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353 results for “Metabolic Pathway”
Four lipidomics datasets (mouse liver, mouse pancreatic islets, mouse soleus muscle and mouse visceral adipose tissue), generated for the publication Mehl et al., "A multiorgan map of metabolic, signalling, and inflammatory pathways that coordinately control fasting glycemia in mice"
<p>Mehl, Thorens et al present a multiomics study aimiing to<span> identify the pathways that are coordinately regulated in pancreatic </span><span>b</span><span>-cells, muscle, liver, and fat to control fasting glycemia we fed C57Bl/6, DBA/2 and Balb/c mice a regular chow or a high fat diet for 3, 10 and 30 days. We measured fasted glycemia, insulinemia and whole-body insulin resistance. Transcriptomic and lipidomic analysis were used in a data fusion approach to identify organ-specific pathways related to the glycemic levels across all conditions investigated. In pancreatic islets, constant insulinemia despite higher glycemic levels were associated with reduced expression of mRNAs encoding hormone and neurotransmitter receptors as well as OXPHOS, cadherins, integrins and gap junction proteins. Higher glycemia and whole-body insulin resistance were associated, in muscle, with reduced expression of mRNAs encoding insulin signaling proteins and enzymes of the glycolysis, Krebs’ cycle and OXPHOS pathways, as well as endocytosis and exocytosis proteins; in hepatocytes, with lower expression of mRNAs of the insulin signaling pathway, of branched chain amino acid catabolism and of OXPHOS; in adipose tissue, with increased expression of mRNAs of innate immunity and lipid catabolism. These data provide a map of the pathways that are coordinately recruited in the investigated tissues to control fasting glycemia and a resource for further studies of interorgan communication in glucose homeostasis. </span></p>
Interstage single ventricle heart disease infants show dysregulation in multiple metabolic pathways: targeted metabolomics analysis - Data
<p>The data in this Zenodo entry corresponds to the data used to produce the results in <a href="https://www.jacc.org/doi/full/10.1016/j.jacadv.2022.100169">https://www.jacc.org/doi/full/10.1016/j.jacadv.2022.100169</a>. The zipped folder contains three files</p> <ul> <li>Metabolite Data.csv - The meatobilte measurements for all the samples</li> <li>Clinical Data.csv - Values for the clinical variables</li> <li>Clinical Data Descriptions.csv - More in depth explanation of clinical variables as well as possible values of the variables</li> </ul> <p><span>This study was supported by the American Heart Association (AHA</span><span>20CDA35310498 and AHA18IPA34170070) and the National Institutes </span><span>of Health (NIH/NCATS Colorado CTSA, No. UL1 TR001082 and NIH/</span><span>NHLBI K23HL12363</span></p>
Supplementary dataset for "Phenylacetic acid metabolism in land plants: novel pathways and metabolites"
<p>Supplementary dataset with measured data for publication "Phenylacetic acid metabolism in land plants: novel pathways and metabolites"</p>
Hepatic transcriptomic analysis reveals differential regulation of metabolic and immune pathways in three strains of chickens with distinct growth rate exposed to mixed parasites infections
<p><span>This dataset was generated from the study investigating hepatic gene expression in three strains of chickens: Ross-308 (R), Lohmann Brown Plus (LB), and Lohmann Dual (LD), 2 weeks after either an experimental infection (n = 18) with both <em>A. galli</em> and <em>H. gallinarum or kept as uninfected control (n = 12)</em>. </span></p>
Merging metabolomics and genomics provides a catalog of genetic factors that infuence molecular phenotypes in pigs linking relevant metabolic pathways
<h3>Content</h3> <p>Metabolites included in the study. Summary statistics of metabolite levels for the Large White and Duroc pig populations are provided.</p>
Metabolic pathway prediction using non-negative matrix factorization with improved precision
<p>We include samples of various data types used in the work "Metabolic pathway prediction using non-negative matrix factorization with improved precision"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/triUMPF">hallamlab/triUMPF</a></p>
Characterizing Metabolic Alterations in Early-stage chronic kidney disease (CKD) patients: A Pathway for Improved Diagnosis and Personalized Treatment.
