Protocol for performing metabolic pathway-based subtyping of breast tumors.

Mohammad Askandar Iqbal, Kirk Smith, Prithvi Singh, Shumaila Siddiqui, Sriram Chandrasekaran

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In one paragraph

Article in STAR protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Mohammad Askandar IqbalThumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates; College of Medicine, Gulf Medical University, Ajman, United Arab Emirates. Electronic address: dr.askandar@gmu.ac.ae.

Kirk SmithDepartment of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.

Prithvi SinghCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi, Delhi, India.

Shumaila SiddiquiCSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.

Sriram ChandrasekaranDepartment of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address: csriram@umich.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Here, we present a protocol for analyzing the global metabolic landscape in breast tumors for the purpose of metabolism-based patient stratification. We describe steps for analyzing 1,454 metabolic genes representing 90 metabolic pathways and subjecting them to an algorithm that calculates the deregulation score of 90 pathways in each tumor sample, thus converting gene-level information into pathway-level information. We then detail procedures for performing clustering analysis to identify metabolic subtypes and using machine learning to develop a signature representing each subtype. For complete details on the use and execution of this protocol, please refer to Iqbal et al.

Indexed as

Breast NeoplasmsMetabolic Networks and PathwaysAlgorithmsCluster AnalysisFemaleGene Expression ProfilingHumansMachine Learningcancermetabolismsystems biology

Identifiers

PMID38970792

DOI10.1016/j.xpro.2024.103173

PMCPMC11452911

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.