SignaFish: A Zebrafish-Specific Signaling Pathway Resource.
Understanding living systems requires an in-depth knowledge of the signaling networks that drive cellular homeostasis, regulate intercellular communication, and contribute to cell fates during development. Several resources exist to provide high-throughput data sets or manually curated interaction information from human or invertebrate model organisms. We previously developed SignaLink, a uniformly curated, multi-layered signaling resource containing information for human and for the model organisms nematode Caenorhabditis elegans and fruit fly Drosophila melanogaster. Until now, the use of the SignaLink database for zebrafish pathway analysis was limited. To overcome this limitation, we created SignaFish ( http://signafish.org ), a fish-specific signaling resource, built using the concept of SignaLink. SignaFish contains more than 200 curation-based signaling interactions, 132 further interactions listed in other resources, and it also lists potential miRNA-based regulatory connections for seven major signaling pathways. From the SignaFish website, users can reach other web resources, such as ZFIN. SignaFish provides signaling or signaling-related interactions that can be examined for each gene or downloaded for each signaling pathway. We believe that the SignaFish resource will serve as a novel navigating point for experimental design and evaluation for the zebrafish community and for researchers focusing on nonmodel fish species, such as cyclids.
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|2 Max Delbrück Center for Molecular Medicine , Berlin, Germany .
Kitti
K
Csályi
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|3 TGAC, The Genome Analysis Centre , Norwich Research Park, Norwich, United Kingdom .
Dávid
D
Fazekas
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .
Tamás
T
Kadlecsik
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|4 European Molecular Biology Laboratory-European Bioinformatics Institute , Hinxton, United Kingdom .|5 Wellcome Trust Genome Campus , Hinxton, United Kingdom .
Dénes
D
Türei
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .
Leila
L
Gul
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .
Balázs
B
Horváth
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|6 Department of Morphology and Physiology, Faculty of Health Sciences, Semmelweis University , Budapest, Hungary .|7 Centre for Molecular Informatics, University of Cambridge , Cambridge, United Kingdom .
Dezső
D
Módos
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|8 Gut Health and Food Safety Programme, Institute of Food Research , Norwich Research Park, Norwich, United Kingdom .
Amanda
A
Demeter
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .
Nóra
N
Pápai
6 Department of Morphology and Physiology, Faculty of Health Sciences, Semmelweis University , Budapest, Hungary .
Katalin
K
Lenti
9 Department of Medical Chemistry, Semmelweis University , Budapest, Hungary .
Péter
P
Csermely
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .
Tibor
T
Vellai
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|3 TGAC, The Genome Analysis Centre , Norwich Research Park, Norwich, United Kingdom .|8 Gut Health and Food Safety Programme, Institute of Food Research , Norwich Research Park, Norwich, United Kingdom .
Tamás
T
Korcsmáros
1 Department of Genetics, Eötvös Loránd University , Budapest, Hungary .|10 MTA-SE Lendület Nephrogenetic Laboratory , Budapest, Hungary .
Máté
M
Varga
D000818:Animals; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D020407:Internet; D015398:Signal Transduction; D015027:Zebrafish / Q000235:genetics*
database; miRNA; pathway; regulation; signaling network; zebrafish