Advanced search
Publication Cover
Journal of Extracellular Vesicles Volume 6, 2017 - Issue 1
Journal homepage
5,217
Views
241
CrossRef citations to date
0
Altmetric
Short Communication

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Mohashin PathanDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, AustraliaORCID Iconhttp://orcid.org/0000-0001-7071-0022View further author information
ORCID Icon,
Shivakumar KeerthikumarDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, AustraliaORCID Iconhttp://orcid.org/0000-0001-9865-9767View further author information
ORCID Icon,
David ChisangaDepartment of Computer Science and Information Technology, La Trobe University, Melbourne, AustraliaORCID Iconhttp://orcid.org/0000-0002-0421-3957View further author information
ORCID Icon,
Riccardo AlessandroDepartment of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, ItalyView further author information
,
Ching-Seng AngThe Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, AustraliaView further author information
,
Philip AskenaseSection of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USAView further author information
,
Arsen O. BatagovBioinformatics Institute, A*STAR, Singapore, SingaporeView further author information
,
Alberto Benito-MartinChildren’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USAView further author information
,
Giovanni CamussiDepartment of Medical Science, University of Torino, Medical School, Torino, ItalyView further author information
,
Aled ClaytonDivision of Cancer and Genetics, School of Medicine, Cardiff University, Velindre Cancer Centre, Cardiff, UKORCID Iconhttp://orcid.org/0000-0002-3087-9226View further author information
ORCID Icon,
Federica CollinoDepartment of Medical Science, University of Torino, Medical School, Torino, Italy;Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, BrazilView further author information
,
Dolores Di VizioDivision of Cancer Biology and Therapeutics, Departments of Surgery, Biomedical Sciences and Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USAView further author information
,
Juan Manuel Falcon-PerezExosomes Lab, Metabolomics Unit, CIC bioGUNE, CIBERehd. Bizkaia Technological Park, Derio 48160, Bikaia and IKERBASQUE Research Foundation, Bilbao, SPAINView further author information
,
Pedro FonsecaDepartment of Oncology-Pathology, Cancer Centrum Karolinska, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, SwedenORCID Iconhttp://orcid.org/0000-0001-9685-8092View further author information
ORCID Icon,
Pamali FonsekaDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, AustraliaORCID Iconhttp://orcid.org/0000-0003-1420-4103View further author information
ORCID Icon,
Simona FontanaDepartment of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, ItalyORCID Iconhttp://orcid.org/0000-0003-4681-2170View further author information
ORCID Icon,
Yong Song GhoDepartment of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of KoreaView further author information
,
An HendrixLaboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, BelgiumView further author information
,
Esther Nolte-’t HoenDepartment of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The NetherlandsView further author information
,
Nunzio IraciDepartment of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy;Department of Clinical Neurosciences, Wellcome Trust-Medical Research Council Stem Cell Institute and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UKORCID Iconhttp://orcid.org/0000-0003-2146-9329View further author information
ORCID Icon,
Kenneth KastaniegaardLaboratory for Medical Mass Spectrometry, Department of Health Science and Technology, Aalborg University, Aalborg, DenmarkORCID Iconhttp://orcid.org/0000-0003-3806-5638View further author information
ORCID Icon,
Thomas KislingerPrincess Margaret Cancer Centre, Toronto, CanadaView further author information
,
Joanna KowalInstitut Curie, PSL Research University, INSERM U932, Paris, FranceORCID Iconhttp://orcid.org/0000-0001-7849-6040View further author information
