Institut Biologi Sistem

 Institute of Systems Biology

Workshop Outline

This introductory workshop will focus on:

  1. Introduction to Pathway and Network Analysis:

    • Brief overview of why pathway and network analysis is important in genomics

    • Introduction to key concepts and principles in pathway analysis

  2. Database and Tools for Pathway and Network Analysis:

    • Explanation of protein-protein interaction (PPI) databases such as STRING and GeneMANIA

    • Demonstration of how to construct PPI networks using these databases

    • Practical exercises on retrieving and interpreting data from these databases

  3. Mapping Genes onto Pathways:

    • Overview of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database

    • Step-by-step guide on how to map identified genes onto KEGG pathways

    • Hands-on exercises for participants to practice mapping genes onto pathways

  4. Functional Annotation of Genes/Proteins:

    • Explanation of functional annotation and its importance in interpreting gene/protein lists

    • Introduction to tools and databases for functional annotation.

    • Practical session demonstrating how to perform functional annotation on gene/protein lists

  5. Gene Ontology (GO) Enrichment Analysis:

    • Overview of Gene Ontology and its significance in understanding gene functions

    • Explanation of GO enrichment analysis and its application

    • Hands-on exercises on performing GO enrichment analysis on gene/protein lists

  6. Pathway Analysis and Visualization:

    • Comprehensive overview of pathway analysis methods

    • Introduction to tools and software for pathway analysis

    • Practical session on conducting pathway analysis and visualizing results

Upon the completion of this workshop, participants will be able to:

  • Construct pathways and PPI network from the list of genes/ proteins

  • Perform GO and pathway analysis on the constructed pathway and PPI network (and use it for hypothesis generation)

  • Understand a complete workflow of data acquisition, pathway construction, pathway analysis, and data interpretation

  • Predict gene function and extend a gene list

Who should attend

Anyone interested in pathway analysis and its applications (researchers, academicians, and students), especially biologists from beginner to advanced levels.

List of Speakers and Trainers

  • Prof. Dr. Zeti Azura Mohamed Hussein is a Professor in Bioinformatics at the Department of Applied Physics, Faculty Science and Technology. She investigates the relationships between disease genes and disease networks using gene network analysis, pathway analysis and network analysis to understand disease pathobiology in human and plants alike which can’t be fully annotated using a single type of data thus the inclusion of big data analysis and omics data integration. Prof. Zeti’s research demonstrates how integrative analysis on omics data can be used to unravel new important knowledge and provide answers on the biological problems of interest. If you are interested to collaborate with her, or be part of her research group, please drop her an email to zeti.hussein@ukm.edu.my or visit her website at https://zetibioinfolab.wordpress.com

  • Dr. Sarahani Harun is currently a research fellow at the Institute of Systems Biology (INBIOSIS). She graduated from the Universiti Kebangsaan Malaysia where she earned a Bachelor in Bioinformatics, Master in Molecular Biology and PhD in Systems Biology. Her research interest involves computational biology that includes pathway analysis in secondary metabolites, i.e., glucosinolates and cyanogenic glycosides to unravel potential genes in the respective biosynthetic pathways. This computational pipeline can be used for new gene discovery to establish genetic resources for crop improvement. She is also interested in analyzing the transcriptome data generated from the oil pest, bagworm (Metisa plana) which is a collaborative project with Felda Global Ventures R&D. The identification of the key regulatory genes from the study would facilitate in controlling the pest infestation in oil palm. Dr. Sarahani can be contacted via email; sarahani@ukm.edu.my.

  • Dr. Rabiatul Adawiah Zainal Abidin is a Senior Research Officer at the Agriomics and Bioinformatics programme, Biotechnology & Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI). She obtained her PhD in Systems Biology from the Universiti Kebangsaan Malaysia in 2021 and BSc in Bioinformatics from University of Malaya in 2006. Dr. Rabiatul uses bioinformatics approach and omics technologies to unlock the wealth of information of local crops (rice, papaya, banana and durian) and livestock. Sometimes, she has been invited as a guest lecture in university to share her experiences for using bioinformatics in agricultural research. She loves data and enjoys research and science environment, especially in agricultural bioinformatics. Dr. Rabiatul can be contacted via email; rabiatul@mardi.gov.my

 

Programme

18th November 2025 (Tuesday)

Time Activity Speaker
9.00 am Introduction to the workshop  Dr. Sarahani Harun
9.10 am Lecture 1: Introduction to pathway databases / tools and data integration Dr. Sarahani Harun
10.10 am Morning break  
10.40 am Practical 1: Leveraging pathway databases and tools
Lecture 2: Introduction to Cytoscape and more pathway databases		 Dr. Sarahani Harun
12.30 pm Lunch break  
2.00 pm Practical 2: Pathway/ network visualization
Editing pathway using Cytoscape
Lecture 3: Introduction to network analysis		 Dr. Sarahani Harun
4.00 pm Summary, Discussion and wrap up Dr. Sarahani Harun
4.30 pm Tea break & END OF DAY 1
  

 

19th November 2025 (Wednesday)

Time Activity Speaker
9.00 am Lecture 4 : Introduction to big data and network biology Prof. Dr. Zeti Azura Mohamed Hussein
10.30 am Morning break
11.00 am Practical 3: Cytoscape – extending pathways/ networks (merging pathways/ networks) Dr. Sarahani Harun
12.30 pm Lunch break
2.00 pm Practical 4: Cytoscape – GO enrichment/ KEGG pathway analysis Dr. Sarahani Harun
4.00 pm Summary, Discussion and wrap up Dr. Sarahani Harun
4.30 pm Tea break & END OF DAY 2
  

 

20th November 2025 (Thursday)

Time Activity Speaker
9.00 am Lecture 5: Gene co-expression network analysis Dr. Rabiatul Adawiah
9.30 am Morning break
10.00 am Practical 5: Gene co-expression network construction - WGCNA Dr. Rabiatul Adawiah
12.30 pm Lunch break
2.00 pm Practical 6:  Gene co-expression network analysis Dr. Rabiatul Adawiah
4.00 pm Summary, discussion and wrap-up  Dr. Rabiatul Adawiah
4.30 pm Closing ceremony
5.00 pm Tea break & END OF WORKSHOP
  

 

Register now or contact us for more details