Summary of Study ST003092

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001921. The data can be accessed directly via it's Project DOI: 10.21228/M8DH8T This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003092
Study TitlePrediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data
Study SummaryBackground Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to the large number of metabolites in a cell and the presence of multiple genes associated with cancer development. Results Here we report the development of a computational workflow that predicts metabolite-gene-pathway sets. Metabolite-gene-pathway sets present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate metabolite-gene-pathway sets. A GEM is a computational model that predicts reaction fluxes at a genome scale, and can be constructed in a cell-specific manner by using omics data. The computational workflow is first validated by comparing the resulting metabolite-gene pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from acute myeloid leukemia and renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the metabolite-gene-pathway sets predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting metabolite-gene-pathway sets is also discussed. Conclusions Validation of the metabolite-gene-pathway set-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting metabolite-gene-pathway sets will help identify novel oncometabolites, and also suggest cancer treatment strategies.
Institute
Korea Advanced Institute of Science and Technology (KAIST)
Last NameLee
First NameSang Mi
Address291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
Emailsandra1996@kaist.ac.kr
Phone+82-42-350-3955
Submit Date2024-02-18
Num Groups2
Total Subjects38
Analysis Type DetailLC-MS
Release Date2024-02-20
Release Version1
Sang Mi Lee Sang Mi Lee
https://dx.doi.org/10.21228/M8DH8T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Disease
SA333209P14Bone marrow AML
SA333210P12Bone marrow AML
SA333211P18Bone marrow AML
SA333212P11Bone marrow AML
SA333213P19Bone marrow AML
SA333214P1Bone marrow AML
SA333215P20Bone marrow AML
SA333216P10Bone marrow AML
SA333217P15Bone marrow AML
SA333218P3Bone marrow AML
SA333219P9Bone marrow AML
SA333220P2Bone marrow AML
SA333221P5Bone marrow AML
SA333222P4Bone marrow AML
SA333223P8Bone marrow AML
SA333224P6Bone marrow AML
SA333225P7Bone marrow MDS/AML
SA333226P36Kidney Renal cell carcinoma
SA333227P35Kidney Renal cell carcinoma
SA333228P34Kidney Renal cell carcinoma
SA333229P37Kidney Renal cell carcinoma
SA333230P33Kidney Renal cell carcinoma
SA333231P41Kidney Renal cell carcinoma
SA333232P32Kidney Renal cell carcinoma
SA333233P40Kidney Renal cell carcinoma
SA333234P39Kidney Renal cell carcinoma
SA333235P38Kidney Renal cell carcinoma
SA333236P23Kidney Renal cell carcinoma
SA333237P25Kidney Renal cell carcinoma
SA333238P24Kidney Renal cell carcinoma
SA333239P22Kidney Renal cell carcinoma
SA333240P21Kidney Renal cell carcinoma
SA333241P26Kidney Renal cell carcinoma
SA333242P27Kidney Renal cell carcinoma
SA333243P30Kidney Renal cell carcinoma
SA333244P29Kidney Renal cell carcinoma
SA333245P28Kidney Renal cell carcinoma
SA333246P31Kidney Renal cell carcinoma
Showing results 1 to 38 of 38
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