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Data Analysis Project Advanced Bioinformatics BIF-30806 2013
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Set Up Basic and Advanced Project Available data sets Deliverables Literature Groups Schedule week 3 & 4
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Purpose Build software pipeline to perform a transcriptome analysis – Code to connect tools and do input/output conversions – Code developed on certain data set, but should be able to run on different input (e.g. different species)
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Basic Project Which are the most highly expressed genes (top 100) in your species of interest under a single condition (or in a single tissue)? Can you find a correlation between gene expression and transcript properties, such as GC content, transcript length, intron length, codon usage, or others? [Optional] Can you visualize the highly expressed genes in an interaction network? TOOLS: Tophat, cufflinks, perl scripts, and possibly others.
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Why?
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Advanced Project Which transcripts/genes show differential expression under both conditions? Can you find out what the functions of these genes are? Can you give a biological explanation of why these genes are differentially expressed under the conditions in your experiment? [Optional] In your data set, can you find modules of co- expressed genes? Try to use the WGCNA package. [Optional] Can you find a functional description and explanation for the identified modules? [Optional] To what extent are the modules conserved in a closely related species? TOOLS: Tophat, cufflinks, cuffdiff, WGCNA, perl scripts, and possibly others
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Why?
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You have a choice Start on basic or advanced project – Of course the basic project can be extended with elements of the advanced project Group members should talk to each other and discuss their choice with Harm/Sandra.
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Deliverables per group Pipeline code, all input/output has to be stored in the “group directory” at the server Final presentation (20 minutes) – Each group member must prepare and presents some slides (5 min per person)
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Deliverables per person Project report – All the work done in the project (intro, M&M, results, discussion/conclusion) – Appendix A: your contribution to the group effort – Appendix B: personal reflection on the project Contribution to group presentation – Prepare and present some slides (5 min per person) The code that you have written
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Data On server: /course/project/ – Arabidopsis – Yeast Other data/species of your choice – Use for example NCBI Short Read Archive (SRA)
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Literature See course website
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Groups See course website
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Schedule week 3 & 4 Presentations – Tue (26-2) afternoon: presenting project plan – Fri (1-3) afternoon: presenting progress – Fri (8-3) all day: final presentation Deadline report & code – Sunday March 10, 23:59 – So, your report has to be in before Monday! – Email your report to “project@bioinformatics.nl”
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