ORCID Icon,
Igor V. KurochkinBioinformatics Institute, A*STAR, Singapore, SingaporeView further author information
,
Tommaso LeonardiDepartment of Clinical Neurosciences, Wellcome Trust-Medical Research Council Stem Cell Institute and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK;European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UKORCID Iconhttp://orcid.org/0000-0002-4449-1863View further author information
ORCID Icon,
Yaxuan LiangCardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USAView further author information
,
Alicia LlorenteDepartment of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway;Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, NorwayView further author information
,
Taral R. LunavatKrefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, SwedenView further author information
,
Sayantan MajiDepartment of Transplantation, Mayo Clinic, Jacksonville, FL, USAView further author information
,
Francesca MonteleoneDepartment of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, ItalyView further author information
,
Anders ØverbyeDepartment of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway;Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, NorwayORCID Iconhttp://orcid.org/0000-0002-2564-3729View further author information
ORCID Icon,
Theocharis PanaretakisDepartment of Oncology-Pathology, Cancer Centrum Karolinska, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, SwedenView further author information
,
Tushar PatelDepartment of Transplantation, Mayo Clinic, Jacksonville, FL, USAView further author information
,
Héctor PeinadoChildren’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA;Microenvironment and Metastasis Group, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, SpainORCID Iconhttp://orcid.org/0000-0002-4256-3413View further author information
ORCID Icon,
Stefano PluchinoDepartment of Clinical Neurosciences, Wellcome Trust-Medical Research Council Stem Cell Institute and National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UKView further author information
,
Simona PrincipePrincess Margaret Cancer Centre, Toronto, CanadaORCID Iconhttp://orcid.org/0000-0003-4681-2170View further author information
ORCID Icon,
Goran RonquistDepartment of Medical Sciences, Uppsala University, Uppsala, SwedenView further author information
,
Felix RoyoExosomes Lab, Metabolomics Unit, CIC bioGUNE, CIBERehd. Bizkaia Technological Park, Derio 48160, Bikaia and IKERBASQUE Research Foundation, Bilbao, SPAINView further author information
,
Susmita SahooCardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USAView further author information
,
Cristiana SpinelliDivision of Cancer Biology and Therapeutics, Departments of Surgery, Biomedical Sciences and Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USAORCID Iconhttp://orcid.org/0000-0002-4655-6173View further author information
ORCID Icon,
Allan StensballeLaboratory for Medical Mass Spectrometry, Department of Health Science and Technology, Aalborg University, Aalborg, DenmarkView further author information
,
Clotilde ThéryInstitut Curie, PSL Research University, INSERM U932, Paris, FranceView further author information
,
Martijn J.C. van HerwijnenDepartment of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The NetherlandsView further author information
,
Marca WaubenDepartment of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The NetherlandsView further author information
,
Joanne L. WeltonDepartment of Biomedical Sciences, Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UKORCID Iconhttp://orcid.org/0000-0002-1445-245XView further author information
ORCID Icon,
Kening ZhaoDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, AustraliaView further author information
&
Suresh MathivananDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, AustraliaCorrespondence[email protected]
View further author information
 show all
Article: 1321455 | Received 22 Feb 2017, Published online: 26 May 2017

