BMS5021 S2 2024 - Topic 3 AssessmentProteomics Data Analysis Project Report

Task Instructions

1. The Brief

Using the SARS-CoV-2 datasets provided throughout the Topic 3 workshops, your task is to write a brief scientific report on how virus infection progresses over time within infected cells, providing information on the expression of virus proteins, significantly up- and down-regulated host proteins, what proteins specific virus proteins interact with, as well as noting your strategy and methods to this analysis.

2. Learning Outcomes // Skill Development

This task addresses the following unit learning outcomes:

ULO1 Describe the relationships between DNA, RNA, and proteins and their roles in cell functioning.

ULO4 Evaluate the merits and limitations of the major bioinformatics databases to solve specific computational biomedical problems.

ULO5 Use bioinformatic tools and databases to analyse nucleotide or protein sequences.

ULO6 Perform elementary statistical analysis on biomolecular and “omics” datasets and represent the outcomes in informative graphical displays and data summaries.

Completing this task will further your skills in using tools & technology, problem identification & solving.

3. Assessment Component

This assessment is worth 40% of your overall grade. You must achieve a mark of 45% in this assessment task to achieve the hurdle. There is only one component to this assessment: an individual written report, submitted via a dropbox on Moodle (this will be available under the Week 12 page). See below.

Component

Group/Individual

Weighting

Submission details

Due date & time

Written report

(2000 words +/- 10%)

Individual

40% of overall unit grade (hurdle)

Submission via Moodle dropbox; .docx or .pdf format.

11:55 p.m. on 28/10/2024

4. Written Report Requirements

Your written report should be 2000 words +/-10%. This task is to be completed individually.

You should include figures (where relevant) to help convey your ideas (ensure these are accompanied by figure legends and referred to in the text), as well as your approach to the data analysis. See below for further details.

Your report should use clear headings and subheadings. Please use APA 7th referencing style (in-text citations & reference list required). Your submission will be passed through Turnitin similarity detection software.Your written report needs to include the following content:

Title

Your title should be clear and concise, and outline the content of the report

Introduction

Introduce the key underlying concepts and data sources

Clearly describe the specific aims of the studies that underpin the datasets/raw files you have been provided with, including identification of the knowledge gap or the intent of the study

Methods and Results

For the Methods, describe your approach to the data analysis, including how mzML files were searched, how output result files were analysed, what software or tools were used for data analysis and/or visualisation

For the Results, consider the following*:

identification of proteins that are confident hits for protein-protein interactions with your assigned SARS-CoV-2 protein

identification of viral proteins in the timecourse dataset and visualisation of their expression profile

visualisation of differentially expressed proteins at each timepoint of the timecourse dataset

comparison of the proteome and translatome datasets

identification of biological functions/pathways/GO enrichments, where relevant, for any of the above points

Discussion

Discuss the findings (results) you have obtained, including*:

the significant proteins that interact with your specific viral bait protein and whether any of these share a similar biological function/form part of a larger protein complex, relevant biological functions including pathways and GO annotation etc.

the significant human proteins whose expression (global proteome and/or translatome) is modulated during the virus infection timecourse

the expression profile change of viral proteins during the infection timecourse

a comparison of the translatome and proteome datasets – what did your analysis show?

Conclusion

Give an overall conclusion(s) that summarises the outcomes and how it addresses the aim of the analysis. Include any limitations of the study and future directions.

*note: these bullet points under the Results (and also Discussion) are suggestions to guide you. You do not need to follow the same order as the bullet points, but ensure sure there is a logical flow to your analysis and discussion.

5. Recommendations for an effective written report

Work to logically sequence your ideas throughout.

For the introduction, a funnel structure is recommended (e.g. the 1st paragraph introduces the general area of study, 2nd paragraph identifies the knowledge gap that prompts this study or the intent of this study, 3rd paragraph identifies the specific aim of this study).

For your results, sequence these as a logical series of sections, each containing a clear, brief summary as to what was done to obtain the data described in each section, followed by a brief description of the key findings, making reference to relevant figures.

Use appropriate language – assume that your audience is a laboratory group and literate in the areas of biology and bioinformatics understanding, though are not experts in this particular area.

Use good quality figures (that have a written figure legend briefly describing the data) to help convey your ideas. For maximum impact, ensure you make reference to these figures in the text of your report.

6. Assessment and Feedback

You will receive feedback in the form of an annotated rubric & written feedback.

7. Marking Guide/Rubric

Please refer to Moodle for the marking rubric. (This will be available in Week 12.)

8. Any Questions?

If you have questions about this task, please:

Add them to the discussion forum on Moodle

Ask in Workshop sessions

Email the unit coordinator/chief examiner.