Filters








126 Hits in 1.3 sec

Automation of ReactomeFIViz via CyREST API

Fred Loney, Guanming Wu
2018 F1000Research  
ReactomeFIViz is a Cytoscape app, providing features for researchers to perform pathway-and network-based data analysis and visualization by leveraging manually curated Reactome pathways and highly reliable  ...  We describe a use case to demonstrate the use of this API in a Python-based notebook, and believe the new API will provide the community a convenient and powerful tool to perform pathway-and network-based  ...  Acknowledgments We would like to thank the whole Reactome team for providing the foundation for ReactomeFIViz.  ... 
doi:10.12688/f1000research.14776.2 fatcat:xwe2vhmcffgtha6vdmh6t54ece

Automation of ReactomeFIViz via CyREST API

Fred Loney, Guanming Wu
2018 F1000Research  
ReactomeFIViz is a Cytoscape app, providing features for researchers to perform pathway-and network-based data analysis and visualization by leveraging manually curated Reactome pathways and highly reliable  ...  We describe a use case to demonstrate the use of this API in a Python-based notebook, and believe the new API will provide the community a convenient and powerful tool to perform pathway-and network-based  ...  Pathway enrichment analysis was performed to collect pathways not shared between them.  ... 
doi:10.12688/f1000research.14776.1 pmid:29946442 pmcid:PMC5998009 fatcat:l2y2r3trdzayxeyb75fcjcosve

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.  ...  Biologists can use this app to uncover network and pathway patterns related to their studies, search for gene signatures from gene expression data sets, reveal pathways significantly enriched by genes  ...  Pathway analysis features Pathway Enrichments Pathway Activities Perform pathway enrichment analysis Perform probabilistic graphical model based pathway modeling Input Gene_List MAF CNV Gene_Expression  ... 
doi:10.12688/f1000research.4431.2 pmid:25309732 pmcid:PMC4184317 fatcat:xk7tmedvkvefnivh3vrciysqvi

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.  ...  Biologists can use this app to uncover network and pathway patterns related to their studies, search for gene signatures from gene expression data sets, reveal pathways significantly enriched by genes  ...  perform pathway enrichment analysis on a list of genes.  ... 
doi:10.12688/f1000research.4431.1 pmid:25309732 pmcid:PMC4184317 fatcat:ge5zyllirjdqjlnxr7sddqo5lm

Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz

Aurora S. Blucher, Shannon K. McWeeney, Lincoln Stein, Guanming Wu
2019 F1000Research  
profiles, using a pathway or network perspective.  ...  This context can be provided using pathways, which are process-oriented representations of biological reactions, or biological networks, which represent pathway-spanning interactions among genes, proteins  ...  Julio Saez-Rodriguez and Attila Gábor at RWTH Aachen University for sharing the Java code of the CytoCopter App and feedback on ReactomeFIViz. We also thank Andy Kaempf and Dr.  ... 
doi:10.12688/f1000research.19592.1 pmid:31372215 pmcid:PMC6644836 fatcat:ghlhbtvc3jcu5iqn5owdwsaum4

Rare copy number variants and congenital heart defects in the 22q11.2 deletion syndrome

Elisabeth E. Mlynarski, Michael Xie, Deanne Taylor, Molly B. Sheridan, Tingwei Guo, Silvia E. Racedo, Donna M. McDonald-McGinn, Eva W. C. Chow, Jacob Vorstman, Ann Swillen, Koen Devriendt, Jeroen Breckpot (+19 others)
2016 Human Genetics  
Rare CNV analysis was performed using Affymetrix SNP Array 6.0 data from 946 22q11DS subjects with CHDs (n = 607) or with normal cardiac anatomy (n = 339).  ...  Compliance with ethical standards Ethical approval All procedures performed in studies involving human participants were in accordance with the ethical standards of the institution and/or national research  ...  A pathway enrichment analysis was run for each individual network module using the ReactomeFIViz built-in "Analyze module functions" tool.  ... 
doi:10.1007/s00439-015-1623-9 pmid:26742502 pmcid:PMC4896312 fatcat:u75hym4ltfbrniixs47d53r6py

Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces

Francesco Raimondi, Joshua G. Burkhart, Matthew J. Betts, Robert B. Russell, Guanming Wu
2021 F1000Research  
Our analysis also uncovered several druggable processes (e.g. GPCR signalling pathways) containing enriched reactions, providing support for new off-label therapeutic options.  ...  In addition, we provided a software tool for users to explore and browse the analysis results in a multi-scale perspective starting from pathways and reactions to protein-protein interactions and protein  ...  Pathway and network knowledgebases provide the foundation to perform pathway and network-based analysis.  ... 
doi:10.12688/f1000research.74395.1 fatcat:trii7fll2fexvppyugnvdhkla4

Genes and pathways identified in thyroid carcinoma based on bioinformatics analysis

J. W. YU, W. MAI, Y. L. CUI, L. Y. KONG
2016 Neoplasma (Bratislava)  
The intersections DEGs were performed by functional enrichment and transcription factor (TF) prediction analyses. These specific DEGs were performed by pathway enrichment analysis.  ...  With the obtained DEGs, we performed gene functional interaction (FI) network analysis.  ...  Subsequently, the DEGs involved in the modules were performed pathway enrichment analysis (FDR < 0.05).  ... 
doi:10.4149/neo_2016_409 pmid:27268919 fatcat:icsz7huyi5hstcvmccrg24xkxa

