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Network-aware reaction pattern recognition reveals regulatory signatures of mitochondrial dysfunction

https://doi.org/10.1101/2020.06.25.171850

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

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El-MAVEN: A Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics

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On Nearest-Neighbor Graphs

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Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

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New software tools, databases, and resources in metabolomics: updates from 2020

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MECR Mutations Cause Childhood-Onset Dystonia and Optic Atrophy, a Mitochondrial Fatty Acid Synthesis Disorder

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Liver-Type Glutaminase GLS2 Is a Druggable Metabolic Node in Luminal-Subtype Breast Cancer

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Regulation of Tumor Initiation by the Mitochondrial Pyruvate Carrier

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Interrogating metabolism as an electron flow system

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Impact of Mitochondrial Fatty Acid Synthesis on Mitochondrial Biogenesis

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ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly

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Evidence that glutamine, not sugar, is the major energy source for cultured HeLa cells.

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Phosphofructokinase mutants of yeast. Biochemistry and genetics.

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AMP deaminase reaction as a control system of glycolysis in yeast. Activation of phosphofructokinase and pyruvate kinase by the AMP deaminase-ammonia system.

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Metabolomic Analysis and Visualization Engine for LC−MS Data

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FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

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Gene Ontology: tool for the unification of biology

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Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

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Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism

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From Krebs to clinic: glutamine metabolism to cancer therapy

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Serine and one-carbon metabolism in cancer

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Flux-dependent graphs for metabolic networks

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Dietary methionine influences therapy in mouse cancer models and alters human metabolism

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Array programming with NumPy

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SciPy 1.0: fundamental algorithms for scientific computing in Python

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The mitochondrial dicarboxylate carrier is essential for the growth of Saccharomyces cerevisiae on ethanol or acetate as the sole carbon source

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High Level Expression and Characterization of the Mitochondrial Citrate Transport Protein from the Yeast Saccharomyces cerevisiae

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Growth and Metastases of Human Lung Cancer Are Inhibited in Mouse Xenografts by a Transition State Analogue of 5′-Methylthioadenosine Phosphorylase

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edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

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Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

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Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

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Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data

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MetExploreViz: web component for interactive metabolic network visualization

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Combining p-values via averaging

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Compartment and hub definitions tune metabolic networks for metabolomic interpretations

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KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGG: Kyoto Encyclopedia of Genes and Genomes

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The Gene Ontology resource: enriching a GOld mine

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Reactome: a knowledgebase of biological pathways

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MetaboAnalyst: a web server for metabolomic data analysis and interpretation

inferredcites →https://doi.org/10.1093/nar/gkq312openalex-snapshot

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

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ChEBI in 2016: Improved services and an expanding collection of metabolites

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

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KEGG: new perspectives on genomes, pathways, diseases and drugs

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HMDB 4.0: the human metabolome database for 2018

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The Reactome Pathway Knowledgebase

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MetExplore: collaborative edition and exploration of metabolic networks

inferredcites →https://doi.org/10.1093/nar/gky310openalex-snapshot

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

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The reactome pathway knowledgebase

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BioModels—15 years of sharing computational models in life science

inferredcites →https://doi.org/10.1101/2020.02.13.944777openalex-snapshot

Co-expression analysis is biased by a mean-correlation relationship

inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

inferredcites →https://doi.org/10.1101/gr.772403openalex-snapshot

PANTHER: A Library of Protein Families and Subfamilies Indexed by Function

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Matplotlib: A 2D Graphics Environment

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Regression Models and Life-Tables

inferredcites →https://doi.org/10.1111/mmi.12402openalex-snapshot

Defects in mitochondrial fatty acid synthesis result in failure of multiple aspects of mitochondrial biogenesis in S accharomyces cerevisiae

inferredcites →https://doi.org/10.1126/science.1218099openalex-snapshot

A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila , and Humans

inferredcites →https://doi.org/10.1126/science.347.6227.1274-copenalex-snapshot

Charting the human proteome: Understanding disease using a tissue-based atlas

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A subcellular map of the human proteome

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A pathology atlas of the human cancer transcriptome

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A Transcriptional Switch in the Expression of Yeast Tricarboxylic Acid Cycle Genes in Response to a Reduction or Loss of Respiratory Function

inferredcites →https://doi.org/10.1158/1940-6207.capr-14-0329openalex-snapshot

Metabolomic Markers of Altered Nucleotide Metabolism in Early Stage Adenocarcinoma

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s40170-015-0135-3openalex-snapshot

The rate of glycolysis quantitatively mediates specific histone acetylation sites

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XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data

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Reproducibility in systems biology modelling

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Integrated omics: tools, advances and future approaches

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SciPy 1.0: fundamental algorithms for scientific computing in Python

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seaborn: statistical data visualization

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Nonparametric Estimation from Incomplete Observations

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Data Structures for Statistical Computing in Python

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Exploring Network Structure, Dynamics, and Function using NetworkX

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Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

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pandas-dev/pandas: Pandas

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Aristotle. On the parts of animals

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The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-981-96-4824-5_4openalex-snapshot

Integrating Metabolomics with Omics Techniques: Exploring Cutting-Edge Technologies in Comprehensive Biological Analysis

inferred← citeshttps://doi.org/10.1007/s11306-021-01796-1openalex-snapshot

New software tools, databases, and resources in metabolomics: updates from 2020

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Microbial metabolomics: recent advancements and applications in infectious diseases and drug discovery

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Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

inferred← citeshttps://doi.org/10.1101/2021.09.17.460635openalex-snapshot

Nitrogen partitioning between branched-chain amino acids and urea cycle enzymes sustains renal cancer progression

inferred← citeshttps://doi.org/10.7554/elife.84282openalex-snapshot

Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms

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