CerebralWeb: a Cytoscape.js']js plug-in to visualize networks stratified by subcellular localization

被引：6
作者：
Frias, Silvia [1 ]
Bryan, Kenneth [2 ]
Brinkman, Fiona S. L. [1 ]
Lynn, David J. [2 ,3 ]
机构：
[1] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada
[2] EMBL Australia Grp, South Australian Hlth & Med Res Inst, Adelaide, SA 5000, Australia
[3] Flinders Univ S Australia, Sch Med, Bedford Pk, SA 5042, Australia
来源：
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2015年
关键词：
INNATEDB; BIOLOGY;
D O I：
10.1093/database/bav041
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualization of molecular interaction networks stratified based on subcellular localization or other user-supplied annotation. The application is designed to be easily integrated into any website and is configurable to support customized network visualization. CerebralWeb also supports the automatic retrieval of Cerebral-compatible localizations for human, mouse and bovine genes via a web service and enables the automated parsing of Cytoscape compatible XGMML network files. CerebralWeb currently supports embedded network visualization on the InnateDB (www.innatedb.com) and Allergy and Asthma Portal (allergen.innatedb.com) database and analysis resources.
引用
收藏
页数：4
相关论文
共 6 条
  • [1] 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
  • [2] Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
    Barsky, Aaron
    Gardy, Jennifer L.
    Hancock, Robert E. W.
    Munzner, Tamara
    [J]. BIOINFORMATICS, 2007, 23 (08) : 1040 - 1042
  • [3] InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation
    Breuer, Karin
    Foroushani, Amir K.
    Laird, Matthew R.
    Chen, Carol
    Sribnaia, Anastasia
    Lo, Raymond
    Winsor, Geoffrey L.
    Hancock, Robert E. W.
    Brinkman, Fiona S. L.
    Lynn, David J.
    [J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D1228 - D1233
  • [4] Cytoscape Web: an interactive web-based network browser
    Lopes, Christian T.
    Franz, Max
    Kazi, Farzana
    Donaldson, Sylva L.
    Morris, Quaid
    Bader, Gary D.
    [J]. BIOINFORMATICS, 2010, 26 (18) : 2347 - 2348
  • [5] InnateDB: facilitating systems-level analyses of the mammalian innate immune response
    Lynn, David J.
    Winsor, Geoffrey L.
    Chan, Calvin
    Richard, Nicolas
    Laird, Matthew R.
    Barsky, Aaron
    Gardy, Jennifer L.
    Roche, Fiona M.
    Chan, Timothy H. W.
    Shah, Naisha
    Lo, Raymond
    Naseer, Misbah
    Que, Jaimmie
    Yau, Melissa
    Acab, Michael
    Tulpan, Dan
    Whiteside, Matthew D.
    Chikatamarla, Avinash
    Mah, Bernadette
    Munzner, Tamara
    Hokamp, Karsten
    Hancock, Robert E. W.
    Brinkman, Fiona S. L.
    [J]. MOLECULAR SYSTEMS BIOLOGY, 2008, 4 (1)
  • [6] Cytoscape: A software environment for integrated models of biomolecular interaction networks
    Shannon, P
    Markiel, A
    Ozier, O
    Baliga, NS
    Wang, JT
    Ramage, D
    Amin, N
    Schwikowski, B
    Ideker, T
    [J]. GENOME RESEARCH, 2003, 13 (11) : 2498 - 2504
1