Signalogs: orthology-based identification of novel signaling pathway components in three metazoans.
BACKGROUND: Uncovering novel components of signal transduction pathways and their interactions within species is a central task in current biological research. Orthology alignment and functional genomics approaches allow the effective identification of signaling proteins by cross-species data integr...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3086880?pdf=render |
| _version_ | 1811285405926948864 |
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| author | Tamás Korcsmáros Máté S Szalay Petra Rovó Robin Palotai Dávid Fazekas Katalin Lenti Illés J Farkas Péter Csermely Tibor Vellai |
| author_facet | Tamás Korcsmáros Máté S Szalay Petra Rovó Robin Palotai Dávid Fazekas Katalin Lenti Illés J Farkas Péter Csermely Tibor Vellai |
| author_sort | Tamás Korcsmáros |
| collection | DOAJ |
| description | BACKGROUND: Uncovering novel components of signal transduction pathways and their interactions within species is a central task in current biological research. Orthology alignment and functional genomics approaches allow the effective identification of signaling proteins by cross-species data integration. Recently, functional annotation of orthologs was transferred across organisms to predict novel roles for proteins. Despite the wide use of these methods, annotation of complete signaling pathways has not yet been transferred systematically between species. PRINCIPAL FINDINGS: Here we introduce the concept of 'signalog' to describe potential novel signaling function of a protein on the basis of the known signaling role(s) of its ortholog(s). To identify signalogs on genomic scale, we systematically transferred signaling pathway annotations among three animal species, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and humans. Using orthology data from InParanoid and signaling pathway information from the SignaLink database, we predict 88 worm, 92 fly, and 73 human novel signaling components. Furthermore, we developed an on-line tool and an interactive orthology network viewer to allow users to predict and visualize components of orthologous pathways. We verified the novelty of the predicted signalogs by literature search and comparison to known pathway annotations. In C. elegans, 6 out of the predicted novel Notch pathway members were validated experimentally. Our approach predicts signaling roles for 19 human orthodisease proteins and 5 known drug targets, and suggests 14 novel drug target candidates. CONCLUSIONS: Orthology-based pathway membership prediction between species enables the identification of novel signaling pathway components that we referred to as signalogs. Signalogs can be used to build a comprehensive signaling network in a given species. Such networks may increase the biomedical utilization of C. elegans and D. melanogaster. In humans, signalogs may identify novel drug targets and new signaling mechanisms for approved drugs. |
| first_indexed | 2024-04-13T02:43:37Z |
| format | Article |
| id | doaj.art-f50abf9955254bbc86c797af0aefe3ba |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T02:43:37Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f50abf9955254bbc86c797af0aefe3ba2022-12-22T03:06:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0165e1924010.1371/journal.pone.0019240Signalogs: orthology-based identification of novel signaling pathway components in three metazoans.Tamás KorcsmárosMáté S SzalayPetra RovóRobin PalotaiDávid FazekasKatalin LentiIllés J FarkasPéter CsermelyTibor VellaiBACKGROUND: Uncovering novel components of signal transduction pathways and their interactions within species is a central task in current biological research. Orthology alignment and functional genomics approaches allow the effective identification of signaling proteins by cross-species data integration. Recently, functional annotation of orthologs was transferred across organisms to predict novel roles for proteins. Despite the wide use of these methods, annotation of complete signaling pathways has not yet been transferred systematically between species. PRINCIPAL FINDINGS: Here we introduce the concept of 'signalog' to describe potential novel signaling function of a protein on the basis of the known signaling role(s) of its ortholog(s). To identify signalogs on genomic scale, we systematically transferred signaling pathway annotations among three animal species, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and humans. Using orthology data from InParanoid and signaling pathway information from the SignaLink database, we predict 88 worm, 92 fly, and 73 human novel signaling components. Furthermore, we developed an on-line tool and an interactive orthology network viewer to allow users to predict and visualize components of orthologous pathways. We verified the novelty of the predicted signalogs by literature search and comparison to known pathway annotations. In C. elegans, 6 out of the predicted novel Notch pathway members were validated experimentally. Our approach predicts signaling roles for 19 human orthodisease proteins and 5 known drug targets, and suggests 14 novel drug target candidates. CONCLUSIONS: Orthology-based pathway membership prediction between species enables the identification of novel signaling pathway components that we referred to as signalogs. Signalogs can be used to build a comprehensive signaling network in a given species. Such networks may increase the biomedical utilization of C. elegans and D. melanogaster. In humans, signalogs may identify novel drug targets and new signaling mechanisms for approved drugs.http://europepmc.org/articles/PMC3086880?pdf=render |
| spellingShingle | Tamás Korcsmáros Máté S Szalay Petra Rovó Robin Palotai Dávid Fazekas Katalin Lenti Illés J Farkas Péter Csermely Tibor Vellai Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PLoS ONE |
| title | Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. |
| title_full | Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. |
| title_fullStr | Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. |
| title_full_unstemmed | Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. |
| title_short | Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. |
| title_sort | signalogs orthology based identification of novel signaling pathway components in three metazoans |
| url | http://europepmc.org/articles/PMC3086880?pdf=render |
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