Literature DB >> 18799481

FunNet: an integrative tool for exploring transcriptional interactions.

Edi Prifti1, Jean-Daniel Zucker, Karine Clement, Corneliu Henegar.   

Abstract

UNLABELLED: We describe here an exploratory tool, called FunNet, which implements an original systems biology approach, aiming to improve the biological relevance of the modular interaction patterns identified in transcriptional co-expression networks. A suitable analytical model, involving two abstraction layers, has been devised to relate expression profiles to the knowledge on transcripts' biological roles, extracted from genomic databases, into a comprehensive exploratory framework. This approach has been implemented into a user-friendly web tool to promote its open use by the community. AVAILABILITY: http://www.funnet.info

Mesh:

Year:  2008        PMID: 18799481     DOI: 10.1093/bioinformatics/btn492

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  39 in total

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Authors:  Huilei Xu; Christoph Schaniel; Ihor R Lemischka; Avi Ma'ayan
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Nov-Dec

2.  MLL3/MLL4-Associated PAGR1 Regulates Adipogenesis by Controlling Induction of C/EBPβ and C/EBPδ.

Authors:  Ji-Eun Lee; Young-Wook Cho; Chu-Xia Deng; Kai Ge
Journal:  Mol Cell Biol       Date:  2020-08-14       Impact factor: 4.272

3.  Irf5 deficiency in macrophages promotes beneficial adipose tissue expansion and insulin sensitivity during obesity.

Authors:  Elise Dalmas; Amine Toubal; Fawaz Alzaid; Katrina Blazek; Hayley L Eames; Kristell Lebozec; Maria Pini; Isabelle Hainault; Emilie Montastier; Raphaël G P Denis; Patricia Ancel; Amélie Lacombe; Yin Ling; Omran Allatif; Céline Cruciani-Guglielmacci; Sébastien André; Nathalie Viguerie; Christine Poitou; Vladimir Stich; Alexandra Torcivia; Fabienne Foufelle; Serge Luquet; Judith Aron-Wisnewsky; Dominique Langin; Karine Clément; Irina A Udalova; Nicolas Venteclef
Journal:  Nat Med       Date:  2015-05-04       Impact factor: 53.440

4.  SMRT-GPS2 corepressor pathway dysregulation coincides with obesity-linked adipocyte inflammation.

Authors:  Amine Toubal; Karine Clément; Rongrong Fan; Patricia Ancel; Veronique Pelloux; Christine Rouault; Nicolas Veyrie; Agnes Hartemann; Eckardt Treuter; Nicolas Venteclef
Journal:  J Clin Invest       Date:  2012-12-10       Impact factor: 14.808

5.  Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia.

Authors:  Xinan Yang; Yong Huang; James L Chen; Jianming Xie; Xiao Sun; Yves A Lussier
Journal:  BMC Bioinformatics       Date:  2009-09-17       Impact factor: 3.169

6.  Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome.

Authors:  Sami Kilpinen; Kalle Ojala; Olli Kallioniemi
Journal:  PLoS One       Date:  2010-12-03       Impact factor: 3.240

7.  Adipose tissue pathways involved in weight loss of cancer cachexia.

Authors:  I Dahlman; N Mejhert; K Linder; T Agustsson; D M Mutch; A Kulyte; B Isaksson; J Permert; N Petrovic; J Nedergaard; E Sjölin; D Brodin; K Clement; K Dahlman-Wright; M Rydén; P Arner
Journal:  Br J Cancer       Date:  2010-04-20       Impact factor: 7.640

8.  The limitations of simple gene set enrichment analysis assuming gene independence.

Authors:  Pablo Tamayo; George Steinhardt; Arthur Liberzon; Jill P Mesirov
Journal:  Stat Methods Med Res       Date:  2012-10-14       Impact factor: 3.021

9.  PEMT, Δ6 desaturase, and palmitoyldocosahexaenoyl phosphatidylcholine are increased in rats during pregnancy.

Authors:  Alan Chalil; Alex P Kitson; Juan J Aristizabal Henao; Kristin A Marks; Jason L Elzinga; Daniel M E Lamontagne-Kam; Daniel Chalil; Flavia Badoud; David M Mutch; Ken D Stark
Journal:  J Lipid Res       Date:  2017-11-22       Impact factor: 5.922

10.  Endoplasmic reticulum stress impairs IL-4/IL-13 signaling through C/EBPβ-mediated transcriptional suppression.

Authors:  Angela M Arensdorf; D Thomas Rutkowski
Journal:  J Cell Sci       Date:  2013-06-26       Impact factor: 5.285

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