---
title: "Integrating Transcriptomics and Metabolomics in Clinical Diagnostics"
id: "pubmed-42765713"
canonical_url: "https://medichelpline.com/clinical-feed/pubmed-42765713"
content_type: "clinical_feed_article"
specialty: "Critical Care"
source_name: "PubMed / NCBI"
source_url: "https://pubmed.ncbi.nlm.nih.gov/42765713/"
doi: "10.1080/10408347.2026.2733903"
published_at: "2026-09-21T00:00:00.000Z"
evidence_level: "Journal Article"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Integrating Transcriptomics and Metabolomics in Clinical Diagnostics
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/pubmed-42765713
- **Specialty:** [Critical Care](https://medichelpline.com/clinical-feed/critical-care.md)
- **Primary Source:** PubMed / NCBI
- **Source URL:** [Original Journal Publication](https://pubmed.ncbi.nlm.nih.gov/42765713/)
- **DOI:** [10.1080/10408347.2026.2733903](https://doi.org/10.1080%2F10408347.2026.2733903)
- **Published At:** 2026-09-21T00:00:00.000Z
- **Evidence Rating:** Journal Article
## Executive GIST (TL;DR)
- **Transcriptomics** and **metabolomics** are integral to understanding disease complexity. - Each field offers partial insights; together, they reveal more comprehensive disease mechanisms. - Review covers methods, workflows, and computational strategies enhancing diagnostic capabilities. - Highlights integration methodologies like correlation-based approaches and machine-learning models. - Discusses barriers including pre-analytical variability, correlation gaps, and lack of standardized frameworks. - Reports limited analytical validation of integrated methodologies in clinical practice. - Emphasizes need for harmonized workflows and regulatory validation for adoption in clinical settings.
## Clinical Analysis & Structured Key Points
Clipboard, Search History, and several other advanced features are temporarily unavailable. [ Skip to main page content ](https://pubmed.ncbi.nlm.nih.gov/42765713/#article-details) ![U.S. flag](https://cdn.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png) An official website of the United States government Here's how you know ![Dot gov](https://cdn.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg) **The .gov means it’s official.** Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site. ![Https](https://cdn.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg) **The site is secure.** The **https://** ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely. [ ![NIH NLM Logo](https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg) ](https://www.ncbi.nlm.nih.gov/) [Log in](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42765713%2F) Show account info Close #### Account Logged in as: **username** * [Dashboard](https://www.ncbi.nlm.nih.gov/myncbi/) * [Publications](https://www.ncbi.nlm.nih.gov/myncbi/collections/bibliography/) * [Account settings](https://www.ncbi.nlm.nih.gov/account/settings/) * [Log out](https://www.ncbi.nlm.nih.gov/account/signout/?back_url=https%3A//pubmed.ncbi.nlm.nih.gov/42765713/) [Access keys](https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys) [NCBI Homepage](https://www.ncbi.nlm.nih.gov) [MyNCBI Homepage](https://pubmed.ncbi.nlm.nih.gov/myncbi/) [Main Content](https://pubmed.ncbi.nlm.nih.gov/42765713/#maincontent) [Main Navigation](https://pubmed.ncbi.nlm.nih.gov/42765713/) [ ![pubmed logo](https://cdn.ncbi.nlm.nih.gov/pubmed/c24ab723-7c80-48cd-9c68-022ded852586/core/images/pubmed-logo-blue.svg) ](https://pubmed.ncbi.nlm.nih.gov/) [ ](https://pubmed.ncbi.nlm.nih.gov/42765713/ "Show search bar") Search: [](https://pubmed.ncbi.nlm.nih.gov/42765713/ "Clear search input")Search [Advanced](https://pubmed.ncbi.nlm.nih.gov/advanced/) [ Clipboard ](https://pubmed.ncbi.nlm.nih.gov/clipboard/) [ User Guide ](https://pubmed.ncbi.nlm.nih.gov/help/) Save Email Send to * [ Clipboard ](https://pubmed.ncbi.nlm.nih.gov/42765713/) * [My Bibliography](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42765713%2F%23open-bibliography-panel) * [Collections](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42765713%2F%23open-collections-panel) * [Citation manager](https://pubmed.ncbi.nlm.nih.gov/42765713/) Display options Display options Format Abstract PubMed PMID ## Save citation to file Format: Summary (text) PubMed PMID Abstract (text) CSV Create file Cancel ## Email citation Email address has not been verified. Go to [ My NCBI account settings ](https://account.ncbi.nlm.nih.gov/settings/) to confirm your email and then refresh this page. To: Subject: Body: Format: Summary Summary (text) Abstract Abstract (text) MeSH and other data Send email Cancel ### Add to Collections * Create a new collection * Add to an existing collection Name your collection: Name must be less than 100 