David Crossman, Ph.D. UAB Heflin Center for Genomic Science. Immersion Course
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1 David Crossman, Ph.D. UAB Heflin Center for Genomic Science Immersion Course
2 What to do with your list of genes Apply a Systems Biology approach to data mine and analyze your data Tools and databases available (some free, others $$) to define the underlying biology behind different omics data These tools and databases will idendfy and prioridze the most relevant pathways, networks and cellular processes affected by your dataset.
3 Pathways & Ontology Analysis Tools Tool Link Price Reactome hkp:// Free IPA hkp://ingenuity.com/ $$$ GeneGo Metacore hkp:// $$$ Cytoscape hkp:// Free GenMAPP hkp:// Free InterMine hkp://intermine.org/ Free KEGG hkp:// Free GO hkp:// Free Panther hkp:// Free DAVID hkp://david.abcc.ncifcrf.gov/ Free And many, many more!!
4 Network Example
5 Variant Pathway Tools Tool Link Price Ingenuity Variant Analysis Clinical Genomics Toolkit hkp://ingenuity.com/ $$$ hkp:// lsresearch.thomsonreuters.com /pages/soludons/21/clinical- genomics- toolkit $$$ Cartagenia hkp:// $$$ Tute Genomics hkp://tutegenomics.com/ $$$ VariantStudio hkp:// informadcs/research/biological- data- interpretadon/ variantstudio.html $$$
6 Demo REACTOME
7 Reactome Open- source, open access. Manually curated. Peer- reviewed pathway database (pathway annotadons are authored by expert biologists). Some of the tools they have: Browse pathways Map IDs to pathways OverrepresentaDon analysis Compare species Analyze expression data
8 Quick links to tools most commonly used. Manual & tutorials Other useful tools
9 Browse Pathways Helpful tutorial This beginning screen says it all on how to browse pathways
10 Analyze Data 1b 2 1c 1a 1. Upload data to Reactome: a. Paste, or b. Choose file from computer (tab- delimited), or c. For demo purposes, click Example 2. Click Analyse 2
11 Analyze Data Results Table can be downloaded in various formats Clicking any of the pathway names will show the respecdve pathway
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13 Compare species This tool will allow you to compare human pathways to any other species pathways they have in their database
14 Compare species Here, I chose mouse and as before, clicking on the pathway name will open the pathway map, and the table/ results can be downloaded.
15 Browse pathways Search for your favorite pathways by following their instrucdons.
16 Demo PANTHER
17 Panther hkp://pantherdb.org/ Tools and data on the PANTHER site can be used to: Get informadon about a gene of interest Explore protein families, molecular funcdons, biological processes, cellular components and pathways Generate lists of genes that belong to a given protein family or subfamily, have a given molecular funcdon or pardcipate in a given biological process or pathway, e.g. generate a candidate gene list for a disease Analyze lists of genes, proteins or transcripts according to categories based on family, molecular funcdon, biological process, cellular component or pathway, e.g. analyze mrna microarray data
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19 Upload muldple gene IDs 1a 1b 1. Upload data to Panther: a. Paste your IDs, or b. Choose a file (tab- delimited) 2. Select Genome(s) 3. Select Analysis type 4. Click submit 2 3 4
20 Table lisdng all the genes in your dataset (scroll to the right to see all the columns Table can be downloaded by the Send list to: dropdown box Click the pie chart icon to view the GO categories in pie charts
21 Pie charts of the 3 GO categories: Molecular FuncDon Biological Process Cellular Component Each wedge can be clicked on to drill further down into the cateogry Clicking on any category name link will list a table of molecules from your dataset found in that pardcular category
22 Demo DAVID
23 DAVID hkp://david.abcc.ncifcrf.gov/ Database for AnnotaDon, VisualizaDon and Integrated Discovery (DAVID) Provides a comprehensive set of funcdonal annotadon tools to beker understand the biological meaning behind large datasets. Tools: GO Pathways Gene- disease associadons Protein funcdonal domains and modfs And much, much more! SystemaDc and integradve analysis of large gene lists using DAVID bioinformadcs resources. Nature Protocols 4, (2009).
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25 Thanks! QuesDons? Contact info: David K. Crossman, Ph.D. BioinformaDcs Director Heflin Center for Genomic Science University of Alabama at Birmingham hkp://
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