Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network, or Pathway Analysis.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1307-8_9
Abstract: The main purpose of pathway or gene set analysis methods is to provide mechanistic insight into the large amount of data produced in high-throughput studies. These tools were developed for gene expression analyses, but they… read more here.
Keywords: gene set; summarizing rna; pathway; pathway analysis ... See more keywords
Differential Pathway Analysis.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9057-3_7
Abstract: Integrating prior knowledge of pathway-level information can enhance power and facilitate interpretation of gene expression data analyses. Here, we provide a practical demonstration of the value of gene set or pathway enrichment testing and extend… read more here.
Keywords: analysis; biology; pathway analysis; gene ... See more keywords
A detailed pathway analysis of the chemical reaction system generating the Martian vertical ozone profile
Sign Up to like & getrecommendations! Published in 2017 at "Icarus"
DOI: 10.1016/j.icarus.2016.12.012
Abstract: Atmospheric chemical composition is crucial in determining a planet’s atmospheric structure, stability, and evolution. Attaining a quantitative understanding of the essential chemical mechanisms governing atmospheric composition is nontrivial due to complex interactions between chemical species.… read more here.
Keywords: chemical; pathway analysis; chemical reaction; profile ... See more keywords
Avoiding the Misuse of Pathway Analysis Tools in Environmental Metabolomics
Sign Up to like & getrecommendations! Published in 2022 at "Environmental Science & Technology"
DOI: 10.1021/acs.est.2c05588
Abstract: W the past 20 years, metabolomics has moved from an exciting innovation within the environmental sciences to something that is almost routine. It can be considered as a means to generate metabolite biomarkers, although it… read more here.
Keywords: pathway analysis; analysis; avoiding misuse; pathway ... See more keywords
Altered Serum Metabolite Profiling and Relevant Pathway Analysis in Rats Stimulated by Honeybee Venom: New Insight into Allergy to Honeybee Venom.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of agricultural and food chemistry"
DOI: 10.1021/acs.jafc.7b04160
Abstract: To improve our understanding of the disturbed metabolic pathways and cellular responses triggered by honeybee venom stimulation, we compared the changes in serum metabolites in rats, either stimulated or not by honeybee venom, by performing… read more here.
Keywords: venom stimulation; venom; honeybee venom; stimulated honeybee ... See more keywords
Addressing reproducibility in single-laboratory phenotyping experiments
Sign Up to like & getrecommendations! Published in 2017 at "Nature Methods"
DOI: 10.1038/nmeth.4259
Abstract: high resolution MS data directly onto pathways, (ii) cross-integration of genomic and proteomic data and (iii) metabolite identity verification via data-dependent MS/MS analysis, either separately or as part of the autonomous workflow5. Our multi-omic analysis… read more here.
Keywords: integration; analysis; supplementary fig; study ... See more keywords
Distinct expression profiles of peptides in placentae from preeclampsia and normal pregnancies
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DOI: 10.1038/s41598-020-74840-0
Abstract: This study sought to identify potential bioactive peptides from the placenta that are involved in preeclampsia (PE) to obtain information about the prediction, diagnosis and treatment of PE. The liquid chromatography/mass spectrometry was used to… read more here.
Keywords: expression profiles; preeclampsia; pathway analysis; distinct expression ... See more keywords
Pathway Analysis of Patients with Severe Acute Respiratory Syndrome.
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DOI: 10.1055/a-1886-2094
Abstract: BACKGROUND Coronaviruses are emerging threats for human health, as demonstrated by the ongoing coronavirus disease 2019 (COVID-19) pandemic that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is closely related to SARS-CoV-1,… read more here.
Keywords: severe acute; pathway analysis; sars cov; analysis ... See more keywords
A comprehensive survey of the approaches for pathway analysis using multi-omics data integration
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac435
Abstract: Abstract Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power… read more here.
Keywords: pathway analysis; multi omics; integration; analysis ... See more keywords
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz598
Abstract: SUMMARY CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models of metabolism. It currently includes the K-shortest EFM… read more here.
Keywords: framework; based models; constraint based; pathway analysis ... See more keywords
Statistical inference of genetic pathway analysis in high dimensions.
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DOI: 10.1093/biomet/asz033
Abstract: Genetic pathway analysis has become an important tool for investigating the association between a group of genetic variants and traits. With dense genotyping and extensive imputation, the number of genetic variants in biological pathways has… read more here.
Keywords: statistical inference; pathway analysis; genetic pathway; analysis ... See more keywords