characters Choose a collection: Unable to load your collection due to an error [Please try again](https://pubmed.ncbi.nlm.nih.gov/42765713/) Add Cancel ### Add to My Bibliography * My Bibliography Unable to load your delegates due to an error [Please try again](https://pubmed.ncbi.nlm.nih.gov/42765713/) Add Cancel ## Your saved search Name of saved search: Search terms: [Test search terms](https://pubmed.ncbi.nlm.nih.gov/42765713/) Would you like email updates of new search results? Saved Search Alert Radio Buttons * Yes * No Email: ([change](https://www.ncbi.nlm.nih.gov/account/settings/)) Frequency: Monthly Weekly Daily Which day? The first Sunday The first Monday The first Tuesday The first Wednesday The first Thursday The first Friday The first Saturday The first day The first weekday Which day? Sunday Monday Tuesday Wednesday Thursday Friday Saturday Report format: Summary Summary (text) Abstract Abstract (text) PubMed Send at most: 1 item 5 items 10 items 20 items 50 items 100 items 200 items Send even when there aren't any new results Optional text in email: Save Cancel ## Create a file for external citation management software Create file Cancel ## Your RSS Feed Name of RSS Feed: Number of items displayed: 5 10 15 20 50 100 Create RSS Cancel RSS Link Copy ### Actions Cite Collections Add to Collections * Create a new collection * Add to an existing collection Name your collection: Name must be less than 100 characters Choose a collection: Unable to load your collection due to an error [Please try again](https://pubmed.ncbi.nlm.nih.gov/42765713/) Add Cancel Permalink Permalink Copy Display options Display options Format Abstract PubMed PMID ### Page navigation * [ Title & authors ](https://pubmed.ncbi.nlm.nih.gov/42765713/#heading) * [ Abstract ](https://pubmed.ncbi.nlm.nih.gov/42765713/#abstract) * [Similar articles](https://pubmed.ncbi.nlm.nih.gov/42765713/#similar) * [ Publication types ](https://pubmed.ncbi.nlm.nih.gov/42765713/#publication-types) Title & authors Abstract Similar articles Publication types Review Crit Rev Anal Chem Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Crit+Rev+Anal+Chem%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Crit+Rev+Anal+Chem%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42765713/) . 2026 Sep 21:1-25. doi: 10.1080/10408347.2026.2733903. Online ahead of print. # Integrating Transcriptomics and Metabolomics for Clinical Disease Detection: A Critical Review of Emerging Diagnostic Methodologies [Kashyap Thummar](https://pubmed.ncbi.nlm.nih.gov/?term=Thummar+K&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#full-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Sneha M Nair](https://pubmed.ncbi.nlm.nih.gov/?term=Nair+SM&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#full-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Foram Ravat](https://pubmed.ncbi.nlm.nih.gov/?term=Ravat+F&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#full-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Janki Goswami](https://pubmed.ncbi.nlm.nih.gov/?term=Goswami+J&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#full-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Bhumika Maheriya](https://pubmed.ncbi.nlm.nih.gov/?term=Maheriya+B&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#full-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Sanjay Chauhan](https://pubmed.ncbi.nlm.nih.gov/?term=Chauhan+S&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#full-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India.") Affiliations Expand ### Affiliation * 1 School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India. * PMID: **42765713** * DOI: [ 10.1080/10408347.2026.2733903 ](https://doi.org/10.1080/10408347.2026.2733903) Item in Clipboard Review # Integrating Transcriptomics and Metabolomics for Clinical Disease Detection: A Critical Review of Emerging Diagnostic Methodologies Kashyap Thummar et al. Crit Rev Anal Chem. 2026. Show details Display options Display options Format Abstract PubMed PMID Crit Rev Anal Chem Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Crit+Rev+Anal+Chem%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Crit+Rev+Anal+Chem%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42765713/) . 