - liver Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000761 NUGC2 - Female - - lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000764 SH10TC - Unknown - Adherent stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000793 KATOIII 907276.0 Male asian Mixed adherent and suspension pleural_effusion Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000847 HGC27 907055.0 Unknown asian Adherent lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000880 AGS 906790.0 Female caucasian Adherent stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000898 SNU719 - Male asian - stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000908 SNU520 - Female asian - stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000911 NUGC3 908455.0 Male - - soft_tissue Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000919 IM95 1240155.0 Male asian Adherent stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000932 SNU1 908444.0 Male asian - stomach Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-000948 2313287 910924.0 Male - - stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-000949 TGBC11TKB 909770.0 Female - Suspension lymph_node Metastasis Gastric Cancer STAD
    Adj359 MBVis
    ACH-001653 SKGT2 1503364.0 Male - Adherent stomach Primary Gastric Cancer STAD
    Adj359 MBVis
    ACH-001664 SNU638 - Male - Adherent ascites Metastasis Gastric Cancer -
    Adj359 MBVis
    ACH-002446 CCLFUPGI0005T - Unknown - Adherent pleura Metastasis Gastric 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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