Figures & data

Figure 1. Features available in FunRich. FunRich is a free standalone functional enrichment analysis tool. Users can obtain customisable graphs, charts, interaction networks and heatmaps. All features of these images including color and font is editable and thus allows for quick representation of analysis. In spite of its ease of use, the images produced are of publication quality and can be directly imported into manuscripts. In addition, users have multiple background database options for more than 13,320 species. One of the features requested by the community is the option to update the background databases in real time. FunRich now allows the users to download data from UniProt, Reactome and Gene Ontology databases in real time. Furthermore, users can perform analyses in the context of biological pathways, gene ontology categories, protein domains, site of expression, cancer signatures, transcription factors, clinical phenotypes, extracellular vesicles, miRNA enrichment, protein interaction network and cross database accession conversion. The custom database option allows users to use any data type for any species thereby allowing for flexibility.

Figure 1. Features available in FunRich. FunRich is a free standalone functional enrichment analysis tool. Users can obtain customisable graphs, charts, interaction networks and heatmaps. All features of these images including color and font is editable and thus allows for quick representation of analysis. In spite of its ease of use, the images produced are of publication quality and can be directly imported into manuscripts. In addition, users have multiple background database options for more than 13,320 species. One of the features requested by the community is the option to update the background databases in real time. FunRich now allows the users to download data from UniProt, Reactome and Gene Ontology databases in real time. Furthermore, users can perform analyses in the context of biological pathways, gene ontology categories, protein domains, site of expression, cancer signatures, transcription factors, clinical phenotypes, extracellular vesicles, miRNA enrichment, protein interaction network and cross database accession conversion. The custom database option allows users to use any data type for any species thereby allowing for flexibility.
Supplemental material

Supplementary_table_1.pdf

Download PDF (102.8 KB)

Related Research Data

Identification of Potential Crucial Genes and Key Pathways in Breast Cancer Using Bioinformatic Analysis
Source: Frontiers Media SA
Systems biology approaches to investigating the roles of extracellular vesicles in human diseases.
Source: Springer Science and Business Media LLC
Alternative splicing links histone modifications to stem cell fate decision.
Source: BMC
Proteomic Profiling of Exosomes Secreted by Breast Cancer Cells with Varying Metastatic Potential.
Source: Wiley
Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
Source: Nature Publishing Group
Impact of outdated gene annotations on pathway enrichment analysis
Source: Springer Science and Business Media LLC
The fungal-specific Hda2 and Hda3 proteins regulate morphological switches in the human fungal pathogen Candida albicans.
Source: bioRxiv
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Source: Proceedings of the National Academy of Sciences
Mechanism Investigation of Tagetes patula L. against Chronic Nonbacterial Prostatitis by Metabolomics and Network Pharmacology.
Source: MDPI AG
Potential biomarkers of ductal carcinoma in situ progression
Source: Springer Science and Business Media LLC
Best practice of identification and proteomic analysis of extracellular vesicles in human health and disease.
Source: Informa UK Limited
Immune Suppressive Extracellular Vesicle Proteins of Leptopilina heterotoma Are Encoded in the Wasp Genome.
Source: Oxford University Press
Stem cell-derived extracellular vesicles inhibit and revert fibrosis progression in a mouse model of diabetic nephropathy
Source: Springer Science and Business Media LLC
Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model
Source: Springer Science and Business Media LLC
Communication of prostate cancer cells with bone cells via extracellular vesicle RNA; a potential mechanism of metastasis
Source: Springer Nature
Methylation analysis highlights novel prognostic criteria in human-metastasized melanoma.
Source: Wiley
Bovine milk-derived exosomes from colostrum are enriched with proteins implicated in immune response and growth.
Source: Springer Science and Business Media LLC
Predicting MicroRNA Target Genes and Identifying Hub Genes in IIA Stage Colon Cancer Patients Using Bioinformatics Analysis.
Source: Hindawi Limited
Deduction of Novel Genes Potentially Involved in Keratinocytes of Type 2 Diabetes Using Next-Generation Sequencing and Bioinformatics Approaches.
Source: Multidisciplinary Digital Publishing Institute
Extracellular vesicles secreted by Saccharomyces cerevisiae are involved in cell wall remodelling.
Source: Nature Publishing Group
Exosomes from metastatic cancer cells transfer amoeboid phenotype to non-metastatic cells and increase endothelial permeability: their emerging role in tumor heterogeneity
Source: Springer Science and Business Media LLC
Exosomes from N-Myc amplified neuroblastoma cells induce migration and confer chemoresistance to non-N-Myc amplified cells: implications of intra-tumour heterogeneity
Source: Informa UK Limited
FunRich: An open access standalone functional enrichment and interaction network analysis tool
Source: Wiley
Genomic analyses identify molecular subtypes of pancreatic cancer
Source: Springer Science and Business Media LLC
Epigenetic profiling and mRNA expression reveal candidate genes as biomarkers for colorectal cancer.
Source: Wiley
Identification and validation of key genes associated with non-small-cell lung cancer.
Source: Wiley
Proteomic Analysis in Morquio A Cells Treated with Immobilized Enzymatic Replacement Therapy on Nanostructured Lipid Systems
Source: MDPI
Analysis of differentially expressed genes among human hair follicle–derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes
Source: BMC
Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis
Source: Portland Press Ltd.

Linking provided by 

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.