Changes between Version 31 and Version 32 of SOPs/go_annotation


Ignore:
Timestamp:
01/26/21 13:01:26 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/go_annotation

    v31 v32  
    11= Identifying enriched biological themes in gene sets =
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     4=== Recommendations ===
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     6* Choose appropriate,
     7   * gene sets (reference) to use depending on the biological question e.g. MSigDB H1 hallmark gene sets
     8   * background genes, some tools do not have the option to select a different background
     9* Gene sets should be approximately 15 to 500 genes
     10* Use gene identifiers that are accepted by the tool
     11* Check or verify the tool’s databases or gene sets are updated or maintained
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    … …  
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    2434* [[https://www.gsea-msigdb.org/gsea/login.jsp|Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.]]
    25 * [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|Explore the Molecular Signatures Database (MSigDB), ]]a collection of annotated gene sets for use with GSEA software.
     35* [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|Explore the Molecular Signatures Database (MSigDB), ]]a collection of annotated gene sets for use with GSEA software.  The H (hallmark), C2 (curated) and C5 (GO) are good gene sets to start the analysis.
    2636* [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA and MSigDB documentation]]
    2737* [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | Guidelines for using RNA-seq datasets with GSEA]]