2026 Sep 21:1-25. doi: 10.1080/10408347.2026.2733903. Online ahead of print. ### Authors [Kashyap Thummar](https://pubmed.ncbi.nlm.nih.gov/?term=Thummar+K&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#short-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Sneha M Nair](https://pubmed.ncbi.nlm.nih.gov/?term=Nair+SM&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#short-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Foram Ravat](https://pubmed.ncbi.nlm.nih.gov/?term=Ravat+F&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#short-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Janki Goswami](https://pubmed.ncbi.nlm.nih.gov/?term=Goswami+J&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#short-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Bhumika Maheriya](https://pubmed.ncbi.nlm.nih.gov/?term=Maheriya+B&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#short-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India."), [Sanjay Chauhan](https://pubmed.ncbi.nlm.nih.gov/?term=Chauhan+S&cauthor_id=42765713)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42765713/#short-view-affiliation-1 "School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India.") ### Affiliation * 1 School of Pharmacy, Gujarat Technological University, Gandhinagar, Gujarat, India. * PMID: **42765713** * DOI: [ 10.1080/10408347.2026.2733903 ](https://doi.org/10.1080/10408347.2026.2733903) Item in Clipboard Cite Display options Display options Format Abstract PubMed PMID ## Abstract Transcriptomics and metabolomics occupy mechanistically complementary positions in the molecular hierarchy of disease: gene expression characterizes upstream regulatory dysregulation, while metabolomics captures the downstream biochemical consequence at the functional endpoint of that cascade. Applied alone, each yields only a partial view of complex, multifactorial disease. This critical review evaluates the workflows, platforms and computational strategies of both disciplines, appraising their diagnostic utility, translational limitations and clinical laboratory adaptability.We examine integration methodologies spanning correlation-based approaches, multiblock latent factor models, network-guided pathway fusion and machine-learning architectures, and set out the parameter sensitivity and reproducibility limitations that the applied literature systematically underreports. These methodological claims are then tested against published practice through two in-depth case studies, in sepsis and non-small cell lung cancer, selected as contrasting exemplars. Persistent barriers are identified and discussed: pre-analytical variability, the transcriptome-metabolome correlation gap (_r_ ≈ 0.3-0.4), incomplete reference databases, the absent proteome layer, and the lack of standardized clinical validation frameworks. We further argue that the missing proteome layer is not only a mechanistic gap but a formal obstacle to causal inference from two-layer data.Emerging solutions, including deep-learning fusion, explainable artificial intelligence and foundation models, are assessed alongside their documented limitations. We report that no biomarker derived from integrated transcriptomic-metabolomic analysis has undergone analytical validation, entered regulatory qualification, or reached clinical implementation, and that where diagnostic performance is reported it belongs to a single-platform model rather than to the integrated signature. Harmonized workflows, standardized reporting and regulatory-grade validation remain prerequisites for clinical adoption. **Keywords:** Bioinformatics software tools; Machine learning; MultiOmics integration; metabolomics; transcriptomics. [PubMed Disclaimer](https://pubmed.ncbi.nlm.nih.gov/disclaimer/) ## Similar articles * [ A tri-omics and machine learning framework identifies prognostic biomarkers and metabolic signatures in sepsis. ](https://pubmed.ncbi.nlm.nih.gov/41611834/) Li X, Ke G, Hu Y, Chen M.Li X, et al.Sci Rep. 2026 Jan 29;16(1):6648. doi: 10.1038/s41598-026-37342-z.Sci Rep. 2026.PMID: 41611834Free PMC article. * [ Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification. ](https://pubmed.ncbi.nlm.nih.gov/26269925/) Wolahan SM, Hirt D, Glenn TC.Wolahan SM, et al.In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25.In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25.PMID: 26269925Free Books & Documents.Review. * [ Omics-based computational approaches for biomarker identification, prediction, and treatment of Long COVID. ](https://pubmed.ncbi.nlm.nih.gov/41368891/) Pinero S, Li X, Zhang J, Winter M, Lee SH, Nguyen T, Liu L, Li J, Le TD.Pinero S, et al.Crit Rev Clin Lab Sci. 2026 Jun;63(4):332-358. doi: 10.1080/10408363.2025.2583083. Epub 2025 Dec 9.Crit Rev Clin Lab Sci. 2026.PMID: 41368891Review. * [ Benchmarking of plasma proteomics workflows reveals complementarity of deep MS and affinity-based assays. ](https://pubmed.ncbi.nlm.nih.gov/42762864/) Monneuse JM, Hage H, Da Silva C, Poncelet M, Levast B, Louis K, Covindarassou S, Ribette T, Ghanem JA, Sarafian M, Saliou A.Monneuse JM, et al.J Proteomics. 2026 Sep 19:105735. doi: 10.1016/j.jprot.2026.105735. Online ahead of print.J Proteomics. 