24 papers · ranked by Valyu relevance
Mike Sportiello, Adam Geber, Rohith Palli, A Karim Embong + 4 more
Many tools exist to perform a rigorous pathway analysis, though traditional gene set enrichment analysis remains among the most common. While useful for many applications, one common situation where it is less so is the metabolic profiling of bulk omics datasets. Rate limiting steps in more linear pathways are the main…
William G. Ryan V., Smita Sahay, John Vergis, Corey Weistuch + 3 more
'Jarek Meller' 'Robert E. McCullumsmith' 'Gerald Lushington'] In bioinformatics, pathway analyses are used to interpret biological data by mapping measured molecules with known pathways to discover their functional processes and relationships. Pathway analysis has become an essential tool for interpreting large-scale…
Tibo Vande Moortele, Pieter Verschaffelt, Qingyao Huang, Nadezhda T. Doncheva + 6 more
Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool…
Tibo Vande Moortele, Pieter Verschaffelt, Qingyao Huang, Nadezhda T. Doncheva + 6 more
'Nadezhda T. Doncheva' 'Tanja Holstein' 'Caroline Jachmann' 'Peter Dawyndt' 'Lennart Martens' 'Bart Mesuere' 'Tim Van Den Bossche'] Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health.…
Lily Taub, Thomas H. Hampton, Sharanya Sarkar, Georgia Doing + 4 more
E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users to assess broad biological stress responses at the KEGG pathway or Gene…
Zhiwei Zheng, Kevin Bryson
Motivation: Pathway enrichment analysis is widely used to interpret gene expression data. Standard approaches, such as GSEA, rely on predefined phenotypic labels and pairwise comparisons, which limits their applicability in unsupervised settings. Existing unsupervised extensions, including single-sample methods…
Maria K. Jaakkola, Anu Kukkonen-Macchi, Tomi Suomi, Laura L. Elo
We introduce a new method for Pathway Analysis of Longitudinal data (PAL), which is suitable for complex study designs, such as longitudinal data. The main advantages of PAL are the use of pathway structures and the suitability of the approach for study settings beyond currently available tools. We demonstrate the…
Gianluca Mattei, Zhuohui Gan, Matteo Ramazzotti, Bernhard O. Palsson + 3 more
'Daniel C. Zielinski' 'Miha Moškon' 'Tadeja Režen'] Pathway analysis is ubiquitous in biological data analysis due to the ability to integrate small simultaneous changes in functionally related components. While pathways are often defined based on either manual curation or network topological properties, an attractive…
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández
'Daniel Domingo-Fernández'] Title: Abstract Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of pathway enrichment lies in its simplicity…
Travis M. Blimkie, Andy An, Robert E. W. Hancock, Stacey D. Finley
R package pathlinkR is designed to aid transcriptomic analyses by streamlining and simplifying the process of analyzing and interpreting differentially expressed genes derived from human RNA-Seq data. It provides an integrated approach to performing pathway enrichment and network-based analyses, while also producing…
Lingran Xiao, Yanfei Wang, Shiying Li, Lingxi Chen + 1 more
The pathway is a biological term that refers to a series of interactions between molecules in a cell that cause a certain product or a change in the cell [NIH20]. Pathway analysis is a powerful method for gene expression analysis [Cir17]. Through pathway maps, the lists of genes that are differently expressed across…
Maria K. Jaakkola, Anu Kukkonen-Macchi, Tomi Suomi, Laura L. Elo
Pathway analysis is a frequent step in studies involving gene or protein expression data, but most of the available pathway methods are designed for simple case versus control studies of two sample groups without further complexity. The few available methods allowing the pathway analysis of more complex study designs…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann‐Apitius, Daniel Domingo‐Fernándéz
'Daniel Domingo‐Fernándéz'] Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of pathway enrichment lies in its simplicity, multiple factors…
Letian Deng, Sanghoon Lee, Kai Wang, Yuehua Zhu + 3 more
Single-cell sequencing (SCS) enables exploring the pathways and processes of cells and cell populations, however, there is a paucity of pathway enrichment methods designed to tolerate the high noise and low gene coverage of this technology. When gene expression data are noisy and signals are sparse, testing pathway…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
Chiara Pastrello, Max Kotlyar, Mark Abovsky, Richard Lu + 1 more
Pathway Data Integration Portal (PathDIP) is an integrated pathway database that was developed to increase functional gene annotation coverage and reduce bias in pathway enrichment analysis. PathDIP 5 provides multiple improvements to enable more interpretable analysis: users can perform enrichment analysis using all…
Vidhi Kulkarni, Igor Tsigelny, Valentina Kouznetsova
Feline mammary carcinoma (FMC) is a prevalent and fatal carcinoma that predominantly affects unsprayed female cats. FMC is the third most common carcinoma in cats but is still underrepresented in research. Current diagnosis methods include physical examinations, imaging tests, and fine-needle aspiration. The diagnosis…
Moushumi Goswami, Divya Dosemane, Sravanthi Davuluri, Akhilesh Bajpai + 1 more
Pathway Databases are essential particularly in the post-genomic era as they provide organized information about biological pathways and processes. However, there are too many pathway databases with varying features. These variations, stemming from multiple factors, create challenges for users in making objective…
Julian Müller, Bernhard Kuster, Matthew The
Protein function is dynamically modulated by post-translational modifications (PTMs). Many different types of PTMs can nowadays be identified and quantified at a large scale using mass spectrometry. It is well known that many PTMs have an effect on protein function and cellular processes, and they should be studied not…
Juan Antonio Villatoro-García, Pablo Pedro Jurado-Bascón, Pedro Carmona‐Sáez
'Pedro Carmona‐Sáez'] The proliferation of omics datasets in public repositories has created unprecedented opportunities for biomedical research but has also posed significant challenges for their integration, particularly due to missing genes and platform-specific discrepancies. Traditional gene expression…
Authors not listed
The identification of kinetically feasible reaction pathways that connect a reactant to its product, including numerous intermediates and transition states, is crucial for predicting chemical reactions and elucidating reaction mechanisms. However, as molecular systems become increasingly complex or larger, the number…
Jiachen Cai, Robert J. B. Goudie, Brian D. M. Tom
application to metabolite measurements in a COVID-19 study Authors: ['Jiachen Cai' 'Robert J. B. Goudie' 'Brian D. M. Tom'] It is of scientific interest to identify essential biomarkers in biological processes underlying diseases to facilitate precision medicine. Factor analysis (FA) has long been used to address this…
Authors not listed
Caenorhabditis elegans (C. elegans) is a well-established nematode model for studying metabolism and neurodegenerative disorders, such as Alzheimer’s (AD) and Parkinson’s disease (PD). Non-targeted metabolomics via liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has proven useful for uncovering…