Platform for Drug Discovery



RECLU: GOAnalysis


Introduction


    RECLU: GOAnalysis

    The GOAnalysis pipeline performs an enrichment analysis on differentially expressed genes obtained by the RECLU ver3.1 pipeline. Basically, this pipeline uses the database containing the Ensembl Transcript ID and gene ontology (GO) terms provided by the Ensembl project. The pipeline tests the independence between differentially expressed genes and GO terms using Fisher's exact test. First, the pipeline classified those genes with differential expression into 4 groups; up-regulated at the top peaks, down-regulated at the top peaks, up-regulated at the bottom peaks, and down-regulated at the bottom peaks. Then implements the enrichment analysis for each group. The pipeline allows BED files at the top and bottom peaks provided by the RECLU ver3.1 pipeline as input files.

    Input formatbed
    Library layoutUnspecified
    SpeciesHuman(hg19),Mouse(mm10)
    Execution timeAbout 20min.


    Results

    Image

    Pipeline history

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Inputs


    Input 1: RECLU Toppeaks data (Required)

  • Check the dataset type explanation: bed
    BED format provides a flexible way to define the data lines that are displayed in an annotation track.
    UCSC Genome/FAQ:Data File Formats

  • Input 2: RECLU Bottompeaks data (Required)

    Check the dataset type explanation: bed
    BED format provides a flexible way to define the data lines that are displayed in an annotation track.
    UCSC Genome/FAQ:Data File Formats

Outputs


    HTML report


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    (1)Toppeaks-Upregurated
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    (2)Toppeaks-Downregurated
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    (3)Bottompeaks-Upregurated
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    (4)Bottompeaks-Downregurated


    CategoryGOのカテゴリ
    AccessionGOのaccession numberクリックするとQuickGOの各termの説明ページにジャンプする
    TermGO term名
    Counts入力遺伝子のうち、このGO termにヒットした遺伝子の数
    %入力遺伝子のうち、このGO termにヒットした遺伝子の割合(%)
    Descendant termsNA: 検出したtermのうち、最leaf term (つまり一番詳細なterm)GO: このtermよりleaf term(もっと詳細なterm)が存在する
    P-value値が小さいほど有意とする指標。多重検定では有意ではないのに有意としてしまう危険がある。
    FDRFalse Discovery Rateで値が小さいほど有意とする指標。P-valueの多重検定の課題を改善した補正値。 この値を参考に候補を絞り込む。



Options


    Image

    GENOME_ID:解析するデータの生物種のreference genomeバージョン。
    moirai/prepareGO logfoldchange:GO解析に用いる発現差遺伝子のlog fold changeの閾値。この値よりもlog fold changeの絶対値が大きい遺伝子を解析に使用。デフォルト値は2.0だが変更可能。
    moirai/prepareGO pvalue:GO解析に用いる発現差遺伝子のP値の閾値。この値よりもP値が小さい遺伝子を解析に使用。デフォルト値は0.05だが変更可能。

Comments


Use case


Related information


    Public
    RR is a language and environment for statistical computing and graphics.(Original site)(external link)

    RIKEN CLST Original
    prepareGO
    windowBedOhmiya
    groupByOrg
    executeGOAnalysis
    goAnalysis.sh
    makeGoAnalysisResult

References