BMS5021 S1 2024 - Topic 3 Assessment Multi-omics Data Integration and Network Analysis in Cancer

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BMS5021 S1 2024 - Topic 3 Assessment

Multi-omics Data Integration and Network Analysis in Cancer

Outline of Written Assessment Criteria - Individual Report

Instructions:

Write an individual 2000-word report based on the analyses you performed during the "Cancer multi-omics data integration and analysis using LinkedOmics" (Week 10) and "Network Analysis using STRING" (Week 11) workshops. The report should integrate the knowledge and skills acquired from both workshops, emphasizing the use of LinkedOmics and STRING to explore cancer biology and identify potential therapeutic targets.

The report should be well-structured, with an introduction, methods, results, discussion, and conclusion sections. Use appropriate headings and subheadings to organize your content. Include relevant figures, tables, and references to support your findings.

2000 words, to be submitted via Moodle by 11:55PM on Thursday 30^th of May 2024.

Report Outline:

1. Title and Introduction (10 marks)

- Write a clear title that outlines the content of your report.

- Briefly introduce the importance of multi-omics data integration and network analysis in cancer research

- State the objectives of your analysis

2. Methods (10 marks)

- Describe the LinkedOmics and STRING platforms and their functionalities

- Describe the specific cancer types and genes you focused on for each type of analyses that you did during the workshops

- Provide a step-by-step description of your analysis workflow for both workshops

3. Results (30 marks)

   - LinkedOmics analysis:

     a. Which genes show changes in RNA expression when gene X is altered in cancer Y?

     b. Which proteins show changes in protein expression when X is altered in cancer Y?

     c. What are the overlaps between the results at RNA and protein expression levels?

     d. Which pathways/biological processes are enriched among the identified genes and proteins?

     e. Which gene and/or protein shows the strongest association with patient survival in your given cancer type?

   - STRING analysis:

     a. Basic description of the PPI network (e.g., number of nodes, edges, and interaction density)

     b. Comparison of networks using different evidence types (e.g., all evidence vs. experimentally validated)

     c. Top 3 pathways and biological processes enriched in the network

     d. Identification of distinct clusters within the network and their associated pathways/processes

     e. Crosstalk between individual PPI networks when using multiple proteins as baits

   - Use appropriate figures, tables, and statistical measures to support your results

4. Discussion (30 marks)

   - Interpret your results and discuss their biological significance

   - Integrate findings from both LinkedOmics and STRING analyses to gain a comprehensive understanding of the cancer biology

   - Compare your findings with the current literature on the specific cancer type and gene

   - Discuss the potential therapeutic implications of your findings

   - Address the limitations of your analysis and suggest future directions for research

5. Conclusion (15 marks)

   - Summarize the main findings of your analysis from both workshops

   - Emphasize the importance of multi-omics data integration and network analysis in understanding cancer biology and identifying therapeutic targets

   - Conclude with a brief statement on the future direction of the work

Presentation and Readability (5 marks)

- Appropriate use of headings and tables.

- Good grammar throughout the text.

- Logical flow of text and organisation of sections.

- Inclusion of figures where appropriate.

- Use of appropriate academic language and references.

Submission Guidelines:

- Format: PDF document

- Font: Arial or Times New Roman, 12 pt

- Line spacing: Single space or 1.5

- Word count: 2000 words (±10%), excluding references, figures, and tables

Assessment Criteria:

- Clarity and completeness of the introduction and objectives (10%)

- Appropriate use of methods and tools from both workshops (10%)

- Quality and presentation of results from both LinkedOmics and STRING analyses (30%)

- Depth and coherence of discussion, integrating findings from both workshops (30%)

- Conclusion and relevance to the field (15%)

- Overall structure, organization, and writing quality (5%)