bioinformatics

In this document, you will find some hints related to the Bioinformatic Practical that may help you for the writing of your report.

Introduction:

· Please consider to include a description of “omics” approach and how they have changed current research;

· Define the problem related to the management and analysis of big dataset;

· Computational biology and System Biology.

· Boolean System and please use the article Tjan et al from the Demonacos’s group for a clear understanding of the topic.

Materials & Methods:

· Describe the databases used to retrieve the information and software applied during the practical.

· Please describe the parameters you have used for each software in each analysis; if you have changed any parameter during the analysis, please state how.

Results:

· Please describe the information retrieve from NCBI gene database relative to CDKN1A (include Table at pg19);

· What are the transcription factors that control CDKN1A? Describe the search we have done and the results u have obtained (include Table at pg 20);

· An excellent representation of the data will include the number of entries, the number of transcription factors and a comparison between the results of the different software.

· Try to choose the best way to represent the results of this search: Tables, Pie charts and Venn Diagrams may represent a good possibility.

· Remember to include the data relative to the change of parameters in this section.

· Is TP53 a TF for CDKN1A?

· Please describe other target genes of TP53

· Describe the interactome of TP53 that you have been able to generate.

Discussion:

· Describe how through computational biology you can describe the function of a complex networks of functional interactions such as the interactome of TP53.

· Please DO NOT REPEAT YOUR RESULTS: you can use some of the interactions you have reported in your interactome as a proof of the great potentials of this computational approach.

· All interactomes are located in the blackboard folder.

Please structure your report based on the below sections:

Abstract (5 marks): Brief summary of the report – should include the background of why this research is important; methods used; major result and conclusion – look at any published research article for an example (~ 250 words).

Introduction (20 marks): Should provide fully referenced background information that is focused on the topic of the lab class and an outline of the aims of the experiment(s). This should not be an extensive literature review. (~750 words or 2 Pages)

Materials & Methods (5 marks): Methods should be written in sentences (no bullet points) in the past-tense and in the third person, i.e. do not use ‘I’ or ‘we’. This should NOT be a reproduction of lab protocols. (The number of words will depend on experiments done)

Results (30 marks): Each result description should start with the purpose of the experiment, description of the results (for example “Addition of hormone resulted in five-fold increase of GILZ gene expression” (Figure 1, compare lane 2 to lane 1)). Result description should finish with a conclusion for each experiment and should be displayed in graphs- tables or figures that are fully labeled with titles and figure legends. The data should be summarised using text that refers to the corresponding figure or table numbers. In assessing the piece of work, great attention will be paid to the presentation, description and analysis of data. (The number of words will depend on experiments done)

Discussion (25 marks): Should consider the outcome of the experiment (did it work? Were the results as expected? Can you identify any technical difficulties?) It should also consider your results in comparison with the published literature. Highlight the significance/ importance of your results. Make a conclusion. (~1000 words)

References and Presentation (15 marks): The required number of references will depend on each lab practical but generally 10 – 20 references will suffice. More will be required for the project reports. We use the Harvard format (see Appendix 2). (10 – 20 references)