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Reactome pathway analysis: a high-performance in-memory approach

Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner, Pablo Marin-Garcia, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob
2017 BMC Bioinformatics  
Conclusion: Through the use of highly optimised, in-memory data structures and algorithms, Reactome has achieved a stable, high performance pathway analysis service, enabling the analysis of genome-wide  ...  Results: Here, we present a new high-performance in-memory implementation of the well-established overrepresentation analysis method.  ...  Authors' contributions AF designed and implemented the proposed analysis method and was the major contributor in writing the manuscript. KS provided technical support and contributed in the writing.  ... 
doi:10.1186/s12859-017-1559-2 pmid:28249561 pmcid:PMC5333408 fatcat:b5h3jwolbvepjfiwp4dyecfi3a

ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis

Guanming Wu, Eric Dawson, Adrian Duong, Robin Haw, Lincoln Stein
2014 F1000Research  
This app provides a suite of features to assist biologists in performing pathway-and network-based data analysis in a biologically intuitive and user-friendly way.  ...  High-throughput experiments are routinely performed in modern biological studies. However, extracting meaningful results from massive experimental data sets is a challenging task for biologists.  ...  Acknowledgements We would like to thank Irina Kalatskaya, Christina Yung and other members in Dr. Lincoln Stein's group for software testing and many feedbacks.  ... 
doi:10.12688/f1000research.4431.1 pmid:25309732 pmcid:PMC4184317 fatcat:ge5zyllirjdqjlnxr7sddqo5lm

Reactome graph database: Efficient access to complex pathway data

Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Timothée Poisot
2018 PLoS Computational Biology  
By adopting graph database technology we are providing a high performance pathway data resource to the community.  ...  Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways.  ...  Reactome annotates processes in a consistent pathway model to create an online resource for researchers as a core reusable pathway dataset for systems biology approaches.  ... 
doi:10.1371/journal.pcbi.1005968 pmid:29377902 pmcid:PMC5805351 fatcat:7znckpg5a5cnrfeekcmakdieyy

Reactome: a knowledge base of biologic pathways and processes

Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu (+2 others)
2007 Genome Biology  
Reactome Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other  ...  Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets.  ...  Acknowledgements The development of Reactome is supported by a grant from the US National Institutes of Health (R01 HG002639), a grant from the European Reactions colored according to the most distant  ... 
doi:10.1186/gb-2007-8-3-r39 pmid:17367534 pmcid:PMC1868929 fatcat:pec5fg3igbgybpklqebttp4bqy

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis [article]

Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Nguyen, Antonio Fabregat, Henning Hermjakob
2020 bioRxiv   pre-print
Data from different species is automatically mapped to a common pathway space. Public data from ExpressionAtlas and Single Cell ExpressionAtlas can be directly integrated in the analysis.  ...  This may be linked to the presence of a specific subset of tumour associated IgG+ plasma cells that lack NFkappaB activation in scRNA-seq data from human melanoma.  ...  All pathway analyses are performed by the worker node in the ReactomeGSA system ( Figure 1 ). Reactome annotation focuses on human pathways.  ... 
doi:10.1101/2020.04.16.044958 fatcat:ge3sjihv6vef5cldmjmicuha4m

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Nguyen, Antonio Fabregat, Henning Hermjakob
2020 Molecular & Cellular Proteomics  
Data from different species is automatically mapped to a common pathway space. Public data from ExpressionAtlas and Single Cell ExpressionAtlas can be directly integrated in the analysis.  ...  This may be linked to the presence of a specific subset of tumour associated IgG+ plasma cells that lack NFkappaB activation in scRNA-seq data from human melanoma.  ...  We performed a comparative pathway analysis of the two TCGA cohorts that were also analysed by CPTAC using a global proteomics approach. transcriptomics measurements.  ... 
doi:10.1074/mcp.tir120.002155 pmid:32907876 pmcid:PMC7710148 fatcat:r3vg6zyu2jfuxoawflgrdwsmo4

ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis

Guanming Wu, Eric Dawson, Adrian Duong, Robin Haw, Lincoln Stein
2014 F1000Research  
This app provides a suite of features to assist biologists in performing pathway-and network-based data analysis in a biologically intuitive and user-friendly way.  ...  High-throughput experiments are routinely performed in modern biological studies. However, extracting meaningful results from massive experimental data sets is a challenging task for biologists.  ...  Acknowledgements We would like to thank Irina Kalatskaya, Christina Yung and other members in Dr. Lincoln Stein's group for software testing and many feedbacks.  ... 
doi:10.12688/f1000research.4431.2 pmid:25309732 pmcid:PMC4184317 fatcat:xk7tmedvkvefnivh3vrciysqvi

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

Sarah Mubeen, Charles Tapley Hoyt, André Gemünd, Martin Hofmann-Apitius, Holger Fröhlich, Daniel Domingo-Fernández
2019 Frontiers in Genetics  
We have performed an in-depth benchmarking of the impact of pathway database choice on statistical enrichment analysis and predictive modeling.  ...  We analyzed five cancer datasets using three major pathway databases and developed an approach to merge several databases into a single integrative one: MPath.  ...  Furthermore, performing the tasks described in this work comes with a high computational cost (Table 1) .  ... 
doi:10.3389/fgene.2019.01203 pmid:31824580 pmcid:PMC6883970 fatcat:u6m5nxsh6zghbnyoyz2cmmehrq