2026.PMID: 42762864 * [ Folic acid supplementation and malaria susceptibility and severity among people taking antifolate antimalarial drugs in endemic areas. ](https://pubmed.ncbi.nlm.nih.gov/36321557/) Crider K, Williams J, Qi YP, Gutman J, Yeung L, Mai C, Finkelstain J, Mehta S, Pons-Duran C, Menéndez C, Moraleda C, Rogers L, Daniels K, Green P.Crider K, et al.Cochrane Database Syst Rev. 2022 Feb 1;2(2022):CD014217. doi: 10.1002/14651858.CD014217.Cochrane Database Syst Rev. 2022.Update in: [Cochrane Database Syst Rev. 2026 Feb 18;2:CD014217. doi: 10.1002/14651858.CD014217.pub2.](https://pubmed.ncbi.nlm.nih.gov/41705996/)PMID: 36321557Free PMC article.Updated. [ See all similar articles ](https://pubmed.ncbi.nlm.nih.gov/?linkname=pubmed_pubmed&from_uid=42765713) ## Publication types * Review Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Review%22%5Bpt%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Review) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42765713/) [x] Cite Copy Download .nbib .nbib Format: AMA APA MLA NLM **Send To** * [Clipboard](https://pubmed.ncbi.nlm.nih.gov/42765713/) * [Email](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42765713%2F%23open-email-panel) * [Save](https://pubmed.ncbi.nlm.nih.gov/42765713/) * [My Bibliography](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42765713%2F%23open-bibliography-panel) * [Collections](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42765713%2F%23open-collections-panel) * [Citation Manager](https://pubmed.ncbi.nlm.nih.gov/42765713/) [x] NCBI Literature Resources [MeSH](https://www.ncbi.nlm.nih.gov/mesh/) [PMC](https://www.ncbi.nlm.nih.gov/pmc/) [Bookshelf](https://www.ncbi.nlm.nih.gov/books) [Disclaimer](https://pubmed.ncbi.nlm.nih.gov/disclaimer/) The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited. Follow NCBI [ Twitter ](https://twitter.com/ncbi) [ Facebook ](https://www.facebook.com/ncbi.nlm) [ LinkedIn ](https://www.linkedin.com/company/ncbinlm) [ GitHub ](https://github.com/ncbi) [ ](https://ncbiinsights.ncbi.nlm.nih.gov/) [Connect with NLM](https://www.nlm.nih.gov/socialmedia/index.html) * [ Twitter ](https://twitter.com/NLM_NIH) * [ SM-Facebook ](https://www.facebook.com/nationallibraryofmedicine) * [ SM-Youtube ](https://www.youtube.com/user/NLMNIH) National Library of Medicine [8600 Rockville Pike Bethesda, MD 20894](https://www.google.com/maps/place/8600+Rockville+Pike,+Bethesda,+MD+20894/@38.9959508,-77.101021,17z/data=!3m1!4b1!4m5!3m4!1s0x89b7c95e25765ddb:0x19156f88b27635b8!8m2!3d38.9959508!4d-77.0988323) [Web Policies](https://www.nlm.nih.gov/web_policies.html) [FOIA](https://www.nih.gov/institutes-nih/nih-office-director/office-communications-public-liaison/freedom-information-act-office) [HHS Vulnerability Disclosure](https://www.hhs.gov/vulnerability-disclosure-policy/index.html) [Help](https://support.nlm.nih.gov/?pagename=pubmed%3Apubmed%3Aabstract%3ANONE) [Accessibility](https://www.nlm.nih.gov/accessibility.html) [Careers](https://www.nlm.nih.gov/careers/careers.html) * [NLM](https://www.nlm.nih.gov/) * [NIH](https://www.nih.gov/) * [HHS](https://www.hhs.gov/) * [USA.gov](https://www.usa.gov/)
## Related Clinical Research

- [Machine learning model predicts early invasive mechanical ventilation in ICU pneumonia patients](https://medichelpline.com/clinical-feed/pubmed-42275910.md) (DOI: 10.1016/j.ijmedinf.2026.106541)
- [Global burden and trends of maternal sepsis and infections (1990–2021) with projections to 2050](https://medichelpline.com/clinical-feed/pubmed-42683240.md) (DOI: 10.1515/med-2026-1443)
- [Understanding Hospice Discharge: A Family's Guide](https://medichelpline.com/clinical-feed/kff-health-news-1-my-husband-was-kicked-out-of-hospice-for-dying-too-slowly.md)
- [Persistent critical illness in mechanically ventilated acute hypoxic respiratory failure: prevalen](https://medichelpline.com/clinical-feed/plos-one-9-persistent-critical-illness-in-acute-hypoxic-respiratory-failure-a.md)
- [20-HETE–GPR75 Signaling Loss Impairs Renal Hemodynamics and Promotes SA-AKI in Sepsis](https://medichelpline.com/clinical-feed/biorxiv-10-loss-of-20-hete-gpr75-signaling-impairs-renal-hemodynamic-adaptation-in-sepsis.md)

## Navigation
- [← Back to Critical Care Feed](https://medichelpline.com/clinical-feed/critical-care.md)
- [← All Clinical Specialties](https://medichelpline.com/clinical-feed.md)
## Medical & Regulatory Disclaimer

> [!CAUTION]
> MedicHelpline content is structured for research, educational, and professional discovery purposes. It does not constitute individual medical advice, clinical diagnosis, or treatment recommendations.
> Always verify dosing, contraindications, and regulatory alerts against official product labeling and primary regulatory sources before clinical decision-making.