CSB352: Lab report 4  This lab report deals with the prediction of function for your assigned gene, with a focus on using gene expression data to do so. You can also summarize your data and insights from your previous reports, and additionally use any general predictive tool of your choice to come up with a plausible biological function for your gene. You can 1) identify gene expression patterns and used this information to help guide function prediction; 2) perform a coexpression analysis against your using microarary data of your choice and subsequently perform a GO enrichment analysis using AgriGO as described for the third lab report; 4) identify any known cis-elements in the promoters of these genes; 5) predict cis-regulatory elements within the promoter sequences of your coexpressed genes; and 6) use integrative tools like GeneMANIA (genemania.org; Warde-Farley et al., 2010, Nucl. Acids Res.) or AraNet (www.functionalnet.org/; Lee et al., 2010, Nature Biotechnol.). You are welcome to use the BioConductor skills you?ve learned, but utilization of webbased tools is equally legitimate. A list of potential websites and tools is provided below.  Be sure to include at least 2 figures in your report. As always, your report should not exceed 4 pages in Times New Roman (12 pt) or Helvetica/Arial (10 pt) double-spaced, not including figures. Introduction (3 marks) ~ ? page  Introduce your assigned and the gene expression datasets that you will be exploring in your expression and coexpression analyses. Why are you investigating this gene and why did you choose these data? What do you hope to identify with regard to transcriptional regulation? For example: In lab 11, our analysis of RD29B coexpressed genes identified regulatory elements responsible for response to water deficit in plants.  Methods (3 marks) ~ ? page  A succinct description of your analysis with enough information for someone to reproduce your result. Be sure to cite web sources of data and tools. Where did you get your gene expression data and how were they collected? Which cis-element prediction tools did you use and what were the settings you settled on for your final prediction run(s). What was the nature of the promoter sequences you used for your predictions?  Results (5 marks) ~ 2 pages  State the results of the experiment and their significance. As before, focus your story around your figures. What did your coexpression analysis yield? What did your ciselement prediction analysis yield? What did your integrative analyses yield? How much do you trust your results and what can you infer or conclude from your data?  Discussion (4 marks) ~ 1 page  State what you learned and might ask/check next if given the time and interest and draw on your results from the past 3 lab reports. What is the likely biological function or functions of your gene? You can include any information from your previous 3 lab reports to determine the role your gene plays in Arabidopsis thaliana. Propose an in vivo  experiment to elucidate the function of your gene/protein. Don?t forget to cite the software tools you use.CSB352H Bioinformatic Methods WS2012 ? Lab Report 4  Potential Data sources and Tools Coexpression tools ? limit your output to the top 50 coexpressed genes (or fewer)  Expression Angler:  http://bar.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi  ACT, Arabidopsis Coexpression Tool:  http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php#CO2  CressExpress: http://www.ssg.uab.edu/coexpression/  ATTEDII, Arabidopsis thaliana trans-factor and cis-element prediction database:  http://www.atted.bio.titech.ac.jp/  Cis-element identification / mapping  Athena: http://www.bioinformatics2.wsu.edu/cgi-bin/Athena/cgi/home.pl  Cistome: http://bar.utoronto.ca/cistome/cgi-bin/BAR_Cistome.cgi  Cis-element prediction  This is by no means a comprehensive list of coexpression-based prediction programs.  There are dozens of web-based and standalone tools out there. Feel free to investigate and use any published open-source tools you like in your analysis.  These are the web-based programs from the lab:  Promomer: http://www.bar.utoronto.ca/ntools/cgi-bin/BAR_Promomer.cgi  Integrative online prediction programs and GO enrichment analysis  GeneMANIA: http://genemania.org/

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