Possible Molecular Markers for the Diagnosis of Pancreatic Ductal Adenocarcinoma

Quan Shen, Miao Yu, Jiang-Kun Jia, Wen-Xi Li, Yu-Wei Tian, Huan-Zhou Xue
2018 Medical Science Monitor  
performed.  ...  The ribosome pathway and the spliceosome pathway were significantly enriched in cluster 1 and cluster 2, respectively.  ...  Pathway analysis of functional network module and PPI network analysis Pathways significantly enriched by each module are shown in Table 2 .  ... 
doi:10.12659/msm.906313 pmid:29671412 pmcid:PMC5928849 fatcat:wngjecr735gmng5yibhg7wk7zq

Detection of differentially expressed genes involved in osteoarthritis pathology

Honglai Tian
2018 Journal of Orthopaedic Surgery and Research  
Significant network modules were identified using ReactomeFIViz, and the pathway of each module was enriched using MATHT. In addition, TFs in the DEGs were identified.  ...  Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed with Multifaceted Analysis Tool for Human Transcriptome (MATHT).  ...  Significant network modules were identified using ReactomeFIViz, and the pathway of each module was enriched using MATHT.  ... 
doi:10.1186/s13018-018-0734-0 pmid:29514675 pmcid:PMC5842536 fatcat:qwxv6codmfgrhgxzednvontjku

Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes

Jaideep Chakladar, Wei Tse Li, Michael Bouvet, Eric Y. Chang, Jessica Wang-Rodriguez, Weg M. Ongkeko
2019 Cancers  
The dysregulation profiles of the subtypes were compared using functional pathways clustering and correlations to relevant clinical variables, genomic alterations, and microRNA regulation.  ...  RNA-sequencing data from The Cancer Genome Atlas (TCGA) were used to identify dysregulated genes in each variant.  ...  [15] , and performed differential expression analysis on niFVPTC vs iFVPTC samples ( Figure S1 ).  ... 
doi:10.3390/cancers11081179 pmid:31443155 pmcid:PMC6721495 fatcat:7wnb4kmr45hsvm3bfdvjtgjqo4

Network-Based Predictors of Progression in Head and Neck Squamous Cell Carcinoma

Nasim Sanati, Ovidiu D. Iancu, Guanming Wu, James E. Jacobs, Shannon K. McWeeney
2018 Frontiers in Genetics  
Pathway Enrichment Analysis of Enriched Modules We performed a pathway enrichment analysis of the modules enriched in DE/DV/DW affected genes.  ...  Pathway Enrichment Analysis Consensus modules' pathway enrichment analysis was assessed utilizing ReactomeFIViz, the Reactome Cytoscape app (ReactomeFIViz-ReactomeWiki 5 ; Wu et al., 2014) .  ...  AUTHOR CONTRIBUTIONS NS conceived of the study and developed or extended code, performed analysis and wrote the majority of the manuscript. GW, OI, and SM provided input into the design and analyses.  ... 
doi:10.3389/fgene.2018.00183 pmid:29910823 pmcid:PMC5992410 fatcat:436ubt3orfeinmradam3m74aw4

Identifying key genes associated with acute myocardial infarction

Ming Cheng, Shoukuan An, Junquan Li
2017 Medicine  
Then, DEGs in each module were subjected to pathway enrichment analysis using DAVID. MiRNAs and transcription factors predicted to regulate target DEGs were identified.  ...  A FI network consists of 21 modules and DEGs in 12 modules were significantly enriched in pathways.  ...  in 2 pathways each; DEGs in Module 2, 4, 7, 11, and 19 were enriched in 1 pathway each Figure 1 . 1 Pathway enrichment analysis of differentially expressed genes A, pathways enriched by the upregulated  ... 
doi:10.1097/md.0000000000007741 pmid:29049183 pmcid:PMC5662349 fatcat:o2wzft26tve23haepffhc6mnje

Screening for Key Pathways Associated with the Development of Osteoporosis by Bioinformatics Analysis

Yanqing Liu, Yueqiu Wang, Yanxia Zhang, Zhiyong Liu, Hongfei Xiang, Xianbo Peng, Bohua Chen, Guyou Jia
2017 BioMed Research International  
Lysosome pathway was the significantly enriched pathways enriched by intersection genes.  ...  KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses were carried out.  ...  KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses were carried out. Besides, Venn diagram analysis and gene functional interaction (FI) network analysis were performed.  ... 
doi:10.1155/2017/8589347 pmid:28466021 pmcid:PMC5390640 fatcat:f7zsffntybfknh3dbl3qj76o6e

Identification of potential gene targets in systemic vasculitis using DNA microarray analysis

Yiwen Feng, Miao Zheng, Shujie Gan, Lei Zhang, Zhong Wan, Yanping Zhang, Qin Qian, Jingdong Tang
2017 Molecular Medicine Reports  
A total of 173 up-and 93 downregulated genes were identified, which were mainly associated with immune response pathways.  ...  Differentially expressed genes (DEGs) were screened in systemic vasculitis compared with controls using BRB ArrayTools, followed by the construction of a protein-protein interaction (PPI) network using  ...  GO and pathway enrichment analysis. GO and pathway analysis demonstrated that up-and downregulated genes were associated with different GO terms and pathways.  ... 
doi:10.3892/mmr.2017.6455 pmid:28440408 pmcid:PMC5436278 fatcat:th3ffg3m2jcxvhgc6w2qju4fmu
« Previous Showing results 1 — 15 out of 126 results