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graphite - a Bioconductor package to convert pathway topology to gene network

Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi
2012 BMC Bioinformatics  
The conversion of pathway topology to a gene/protein networks (where nodes are a simple element like a gene/ protein) is a critical and challenging task that enables topology-based gene set analyses.  ...  The resulting networks represent a uniform resource for pathway analyses. Indeed, graphite provides easy access to three recently proposed topological methods.  ...  This work was funded by University of Padova [CPDR070805 to G. Sales, 60A06-8475/11 and CPDR075919 to C. Romualdi]  ... 
doi:10.1186/1471-2105-13-20 pmid:22292714 pmcid:PMC3296647 fatcat:hkbk3e5rgze5vmmwj7b52n5zbu

Graphite Web: web tool for gene set analysis exploiting pathway topology

Gabriele Sales, Enrica Calura, Paolo Martini, Chiara Romualdi
2013 Nucleic Acids Research  
Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments.  ...  Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges.  ...  The authors want to thank the University of Padova for support of this work [CPDR075919 and CPDA119031 to C.R.; CPDR070805 to G.S.].  ... 
doi:10.1093/nar/gkt386 pmid:23666626 pmcid:PMC3977659 fatcat:acv5nfnqincd5k7kibg6psiuny

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

Frank Kramer, Michaela Bayerlová, Tim Beißbarth
2014 Biology  
A total of 12 packages integrating pathway data are reviewed in this manuscript.  ...  Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the  ...  The graphite package offers its parsed data as pathway objects, which are imported from KGML-and BioPAX-encoded data and converted to R objects.  ... 
doi:10.3390/biology3010085 pmid:24833336 pmcid:PMC4009765 fatcat:op62z6xt7jgwnkmdbabf4veaiq

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms

Luca Bianco, Samantha Riccadonna, Enrico Lavezzo, Marco Falda, Elide Formentin, Duccio Cavalieri, Stefano Toppo, Paolo Fontana
2016 Bioinformatics  
The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways.  ...  pathway topology.  ...  ., 2012) or graphite (Sales et al., 2012) , exploit also the pathway topology.  ... 
doi:10.1093/bioinformatics/btw636 pmid:28158604 pmcid:PMC5408796 fatcat:4jfqxnqbtvbcbbzsunetcn4ghq

KEGG2Net: Deducing gene interaction networks and acyclic graphs from KEGG pathways

Sree K Chanumolu, Mustafa Albahrani, Handan Can, Hasan H Otu
2021 EMBnet journal  
We developed KEGG2Net, a web resource that generates a network involving only the genes represented on a KEGG pathway with all of the direct and indirect gene-gene interactions deduced from the pathway  ...  Our results indicate that an ensemble method for cycle removal performs as the best approach to convert the gene interaction networks into DAGs.  ...  Discussion In this work, we provide a web resource that converts KEGG pathways into gene interaction networks Suominen and Mader, 2014), a greedy local heuristic to the minimum feedback arc set (MFAS)  ... 
doi:10.14806/ej.26.0.949 pmid:33880340 pmcid:PMC8055051 fatcat:duecdriujzcfbpllhoet47t7aq

RCy3: Network Biology using Cytoscape from within R [article]

Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
2019 bioRxiv   pre-print
Two-way conversion with networks from igraph and graph ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages.  ...  RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment.  ...  Acknowledgments We would like to acknowledge contributions by other developers on the original implementation of RCy3 by Paul Shannon, Tanja Muetze and Georgi Kolishkovski.  ... 
doi:10.1101/793166 fatcat:phif3sc4nzbyjczavcketlxpza

Along signal paths: an empirical gene set approach exploiting pathway topology

Paolo Martini, Gabriele Sales, M. Sofia Massa, Monica Chiogna, Chiara Romualdi
2012 Nucleic Acids Research  
From a biological point of view only some portions of a pathway are expected to be altered; however, few methods using pathway topology have been proposed and none of them tries to identify the signal  ...  Gene set analysis using biological pathways has become a widely used statistical approach for gene expression analysis.  ...  We also thank the University of Padova for support of this work [CPDR075919 and CPDA119031 to C.R. and M.C.; CPDR070805 to G.S.].  ... 
doi:10.1093/nar/gks866 pmid:23002139 pmcid:PMC3592432 fatcat:pq2ot5fjlzg7jli6yhlc4lv634

multiGSEA: A GSEA-based pathway enrichment analysis for multi-omics data [article]