<p>The raw NMR data that I have uploaded contains the final concentration results that have been used for this study.</p>
The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
<p>The plant genus <em>Oenothera</em> has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 <em>Oenothera</em> species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section <em>Oenothera </em>exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to <em>Oenothera </em>diversification and rapid gene family evolution.</p>
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
<p>This repository contains signalling to metabolic pathways interconnecting (S-M) protein-protein interaction (PPI) paths. The repository consists of two file:</p> <p><a href="https://zenodo.org/api/files/61dbb365-104e-4c41-ad0a-79f4c657bbee/S-M_paths_z-score_greater_equal_1.txt">S-M_paths_z-score_greater_equal_1.txt </a>: It contains all the S-M paths having z-score >= 1.</p> <p><a href="https://zenodo.org/api/files/61dbb365-104e-4c41-ad0a-79f4c657bbee/S-M_paths_z-score_greater_equal_3.txt">S-M_paths_z-score_greater_equal_3.txt </a>: It contains all the S-M paths having z-score >=3</p>
Raw data of metabolic pathways and candidate olfactory genes in Holotrichia parallela (Coleoptera: Scarabaeidae)
<p>Analysis of antennal transcriptome data caused the discovery of metabolic and signaling pathways and the identification of olfactory genes. According to KEGG pathway enrichment analysis, KEGG pathways and KEGG modules were annotated. Based on the FuncTree software analysis, the functional potential of<em> H. parallela</em> unigenes was visualized across different functional layers, including biological progress, KEGG module and KEGG pathway. We successfully identified a series of putative olfactory genes, including OBPs, CSPs SNMPs and ODEs. The relationship between <em>H. parallela</em> with other species was predicted and many olfactory genes with various functions were analyzed based on phylogenetic analysis. Heat maps and qRT-PCR experiments were performed to display and verify biased or specific expression profiles between sexes and between olfactory and non olfactory tissues.</p>
Time series transcriptomes resolve metabolic pathways underlying crocin's anti-cancer activity | Dataset: sequencing reads (2,6,12,24 hr crocin treatments)
<p><span>Natural products like saffron show promise in treating hepatocellular carcinoma (HCC), but their mechanisms remain unclear. Here, we used time-series transcriptomics to elucidate crocin's anti-cancer mechanisms in HCC cells. We treated HepG2 cells with 1 and 2 mM crocin for 2, 6, 12, and 24 hours and analyzed transcriptomic profiles at each timepoint. The strongest transcriptional response occurred at 2 hours with 1 mM crocin, with diminishing effects at later timepoints. We observed upregulation of metabolic-, adhesion-, and endocytosis-related genes across all timepoints. Pathway analysis revealed activation of DNA damage checkpoints and senescence while proliferation pathways were suppressed. Notably, 52 genes involved in non-alcoholic fatty liver disease were downregulated at 24 hours (FDR p = 8 × 10⁻⁸), suggesting reversal of carcinogenic pathways. Strikingly, crocin consistently downregulated spliceosomal machinery genes across all timepoints while upregulating senescence and autophagy pathways. This spliceosome targeting represents a clinically relevant mechanism, as aberrant splicing drives oncogenesis in more than 90% of cancers. The transcription factor PAX5 was significantly upregulated while oncogenic ELK1 targets were downregulated. Our findings show that crocin treatment is accompanied by HCC cell senescence induction through coordinated spliceosome disruption and metabolic reprogramming, providing novel therapeutic targets for hepatocellular carcinoma.</span></p> <p><strong><span>Keywords: </span></strong><span>Hepatocellular carcinoma (HCC), crocin, transcriptomics, spliceosome, senescence, natural anti-cancer compounds</span></p>
High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds
<h3><em><strong>Content</strong></em></h3> <p>Dataset of the study: "High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds.</p>
Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models
<p>GraphPad Prism files containing source data for figures included in the manuscript "Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models", by Dwidar et al., published in mBio.</p>
Data from: Mycorrhization and chemical seed priming boost tomato stress tolerance by changing primary and defence metabolic pathways
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Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy
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Data for: The galactokinase enzyme of yeast senses metabolic flux to stabilize GAL pathway regulation
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The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
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Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
<p>We include samples of various data types used in the work "Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/pathway2vec">hallamlab/pathway2vec</a></p>
Metabolic pathway inference using multi-label classification with rich pathway features
<p>We include samples of various data types used in the work "Metabolic pathway inference using multi-label classification with rich pathway features"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/mlLGPR">hallamlab/mlLGPR</a></p>
Relabeling metabolic pathway data with groups to improve prediction outcomes
<p>We include samples of various data types used in the work "Relabeling metabolic pathway data with groups to improve prediction outcomes"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/reMap">hallamlab/reMap</a></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.