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- Weishaupt, HolgerUppsala universitet,Science for Life Laboratory, SciLifeLab,Neuroonkologi,Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Dag Hammarskjoldsvag 20, S-75185 Uppsala, Sweden. (author)
Loss of Conservation of Graph Centralities in Reverse-engineered Transcriptional Regulatory Networks
- Article/chapterEnglish2017
Publisher, publication year, extent ...
- 2017-04-03
- Springer,2017
- printrdacarrier
Numbers
- LIBRIS-ID:oai:DiVA.org:mdh-36593
- https://urn.kb.se/resolve?urn=urn:nbn:se:mdh:diva-36593URI
- https://doi.org/10.1007/s11009-017-9554-7DOI
- https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-340897URI
Supplementary language notes
- Language:English
- Summary in:English
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Notes
- Graph centralities are commonly used to identify and prioritize disease genes in transcriptional regulatory networks. Studies on small networks of experimentally validated protein-protein interactions underpin the general validity of this approach and extensions of such findings have recently been proposed for networks inferred from gene expression data. However, it is largely unknown how well gene centralities are preserved between the underlying biological interactions and the networks inferred from gene expression data. Specifically, while previous studies have evaluated the performance of inference methods on synthetic gene expression, it has not been established how the choice of inference method affects individual centralities in the network. Here, we compare two gene centrality measures between reference networks and networks inferred from corresponding simulated gene expression data, using a number of commonly used network inference methods. The results indicate that the centrality of genes is only moderately conserved for all of the inference methods used. In conclusion, caution should be exercised when inspecting centralities in reverse-engineered networks and further work will be required to establish the use of such networks for prioritizing disease genes.
Subject headings and genre
- NATURVETENSKAP Matematik Sannolikhetsteori och statistik hsv//swe
- NATURAL SCIENCES Mathematics Probability Theory and Statistics hsv//eng
- NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
- NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
- NATURVETENSKAP Data- och informationsvetenskap Bioinformatik hsv//swe
- NATURAL SCIENCES Computer and Information Sciences Bioinformatics hsv//eng
- Transcriptional regulatory network inference
- Simulated gene expression
- Graph centrality
- Mathematics/Applied Mathematics
- matematik/tillämpad matematik
Added entries (persons, corporate bodies, meetings, titles ...)
- Johansson, PatrikUppsala universitet,Neuroonkologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)patjo183 (author)
- Engström, Christopher,1987-Mälardalens högskola,Utbildningsvetenskap och Matematik,Mälardalen Univ, Sch Educ Culture & Commun UKK, Div Appl Math, Box 883, S-72123 Vasteras, Sweden.(Swepub:mdh)cem02 (author)
- Nelander, SvenUppsala universitet,Science for Life Laboratory, SciLifeLab,Neuroonkologi(Swepub:uu)svene843 (author)
- Silvestrov, Sergei,1970-Mälardalens högskola,Utbildningsvetenskap och Matematik,Mälardalen Univ, Sch Educ Culture & Commun UKK, Div Appl Math, Box 883, S-72123 Vasteras, Sweden.(Swepub:mdh)ssv01 (author)
- Swartling, Fredrik J.,1975-Uppsala universitet,Neuroonkologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)fredjoha (author)
- Uppsala universitetScience for Life Laboratory, SciLifeLab (creator_code:org_t)
Related titles
- In:Methodology and Computing in Applied Probability: Springer19:4, s. 1095-11051387-58411573-7713
Internet link
- https://doi.org/10.1007/s11009-017-9554-7Fulltext
- https://doi.org/10.1007/s11009-017-9554-7Open access to free full text
- https://link.springer.com/content/pdf/10.1007%2Fs11009-017-9554-7.pdf
- https://uu.diva-portal.org/smash/get/diva2:1180924/FULLTEXT01.pdffulltext:print
- https://urn.kb.se/resolve?urn=urn:nbn:se:mdh:diva-36593
- https://doi.org/10.1007/s11009-017-9554-7
- https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-340897
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