Sebastian Canzler, Jörg Hackermüller
2020 bioRxiv   pre-print
Here, we present the multiGSEA package aiding to calculate a combined GSEA-based pathway enrichment on multiple omics layer.  ...  Gaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods.  ...  Within the first step of the multiGSEA workflow, we make use of the graphite package to retrieve pathway definitions from up to eight public databases.  ... 
doi:10.1101/2020.07.17.208215 fatcat:tuvi55fgsvf3zoviley3n5l3qy

Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis

Punit Tyagi, Mangesh Bhide
2021 PeerJ  
, network topology-based pathway analysis, and multiple databases support (KEGG, Reactome, PANTHER, biocarta, NCI-Nature Pathway Interaction Database PharmGKB and STRINGdb) for extensive pathway enrichment  ...  In a nutshell, we present the OMnalysis as a well-organized user interface, supported by peer-reviewed R packages with updated databases for quick interpretation of the differential transcriptomics and  ...  It is compatible with any operating ACKNOWLEDGEMENTS We would like to thank Dr.  ... 
doi:10.7717/peerj.12415 pmid:34820180 pmcid:PMC8588854 fatcat:jnztz4ixlfcoleviz2iawpwsq4

RCy3: Network biology using Cytoscape from within R

Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
2019 F1000Research  
Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages.  ...  RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment.  ...  Acknowledgments We would like to acknowledge contributions by other developers on the original implementation of RCy3 by Paul Shannon, Tanja Muetze and Georgi Kolishkovski.  ... 
doi:10.12688/f1000research.20887.1 pmid:31819800 pmcid:PMC6880260 fatcat:ukb4gkakh5fgllz3fdeoayxiem

The metaRbolomics Toolbox in Bioconductor and beyond

Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski (+7 others)
2019 Metabolites  
and identification, and biochemical network and pathway analysis.  ...  In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.  ...  based on partial correlation and followed by a network topology analysis.  ... 
doi:10.3390/metabo9100200 pmid:31548506 pmcid:PMC6835268 fatcat:3b2gnq6qdrcfbcq6hewgoobdce

Integration of networks and pathways with StarBioTrek package

Claudia Cava, Isabella Castiglioni
2019 The R Journal  
StarBioTrek is an R package for the integration of biological pathways and networks which provides a series of functions to support the user in their analyses.  ...  In particular, it implements algorithms to identify pathways cross-talk networks and gene network drivers in pathways.  ...  Integration between pathways and networks from protein-protein interaction The function GetPathNet allows us to obtain a list of interacting genes (protein-protein interactions from graphite package) for  ... 
doi:10.32614/rj-2019-025 fatcat:wg3blqayvjc3bd2lioxomlap3q

RCy3: Network biology using Cytoscape from within R

Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
2019 F1000Research  
Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages.  ...  RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment.  ...  Acknowledgments We would like to acknowledge contributions by other developers on the original implementation of RCy3 by Paul Shannon, Tanja Muetze and Georgi Kolishkovski.  ... 
doi:10.12688/f1000research.20887.3 fatcat:rb7y3qtpxjes5cdmfbrosm7rku

RCy3: Network biology using Cytoscape from within R

Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
2019 F1000Research  
Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages.  ...  RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment.  ...  Acknowledgments We would like to acknowledge contributions by other developers on the original implementation of RCy3 by Paul Shannon, Tanja Muetze and Georgi Kolishkovski.  ... 
doi:10.12688/f1000research.20887.2 fatcat:wrs7hiwmsrglfk5xvzoitg752e

Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles

Enrica Calura, Paolo Martini, Gabriele Sales, Luca Beltrame, Giovanna Chiorino, Maurizio D'Incalci, Sergio Marchini, Chiara Romualdi
2014 Nucleic Acids Research  
To fill these gaps, we present 'micrographite' a new pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles.  ...  Here, micrographite is used to study and dissect the epithelial ovarian cancer gene and miRNA transcriptome defining and validating a new regulatory circuit related to ovarian cancer histotype specificity  ...  Pathway topologies derived from graphite, a Bioconductor package that we recently developed to store, manage and convert pathway annotations (from BioPax or KGML formats) into gene-gene networks. graphite  ... 
doi:10.1093/nar/gku354 pmid:24803669 pmcid:PMC4066781 fatcat:kk6lwxk3lnhkvak5ecmiidohrm
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