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models

Katharina Baum, Jagath C. Rajapakse, Francisco Azuaje
2019 F1000Research  
We apply SBM-based analysis independently to three correlation-based networks of breast cancer data originating from high-throughput measurements of different molecular layers: either transcriptomics,  ...  Biological entities such as genes, promoters, mRNA, metabolites or proteins do not act alone, but in concert in their network context.  ...  In order to assess the usefulness of this approach, the authors evaluate the biological meaning of the modules obtained performing a functional enrichment analysis for each module of the network.  ... 
doi:10.12688/f1000research.18705.2 fatcat:tq5vad6u4zhi5mgyjhkbxanwou

Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer

Xi Yang, Quan Qi, Yuefen Pan, Qing Zhou, Yinhang Wu, Jing Zhuang, Jiamin Xu, Mingyue Pan, Shuwen Han
2021 Frontiers in Immunology  
tissue and 1252 T cells from the peripheral blood of CRC patients, unsupervised clustering analysis was performed to identify functionally distinct T cell populations, followed by correlations and ligand-receptor  ...  A larger number of tumor-infiltrating CD8+ Tex (88.94%) cells were found in the colon cancer than in the rectal cancer (11.06%).  ...  AUTHOR CONTRIBUTIONS All authors participated in the conception and design, data acquisition, analysis and interpretation of the study. XY, QQ, YP, and QZ wrote the manuscript.  ... 
doi:10.3389/fimmu.2020.620196 pmid:33584715 pmcid:PMC7873865 fatcat:pipw4uiojzbgdpsio22hox5coe

A human functional protein interaction network and its application to cancer data analysis

Guanming Wu, Xin Feng, Lincoln Stein
2010 Genome Biology  
A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system.  ...  Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases.  ...  This work was supported by a NIH grant (P41 HG003751).  ... 
doi:10.1186/gb-2010-11-5-r53 pmid:20482850 pmcid:PMC2898064 fatcat:vntehsevq5gcrfppuzcikesvde

Transcriptomic analysis of probable asymptomatic and symptomatic Alzheimer brains

Hamel Patel, Angela K. Hodges, Charles Curtis, Sang Hyuck Lee, Claire Troakes, Richard J.B. Dobson, Stephen J Newhouse
2019 Brain, behavior, and immunity  
Co-expression analysis identified an overactivation of the brain "glutamate-glutamine cycle", and disturbances in the brain energy pathways in both AsymAD and AD subjects, while the connectivity of key  ...  Differential expression analysis identified a significant increase of transcriptomic activity in the frontal cortex of AsymAD subjects, suggesting fundamental changes in AD may initially begin within the  ...  Using DE analysis, coupled with a "systems-biology" approach, we were able to detect disturbances in the energy pathways and the "glutamate-glutamine cycle" in the brains of subjects with mild and severe  ... 
doi:10.1016/j.bbi.2019.05.009 pmid:31063847 fatcat:yyngiay3jva77pv7wvsdgyqlp4

Transcriptomic analysis of probable asymptomatic and symptomatic Alzheimer brains [article]

Hamel Patel, Angela K Hodges, Charles Curtis, Sang hyuck Hyuck Lee, Claire Troakes, Richard Dobson, Stephen J Newhouse
2019 biorxiv/medrxiv   pre-print
Co-expression analysis identified an overactivation of the brain glutamate-glutamine cycle, and disturbances in the brain energy pathways in both AsymAD and AD subjects, while connectivity of key hub genes  ...  Differential expression analysis identified a significant increase of transcriptomic activity in the frontal cortex of AsymAD subjects, suggesting fundamental changes in AD may initially begin within the  ...  Using DE analysis, coupled with a "systems-biology" approach, we were able to detect disturbances in the energy pathways and the "glutamate-glutamine cycle" in the brains of subjects with mild and severe  ... 
doi:10.1101/621912 fatcat:bkrymaf56nczbhxahhoz6rna5u

DecoPath: A web application for decoding pathway enrichment analysis [article]

Sarah Mubeen, Vinay Srinivas Bharadhwaj, Yojana Gadiya, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Daniel Domingo-Fernández
2021 bioRxiv   pre-print
These shortcomings call for approaches that investigate the differences and agreements across databases and enrichment methods as their selection in the experimental design of a pathway analysis can be  ...  a crucial first step in ensuring the results of such an analysis are meaningful.  ...  Acknowledgements We are very grateful to the curators of KEGG, Reactome, WikiPathways, and PathBank for generating the raw content which was used in this work.  ... 
doi:10.1101/2021.05.22.445243 fatcat:fojdobmd4ravbkkeixoxi5g2w4

pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species

2019 Nucleic Acids Research  
A total of 6401 core and ortholog pathways have been curated from the literature or by annotating orthologs of human proteins in the literature-curated pathways.  ...  pathway-enrichment analysis.  ...  PathDIP 4 provides users a pipeline through integration of mirDIP (33), a miRNA-target database, and pathDIP 4, to perform pathway annotation and enrichment analysis of miRNA targets in one step.  ... 
doi:10.1093/nar/gkz989 pmid:31733064 pmcid:PMC7145646 fatcat:ehdvbpx7uvbidds5n7nrjte3zq
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