| | 1 | = Identifying enriched biological themes in gene sets = |
| | 2 | |
| | 3 | |
| | 4 | === DAVID === |
| | 5 | [[http://david.abcc.ncifcrf.gov/home.jsp | DAVID]] |
| | 6 | |
| | 7 | * DAVID is generally the best place to start your enrichment analysis. |
| | 8 | * Instructions for using DAVID can be found under //Functional Annotation// on the DAVID web site. |
| | 9 | * You'll probably end up running DAVID multiple times, with different types of annotations, to get the more informative combination. |
| | 10 | * Full output can be downloaded and viewed as a spreadsheet. |
| | 11 | |
| | 12 | === Gene Set Enrichment Analysis (GSEA) === |
| | 13 | [[http://www.broadinstitute.org/gsea/index.jsp|Broad GSEA]] |
| | 14 | |
| | 15 | [[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA Wiki]] |
| | 16 | |
| | 17 | ==== Ranked List ==== |
| | 18 | 1. Create a two column file with gene names as first column and numeric values for second column (eg. weight, p-value, etc), does not need to be sorted. |
| | 19 | * Assigning weights: There is no standard way to assign weights, however, it should reflect some logical order. GSEA uses the correlation (between expression and phenotype) to assign weights, if the list is not pre-ordered or ranked. A similar scheme can be used to rank the genes, other options includes using the t-score, or a scoring scheme that takes into account both log ratio and p-value. |
| | 20 | * If a gene list is not unique, duplicate genes can be given a //shared// weight, for eg. if a gene occurs four times in the list it is given a weight of 0.25, if it is unique a weight of 1 is given. |
| | 21 | 2. Run GSEA: Tools -> GseaPreranked |
| | 22 | |
| | 23 | ==== Unranked List ==== |
| | 24 | |
| | 25 | GSEA will rank the genes |
| | 26 | |
| | 27 | 1. Create necessary files in correct format for expression, phenotype and chip annotation (see GSEA wiki) |
| | 28 | 1. Use MSigDB for gene sets or create custom gene sets in correct format |
| | 29 | 1. Run GSEA, use default options to start |
| | 30 | |
| | 31 | === BiNGO === |
| | 32 | [[http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=BiNGO|BiNGO Plugin]] \\ |
| | 33 | You need to have [[http://cytoscape.org | Cytoscape]] installed to use BiNGO |
| | 34 | 1. Start BiNGO via Cytoscape , Plugins->Start BiNGO |
| | 35 | 1. Get genes from cluster/network or paste gene list |
| | 36 | 1. Select the correct options (eg. species) |
| | 37 | 1. Run BiNGO |
| | 38 | |
| | 39 | === GeneGO === |
| | 40 | [[http://portal.genego.com/ | GeneGO Login (Password Required)]] |
| | 41 | 1. Upload gene list and activate |
| | 42 | 1. One-click analysis -> Select GeneGo Pathway Maps |
| | 43 | |
| | 44 | |
| | 45 | == Useful Links == |
| | 46 | |
| | 47 | [[http://go.princeton.edu/cgi-bin/GOTermFinder | GO Term Finder]] : significant GO terms shared among a list of genes from your organism.[[BR]] |
| | 48 | |
| | 49 | [[http://go.princeton.edu/cgi-bin/GOTermMapper | GO Term Mapper]] : maps the granular GO annotations for genes in a list to a set of GO slim terms, allowing you to bin your genes into broad categories. |
| | 50 | |
| | 51 | |
| | 52 | |
| | 53 | == More Information == |
| | 54 | |
| | 55 | Hot Topics: [[http://iona.wi.mit.edu/bio/education/hot_topics/enrichment/Gene_list_enrichment_Mar10.pdf | Gene List Enrichment ]] |
