oru.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Capturing context-specific regulation in molecular interaction networks
Örebro University, School of Medical Sciences.ORCID iD: 0000-0003-2437-1300
Örebro University, School of Medical Sciences.ORCID iD: 0000-0002-7173-5579
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Motivation: Gene expression changes over time in response to perturbations. These changes are coordinated into functional modules via regulatory interactions. The genes within a functional module are expected to be differentially expressed in a manner coherent with their regulatory network. This perspective presents a promising approach to increase power to detect differential signals as well as for describing regulated modules from a mechanistic point of view.

Results: We present an effective procedure for identifying differentially activated subnetworks in molecular interaction networks. Differential gene expression coherent with the regulatory nature of the network is identified. Sequentially controlling error on genes and links results in more efficient inference. By focusing on local inference, our method is ignorant of the global topology, and as a result equally effective on exponential and scale-free networks. We apply our procedure both to systematically simulated data, comparing its performance to alternative methods, and to the transcription regulatory network in the context of particle-induced pulmonary inflammation, recapitulating and proposing additional candidates to some previously obtained results.

National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:oru:diva-65214DOI: 10.1101/254730OAI: oai:DiVA.org:oru-65214DiVA, id: diva2:1185427
Available from: 2018-02-24 Created: 2018-02-24 Last updated: 2018-03-16Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full text

Authority records BETA

Rush, StephenRepsilber, Dirk

Search in DiVA

By author/editor
Rush, StephenRepsilber, Dirk
By organisation
School of Medical Sciences
Bioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 24 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf