UKM Medical Molecular Biology Institute

 Leading Institute in Molecular Medicine

Network Biology Workshop

  •  

  • Introduction

    In the past decade, network biology has emerged as a major theme in biology and disease. Unprecedented technological progress in generating biological data has led to an explosion of high-throughput omics datasets. However, the ability to extract meaningful information from such vast amounts of data to understand the etiology of the disease remains a challenge in biomedical science. The computational analysis of high-throughput datasets using the network-based approach has gained widespread adoption to unravel the mechanisms that orchestrate the activities of biomolecules, the so-called biological entities (i.e., DNA, mRNA, protein, and metabolite) in cells. A holistic way to portray such activities is by navigating the interactions between the nodes (biological entities) via links called edges. A biological network may also represent a wide range of biological data to address biological questions of disease studies by scrutinizing candidate disease-causing genes, disease-associated subnetworks, and therapeutic targets. Their increasing importance is proven by the rapid increase in published articles on biological network-related subjects over the past 20 years. Following the great interest in biological networks, many open-source databases and state-of-the-art tools were developed for hosting and dissecting such interactome data. Hence, this workshop offers extensive hands-on training on constructing and analyzing cellular networks using a diverse set of analyses, including finding over-represented pathways or gene ontology, gene set enrichment analysis, regulatory network analysis, gene function prediction and pathway analysis.

    At the end of this workshop, the participants will be able to:

    • Grasp an idea of the importance of network biology as a developing area of biomedical research.
    • Retrieve a collection of data types from open-source databases that store omics/interactomics data.
    • Use biological network tools, i.e., Cytoscape and CEMiTool, for network construction.
    • Use guilt-by-association approaches to discover candidates of disease-causing target genes.
    • Interpret biological data of complex phenotypes.

     

    Target Group

    This workshop is aimed at researchers interested in network analysis, protein-protein interactions, co-expression analysis and other related areas. Clinicians, academicians, postdocs, and postgraduate students are invited to apply. We are targeting a maximum of 15 participants to attend this network biology workshop.

  • 18 th – 19 th January 2023 : Wednesday & Thursday

    8.00 am – 4.30 pm (everyday)

     

    RM 490 per person (UKM students and staff)

    RM 550 per person (Non-UKM)

    (Registration fee is inclusive of training materials and meals)

     

    Register

  •  

    Day 1 (18/01/2023)
    Time Activities Speaker
    8:00 – 9:00 am Registration and Breakfast
    9:00 – 9:30 am Welcome speech by the Director of UMBI

    (Bioinformatics laboratory, Level 3)

    		 AP. Dr. Nor Azian Abdul Murad
    9:30 – 11:00 am Lecture 1: Introduction to Network Biology and Its Application in Medicine

    (Bioinformatics laboratory, Level 3)

    ●        Brief introduction of network biology in the age of biomedical big data

    ●        Types and principles of biological networks, available databases, tools, and approaches

    ●        Advancement/applications of network biology in medical research (i.e., cancer, non-communicable disease & infectious disease)

    		 Dr Redha
    11:00 – 11:30 am Break
     

    11:30 – 1:00 pm

     

     

     

    		  Lecture 2 and Practical Session 1: Network Analysis with Cytoscape I

    (Bioinformatics laboratory, Level 3)

    ●        Introduction to Cytoscape and guided tour of available Cytoscape apps

    ●        Network analysis using RNA-Seq data

    i.        Identification of differentially expressed genes (DEGs)

    ii.        Importing network data from public DB (i.e., STRING)

    iii.        Network construction

    iv.        Integration of experimental data (DEGs) on network

    v.        Network-based functional enrichment analysis (i.e., STRING enrichement, ClueGO, BINGO)

    vi.        Network cluster detection

    		  

    Dr Redha

    Mdm Alyaa

    Mdm Mira
    1:00 – 2:15 pm Lunch
    2:15 – 4:30 pm Practical session 2:

    Part 1: Network Analysis with Cytoscape II

    (Bioinformatics laboratory, Level 3)

    ●        Gene/variant-disease association network analysis (i.e., HIPPIE, DisGeNET)

    i.            Generate gene/variant-disease associated network

    ii.            Disease enrichment analysis in gene/variant associated network

     

