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1000 Titel
  • ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work
1000 Autor/in
  1. Warsow, Gregor |
  2. Greber, Boris |
  3. Falk, Steffi S. I. |
  4. Harder, Clemens |
  5. Siatkowski, Marcin |
  6. Schordan, Sandra |
  7. Som, Anup |
  8. Endlich, Nicole |
  9. Schöler, Hans |
  10. Repsilber, Dirk |
  11. Endlich, Karlhans |
  12. Fuellen, Georg |
1000 Erscheinungsjahr 2010
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2010-11-30
1000 Erschienen in
1000 Quellenangabe
  • 4: 164
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2010
1000 Lizenz
1000 Verlagsversion
  • https://dx.doi.org/10.1186/1752-0509-4-164 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012047/ |
1000 Ergänzendes Material
  • https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-164#Declarations |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • BACKGROUND: Experimentalists are overwhelmed by high-throughput data and there is an urgent need to condense information into simple hypotheses. For example, large amounts of microarray and deep sequencing data are becoming available, describing a variety of experimental conditions such as gene knockout and knockdown, the effect of interventions, and the differences between tissues and cell lines. RESULTS: To address this challenge, we developed a method, implemented as a Cytoscape plugin called ExprEssence. As input we take a network of interaction, stimulation and/or inhibition links between genes/proteins, and differential data, such as gene expression data, tracking an intervention or development in time. We condense the network, highlighting those links across which the largest changes can be observed. Highlighting is based on a simple formula inspired by the law of mass action. We can interactively modify the threshold for highlighting and instantaneously visualize results. We applied ExprEssence to three scenarios describing kidney podocyte biology, pluripotency and ageing: 1) We identify putative processes involved in podocyte (de-)differentiation and validate one prediction experimentally. 2) We predict and validate the expression level of a transcription factor involved in pluripotency. 3) Finally, we generate plausible hypotheses on the role of apoptosis, cell cycle deregulation and DNA repair in ageing data obtained from the hippocampus. CONCLUSION: Reducing the size of gene/protein networks to the few links affected by large changes allows to screen for putative mechanistic relationships among the genes/proteins that are involved in adaptation to different experimental conditions, yielding important hypotheses, insights and suggestions for new experiments. We note that we do not focus on the identification of 'active subnetworks'. Instead we focus on the identification of single links (which may or may not form subnetworks), and these single links are much easier to validate experimentally than submodules.
1000 Fachgruppe
  1. Biologie |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/creator/V2Fyc293LCBHcmVnb3I=|https://frl.publisso.de/adhoc/creator/R3JlYmVyLCBCb3Jpcw==|https://frl.publisso.de/adhoc/creator/RmFsaywgU3RlZmZpIFMuIEku|https://frl.publisso.de/adhoc/creator/SGFyZGVyLCBDbGVtZW5z|https://frl.publisso.de/adhoc/creator/U2lhdGtvd3NraSwgTWFyY2lu|https://frl.publisso.de/adhoc/creator/U2Nob3JkYW4sIFNhbmRyYQ==|https://frl.publisso.de/adhoc/creator/U29tLCBBbnVw|https://frl.publisso.de/adhoc/creator/RW5kbGljaCwgTmljb2xl|https://frl.publisso.de/adhoc/creator/U2Now7ZsZXIsIEhhbnM=|https://frl.publisso.de/adhoc/creator/UmVwc2lsYmVyLCBEaXJr|https://frl.publisso.de/adhoc/creator/RW5kbGljaCwgS2FybGhhbnM=|https://frl.publisso.de/adhoc/creator/RnVlbGxlbiwgR2Vvcmc=
1000 Förderer
  1. DFG |
  2. BMBF |
  3. European Foundation for the Study of Diabetes (EFSD)/Novo Nordisk |
1000 Fördernummer
  1. FU583/2-1
  2. 01GN0901; 01GN0805
  3. -
1000 Förderprogramm
  1. SPP 1356: Pluripotency and Cellular Reprogramming
  2. Generation of pluri- and multipotent stem cells
  3. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer DFG |
    1000 Förderprogramm SPP 1356: Pluripotency and Cellular Reprogramming
    1000 Fördernummer FU583/2-1
  2. 1000 joinedFunding-child
    1000 Förderer BMBF |
    1000 Förderprogramm Generation of pluri- and multipotent stem cells
    1000 Fördernummer 01GN0901; 01GN0805
  3. 1000 joinedFunding-child
    1000 Förderer European Foundation for the Study of Diabetes (EFSD)/Novo Nordisk |
    1000 Förderprogramm -
    1000 Fördernummer -
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6403509.rdf
1000 Erstellt am 2017-07-18T11:15:28.811+0200
1000 Erstellt von 21
1000 beschreibt frl:6403509
1000 Bearbeitet von 218
1000 Zuletzt bearbeitet Wed May 16 10:30:50 CEST 2018
1000 Objekt bearb. Wed May 16 10:30:50 CEST 2018
1000 Vgl. frl:6403509
1000 Oai Id
  1. oai:frl.publisso.de:frl:6403509 |
1000 Sichtbarkeit Metadaten public
1000 Sichtbarkeit Daten public
1000 Gegenstand von

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