CSB352H Bioinformatic Methods
Summer 2025
CSB352: Lab Report 2
For this lab report, you need to articulate the details and outcome of in silico experiments involving the most informative results for your assigned gene from 1) the analysis of protein domains; 2) examination of protein-protein interaction (PPI) data with a GO enrichment analysis using AgriGO as described below; 3) identification of interesting gene expression patterns and using this information to help guide function prediction; 4) performing a coexpression analysis against an expression database of your choice and subsequently performing a GO enrichment analysis using AgriGO; 5) using 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.). Your report should be no longer than 6 pages, double-spaced, not including references and figures, of which there is a requirement of exactly 3 (of your choosing, with 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 look at a couple papers, before formulating your function hypothesis. You should cite at least 2 primary sources plus all tools/websites/data sources used, using the journal Nature’s reference format.
Introduction: (6 marks)
Introduce 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 is unknown. Or this could be a more expressed desire to characterize the function via the examination of protein domains and protein-protein interaction data. 2) How did you attempt to answer your question? You could also mention findings from your first lab report here.
Methods: (8 marks)
A description of your analysis with enough information for someone to reproduce 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 of 3 and minimum interaction level of 2 ”, for instance. Be sure to cite web sources of data and tools.
Results and Discussion: (16 marks)
State the results of the experiment and their significance. Focus your “story” around your 3 figures but do mention your other analyses. What results did you find? What can you infer or conclude from your data - what might your gene do? Negative results can also be informative. Each figure should include a caption that describes the figure. The caption should be detailed enough that the readers do not need to read the text in order to understand the figure. State what you learned and what you might ask/check next if given the time and interest. Attempt to provide a hypothesis for in vivo activity and propose a follow up experiment, be it in silico or in vivo.