NDLI: Robustness evaluations of pathway activity inference methods on gene expression data

Content Provider	Springer Nature : BioMed Central
Author	Hui, Tay Xin Kasim, Shahreen Aziz, Izzatdin Abdul Fudzee, Mohd Farhan Md Haron, Nazleeni Samiha Sutikno, Tole Hassan, Rohayanti Mahdin, Hairulnizam Sen, Seah Choon
Abstract	Background With the exponential growth of high-throughput technologies, multiple pathway analysis methods have been proposed to estimate pathway activities from gene expression profiles. These pathway activity inference methods can be divided into two main categories: non-Topology-Based (non-TB) and Pathway Topology-Based (PTB) methods. Although some review and survey articles discussed the topic from different aspects, there is a lack of systematic assessment and comparisons on the robustness of these approaches. Results Thus, this study presents comprehensive robustness evaluations of seven widely used pathway activity inference methods using six cancer datasets based on two assessments. The first assessment seeks to investigate the robustness of pathway activity in pathway activity inference methods, while the second assessment aims to assess the robustness of risk-active pathways and genes predicted by these methods. The mean reproducibility power and total number of identified informative pathways and genes were evaluated. Based on the first assessment, the mean reproducibility power of pathway activity inference methods generally decreased as the number of pathway selections increased. Entropy-based Directed Random Walk (e-DRW) distinctly outperformed other methods in exhibiting the greatest reproducibility power across all cancer datasets. On the other hand, the second assessment shows that no methods provide satisfactory results across datasets. Conclusion However, PTB methods generally appear to perform better in producing greater reproducibility power and identifying potential cancer markers compared to non-TB methods.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05632-w.pdf
Ending Page	24
Page Count	24
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-024-05632-w
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-01-12
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Pathway analysis Reproducibility power Robustness PubMed text data mining Literature validation Pathway activity inference Cancer classification Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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