SignaFish: A Zebrafish-Specific Signaling Pathway Resource

Csályi, Kitti; Fazekas, Dávid; Kadlecsik, Tamás; Türei, Dénes; Gul, Lejla; Horváth, Balázs; Módos, Dezső; Demeter, Attila; Pápai, Nóra; Lenti, Katalin; Csermely, Péter; Vellai, Tibor; Korcsmáros, Tamás; Varga, Máté

doi:10.1089/zeb.2016.1277

Cited by 7 publications

(6 citation statements)

References 12 publications

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“…ZFIN links to SignaFish for interactions when known. 44 Antibodies targeting the gene, plasmids with the coding region at Addgene, and constructs containing the gene are linked in their respective sections. There is also a section that links BACs, ESTs, and cDNAs associated with the gene as well as a section that links to sequences at GenBank and UniProt.…”

Section: Gene Pagementioning

confidence: 99%

Zebrafish information network, the knowledgebase for Danio rerio research

et al. 2022

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The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for Danio rerio genetic and genomic data. ZFIN has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at ZFIN include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. ZFIN makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, ZFIN and six other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here we provide an overview of the data available at ZFIN including recent updates to the gene page to provide access to single-cell RNA sequencing (scRNA-seq) data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.

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Section: Gene Pagementioning

confidence: 99%

Zebrafish information network, the knowledgebase for Danio rerio research

et al. 2022

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“…SignaLink3 is the largest signaling resource for D. melanogaster with over 1400 unique proteins and 30 miRNAs. Next to D. melanogaster SignaLink is the only currently available signaling network resource for C. elegans as well as D. rerio with the full integration of our previously separate resource, SignaFish ( 30 ). Annotations of pathways are also sparser in model organisms than in humans, however pathways such as RTK, WNT/Wingless and Notch can be explored in detail in these species as well (Figure 2A ).…”

Section: Description and Contentmentioning

confidence: 99%

SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks

Csabai

Fazekas

Kadlecsik

et al. 2021

Nucleic Acids Research

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Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only a part of the complex network of intertwining pathways, leaving out key interactions or processes. Hence, we have developed SignaLink3 (http://signalink.org/), a value-added knowledge-base that provides manually curated data on signaling pathways and integrated data from several types of databases (interaction, regulation, localisation, disease, etc.) for humans, and three major animal model organisms. SignaLink3 contains over 400 000 newly added human protein-protein interactions resulting in a total of 700 000 interactions for Homo sapiens, making it one of the largest integrated signaling network resources. Next to H. sapiens, SignaLink3 is the only current signaling network resource to provide regulatory information for the model species Caenorhabditis elegans and Danio rerio, and the largest resource for Drosophila melanogaster. Compared to previous versions, we have integrated gene expression data as well as subcellular localization of the interactors, therefore uniquely allowing tissue-, or compartment-specific pathway interaction analysis to create more accurate models. Data is freely available for download in widely used formats, including CSV, PSI-MI TAB or SQL.

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“…The transcript section links to several genome browsers as well as displaying the transcript diagrams and links to ZFIN Transcript Pages and withdrawn transcripts. ZFIN links to SignaFish (Csályi et. al 2016) for interactions when known.…”

Section: Orthology and Other Data Sectionsmentioning

confidence: 99%

Zebrafish Information Network, the knowledgebase for Danio rerio research

Bradford

Slyke

Singer

et al. 2021

Preprint

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The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for zebrafish genetic and genomic data. ZFIN expertly curates, integrates, and displays zebrafish data including genes, alleles, human disease models, gene expression, phenotype, gene function, orthology, morpholino, CRISPR, TALEN, and antibodies. ZFIN makes zebrafish research data Findable, Accessible, Interoperable, and Reusable (FAIR) through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. ZFIN is a founding member of the Alliance of Genome Resources, providing zebrafish data for integration into the cross species platform as well as contributing to model organism data harmonization efforts.

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SignaFish: A Zebrafish-Specific Signaling Pathway Resource

Cited by 7 publications

References 12 publications

Zebrafish information network, the knowledgebase for Danio rerio research

Zebrafish information network, the knowledgebase for Danio rerio research

SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks

Zebrafish Information Network, the knowledgebase for Danio rerio research

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