NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies

被引:17
作者
Zuniga-Leon, Eduardo [1 ]
Carrasco-Navarro, Ulises [1 ]
Fierro, Francisco [1 ]
机构
[1] Univ Autonoma Metropolitana, Unidad Iztapalapa, Dept Biotecnol, Ciudad De Mexico 09340, Mexico
来源
GENES | 2018年 / 9卷 / 12期
关键词
Gene Ontology; KEGG pathways; enrichment analysis; proteomic analysis; plot visualization; GOA DATABASE; SETS;
D O I
10.3390/genes9120569
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representation or enrichment tools have played a successful role in the functional analysis of large gene/protein lists, which is evidenced by thousands of publications citing these tools. However, in most cases the results of these analyses are long lists of biological terms associated to proteins that are difficult to digest and interpret. Here we present NeVOmics, Network-based Visualization for Omics, a functional enrichment analysis tool that identifies statistically over-represented biological terms within a given gene/protein set. This tool provides a hypergeometric distribution test to calculate significantly enriched biological terms, and facilitates analysis on cluster distribution and relationship of proteins to processes and pathways. NeVOmics is adapted to use updated information from the two main annotation databases: Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). NeVOmics compares favorably to other Gene Ontology and enrichment tools regarding coverage in the identification of biological terms. NeVOmics can also build different network-based graphical representations from the enrichment results, which makes it an integrative tool that greatly facilitates interpretation of results obtained by OMICs approaches. NeVOmics is freely accessible at https://github.com/bioinfproject/bioinfo/.
引用
收藏
页数:14
相关论文
共 26 条
  • [1] [Anonymous], 2009, INT ASS ADV ART INT
  • [2] Gene Ontology: tool for the unification of biology
    Ashburner, M
    Ball, CA
    Blake, JA
    Botstein, D
    Butler, H
    Cherry, JM
    Davis, AP
    Dolinski, K
    Dwight, SS
    Eppig, JT
    Harris, MA
    Hill, DP
    Issel-Tarver, L
    Kasarskis, A
    Lewis, S
    Matese, JC
    Richardson, JE
    Ringwald, M
    Rubin, GM
    Sherlock, G
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [3] UniProt: the universal protein knowledgebase
    Bateman, Alex
    Martin, Maria Jesus
    O'Donovan, Claire
    Magrane, Michele
    Alpi, Emanuele
    Antunes, Ricardo
    Bely, Benoit
    Bingley, Mark
    Bonilla, Carlos
    Britto, Ramona
    Bursteinas, Borisas
    Bye-A-Jee, Hema
    Cowley, Andrew
    Da Silva, Alan
    De Giorgi, Maurizio
    Dogan, Tunca
    Fazzini, Francesco
    Castro, Leyla Garcia
    Figueira, Luis
    Garmiri, Penelope
    Georghiou, George
    Gonzalez, Daniel
    Hatton-Ellis, Emma
    Li, Weizhong
    Liu, Wudong
    Lopez, Rodrigo
    Luo, Jie
    Lussi, Yvonne
    MacDougall, Alistair
    Nightingale, Andrew
    Palka, Barbara
    Pichler, Klemens
    Poggioli, Diego
    Pundir, Sangya
    Pureza, Luis
    Qi, Guoying
    Rosanoff, Steven
    Saidi, Rabie
    Sawford, Tony
    Shypitsyna, Aleksandra
    Speretta, Elena
    Turner, Edward
    Tyagi, Nidhi
    Volynkin, Vladimir
    Wardell, Tony
    Warner, Kate
    Watkins, Xavier
    Zaru, Rossana
    Zellner, Hermann
    Xenarios, Ioannis
    [J]. NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) : D158 - D169
  • [4] The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
    Camon, E
    Magrane, M
    Barrell, D
    Lee, V
    Dimmer, E
    Maslen, J
    Binns, D
    Harte, N
    Lopez, R
    Apweiler, R
    [J]. NUCLEIC ACIDS RESEARCH, 2004, 32 : D262 - D266
  • [5] GeneMerge - post-genomic analysis, data mining, and hypothesis testing
    Castillo-Davis, CI
    Hartl, DL
    [J]. BIOINFORMATICS, 2003, 19 (07) : 891 - 892
  • [6] UpSetR: an R package for the visualization of intersecting sets and their properties
    Conway, Jake R.
    Lex, Alexander
    Gehlenborg, Nils
    [J]. BIOINFORMATICS, 2017, 33 (18) : 2938 - 2940
  • [7] Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation
    Dolan, Whitney L.
    Chapple, Clint
    [J]. G3-GENES GENOMES GENETICS, 2018, 8 (09): : 3093 - 3108
  • [8] GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    Eden, Eran
    Navon, Roy
    Steinfeld, Israel
    Lipson, Doron
    Yakhini, Zohar
    [J]. BMC BIOINFORMATICS, 2009, 10
  • [9] Contribution of platelets to tumour metastasis
    Gay, Laurie J.
    Felding-Habermann, Brunhilde
    [J]. NATURE REVIEWS CANCER, 2011, 11 (02) : 123 - 134
  • [10] circlize implements and enhances circular visualization in R
    Gu, Zuguang
    Gu, Lei
    Eils, Roland
    Schlesner, Matthias
    Brors, Benedikt
    [J]. BIOINFORMATICS, 2014, 30 (19) : 2811 - 2812