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    20230209_pilot_DEG

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    汤慧仪

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    20230209_pilot_DEG

    Uploaded by

    汤慧仪
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    1 views5 pages

    20230209_pilot_DEG

    Uploaded by

    汤慧仪

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    You are on page 1of 5

    EggPlants Pilot

    2023.02.09
    Pei-Yu Lin
    Workflow
    Core gene identification Essential gene prediction Local EGs detection

    Analysing network
    Start statistics between global
    Network statistic analysis and local EGs
    Collecting 281 plant genomes
    Collecting 281 plant genomes

    (11M genes) Essential gene prediction by GLM Identifying global


    and local EGs
    Pairwise gene comparison
    Computational
    Ranked
    & experimental
    essential genes Associating local EGs
    Build a gene similarity network validation
    with specific branches
    and functions
    Network clustering by Louvain
    Build up GUI (browse,
    query, database pages)
    Core gene subnets

    EggPlants online database

    Stop
    Essential gene collection
    • Source: DEG database (http://origin.tubic.org/deg/public/index.php )
    • Species:
    Species Known EGs Abbreviation Download
    Arabidopsis thaliana 356 DEG2003xxxx link
    Mapping known EGs to subnets
    • Tool: MMseqs2 (https://github.com/soedinglab/MMseqs2) 5 mins (88 cores 1.48 T)
    • mmseqs easy-search all_plants.fa.gz DEG20.aa.gz deg.m8 tmp
    • Tool: map_eg.R (https://github.com/beritlin/FunCore/blob/master/map_eg.R)

    • Output: (examaple)

    group # species # nodes DEG


    8117 3 3 0
    6783 6 16 1
    Results
    • Table
    Local (N= ) Global (N= ) P-value
    Cut off -
    # nodes
    # species

    • Figures

    With known EG
    # subnets

    Without known EG

    # species

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