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

    Image

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


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




Options

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