For this lab report, you need to articulate the details and outcome of in silico experimentsinvolving the most informative results for your assigned gene from 1) the analysis ofprotein domains; 2) examination of protein-protein interaction (PPI) data with a GOenrichment analysis using AgriGO as described below; 3) identification of interestinggene expression patterns and using this information to help guide function prediction; 4)performing a coexpression analysis against an expression database of your choice andsubsequently performing a GO enrichment analysis using AgriGO; 5) identifying anyknown cis-elements in the promoters of these genes; 6) using integrative tools likeGeneMANIA (genemania.org; Warde-Farley et al., 2010, Nucl. Acids Res.) or AraNet(www.functionalnet.org/; Lee et al., 2010, Nature Biotechnol.). Your report will be 6pages of Times Roman 12 point text or Arial 11 point text, double-spaced, not includingreferences and figures, of which there is a requirement of exactly 3 (of your choosing,with informative legends).Have fun, but do think scientifically and logically about your questions and approaches.And do, of course, visit PubMed, browse some abstracts in an area of interest, even lookat a couple papers, before formulating your function hypothesis. You should cite at least2 primary sources plus all tools/websites/data sources used, using the journal Nature’sreference format.Introduction (6 marks) ~ ¾ pageIntroduce your gene of interest and state 1) What question you are asking and why?This could be as simple as: “What is the function of this protein?”, if its function isunknown. Or this could be a more expressed desire to characterize the function via theexamination of protein domains and protein-protein interaction data. 2) How did youattempt to answer your question? You could also mention findings from your first labreport here.Methods (8 marks) ~ ¾ pageA succinct description of your analysis with enough information for someone toreproduce your result. It’s enough to say “I retrieved all interactions for my gene ofinterest from Arabidopsis PPI data in BioGRID, filtering by a minimum evidence level of3 and minimum interaction level of 2”, for instance. Be sure to cite actual, publishedpapers for web sources of data and tools.Results and Discussion (16 marks) ~ 3.5 pages for Results / ~ 1 page for Discussion
State the results of the experiment and their significance. Focus your “story” around your3 figures but do mention your other analyses. What results did you find? What can youinfer or conclude from your data: what might your gene do, in other words? Negativeresults can also be informative. State what you learned and what you might ask/checknext if given the time and interest. Attempt to provide a hypothesis for in vivo activityand propose a follow up experiment, be it in silico or in vivo, to test this hypothesis.
Potential Data sources and Tools*Domain AnalysisUse tools described in Class 7, e.g. InterProScan.Protein-Protein InteractionsArabidopsis Interactions Viewer: http://bar.utoronto.ca/interactions/BioGRID (as per Class 8): http://thebiogrid.org/Note: if you only get a few interactors for your assigned gene, try repeating your queryincluding those interactors along with your query gene/protein product, to identifyinteractors of interactors. This might be necessary to do a meaningful GO enrichmentanalysis.GO Enrichment AnalysisA useful tool for performing GO enrichment analysis for lists of Arabidopsis genes orproteins is AgriGO (Du et al., 2010, Nucleic Acids Research; doi:http://dx.doi.org/10.1093/nar/gkq310) as per Class 11 athttp://systemsbiology.cau.edu.cn/agriGOv2/classification_analysis.php?category=Plant&&family=Brassicaceae.Expression AnalysisBio-Analytic Resource eFP Browser: http://bar.utoronto.ca/efp/. In which Data Source isexpression the strongest or most leptokurtic in a particular sample, cell type, or tissue?Coexpression toolsLimit your output to the top 50 coexpressed genes (or fewer). It might be more useful todo a condition-dependent analysis, limiting the samples that you are using to specificaspects of biology, e.g. abiotic stress if your gene of interest seems to be induced inresponse to abiotic stress.Expression Angler:http://bar.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgiATTEDII, Arabidopsis thaliana coexpression database: http://atted.jpCis-element identification / mappingAthena: http://bioinformatics1.smb.wsu.edu/cgi-bin/Athena/cgi/home.plCistome: http://bar.utoronto.ca/cistome_legacy/cgi-bin/BAR_Cistome.cgiIntegrative online prediction programsGeneMANIA: http://genemania.org/AraNet: http://www.inetbio.org/aranet/* All of these tools have papers associated with them. Cite them if you use them!