    Part 2: Introduction to R

    ●        How to install R, R Studio and Bioconductor

    ●        R packages

    ●        Data retrieval (gene/variant-disease associations, GDAs/VDAs, disease enrichment)

    ●        Plotting and data visualization in R (i.e., GOplot)

    		 Dr Redha

    Mdm Alyaa

    Mdm Mira
    4:30 pm End of Day 1

     

    Day 2 (19/01/2023)
    Time Activities Speaker
    8:00 – 9:00 am Breakfast
    9:00 – 10:30 am  Lecture 3 and Practical Session 3: Gene-disease prioritization by co-expression analysis I

    (Bioinformatics laboratory, Level 3)

    ●        Brief introduction of modular co-expression analysis

    ●        Installation of CEMiTool, R package

    ●        Data preparation (RNA-seq/Microarray data, phenotype (i.e., sample group))

    ●        Gene co-expression module analysis

    ●        Identification of module hubs

    ●        Gene set enrichment analysis (GSEA)

    ●        Expression profile plot

    		 Dr Redha

    Mdm Alyaa

    Mdm Mira
    10:30 – 11:00 am Break
    11:00 – 1:30 pm  Practical Session 4 (Cont’d): Gene-disease prioritization by co-expression analysis II

    (Bioinformatics laboratory, Level 3)

    ●        Over-representation analysis (ORA)

    ●        Generate gene network

    ●        Visualization of network hubs

    		 Dr Redha

    Mdm Alyaa

    Mdm Mira
    1:30 – 2:30 pm Lunch
    2:30 – 4:30 pm  Practical Session 5: Pathway analysis

    (Bioinformatics laboratory, Level 3)

    ●        Introduction to pathway analysis

    ●        KEGG pathway analysis

    ●        Pathway enrichment analysis (i.e., GSEA, g:profiler, and EnrichmentMap)

     

    Practical Session 6: Gene regulatory network

    (Bioinformatics laboratory, Level 3)

    ·         Brief introduction of gene regulatory network analysis

    ·         Generate transcription target interaction and motif analysis

    		 Dr Redha

    Mdm Alyaa

    Mdm Mira

     
    4:30 pm End of Day 2

  • The Network Biology Workshop will be held at UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, that is located just a 15-minute drive away from the heart of Kuala Lumpur city center.

    For more information about the venue, please visit the UMBI website at https://www.ukm.my/umbi/.

    Please take note that accommodation is NOT provided. Kindly refer to the Accommodation tab for further information.

    WAZE: https://www.waze.com/directions/malaysia/kuala-lumpur/umbi-ukm/66650143.666632502.6392182.html

    GOOGLE MAP: https://goo.gl/maps/soeAgH9K4292

  • Hotels nearby UMBI:

    • Hotel Sri Permaisuri Cheras (3-star hotel)
    • Hotel EST Kuala Lumpur
    • International Youth Centre (IYC) Residence
    • Hotel Maple Inn
    • V Hotel Kuala Lumpur
    • Crystal Garden Hotel
    • Low Budget hotels are also available nearby the UMBI. Please refer to any hotel booking website for further information.

    **Important Note: KINDLY BE NOTED THAT THE ORGANIZER WILL NOT BE LIABLE FOR ANY CLAIM OR RESPONSIBILITY IN REGARDS OF THE LISTED ACCOMMODATION ABOVE. FOR ACCOMMODATION BOOKING AND RESERVATION, PLEASE CLICK THE APPROPRIATE LINKS AND FOLLOW THE GUIDELINES ON THE RESPECTIVE WEBSITE.

  • Contact details:

     

    Dr. Muhammad Redha Abdullah Zawawi: +603-91459058 (mraz@ukm.edu.my)

    UKM Medical Molecular Biology Institute (UMBI)

    Jalan Yaacob Latiff, Bandar Tun Razak

    56000, Cheras, Kuala Lumpur, Malaysia

     

    Ms. Nurul Amirah Zamri: +603-91459023 (nurulamirah@ukm.edu.my)

    Administrative Assistant (Office Administration)

    UKM Medical Molecular Biology Institute (UMBI)

    Jalan Yaacob Latiff, Bandar Tun Razak

    56000, Cheras, Kuala Lumpur, Malaysia

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