Research

PhD Thesis

“Exploratory Analysis of transcriptomic data: from their visualisation to the integration of external information”

Abstract

We propose new methodologies of exploratory statistics which are dedicated to the analysis of transcriptomic data (DNA microarray data). Transcriptomic data provide an image of the transcriptome which itself is the result of phenomena of activation or inhibition of gene expression.

However, the image of the transcriptome is noisy. That is why, firstly we focus on the issue of transcriptomic data denoising, in a visualisation framework. To do so, we propose a regularised version of principal component analysis. This regularised version allows to better estimate and visualise the underlying signal of noisy data.

In addition, we can wonder if the knowledge of only the transcriptome is enough to understand the complexity of relationships between genes. That is why we propose to integrate other sources of information about genes, and in an active way, in the analysis of transcriptomic data. Two major mechanisms seem to be involved in the regulation of gene expression, regulatory proteins (for instance transcription factors) and regulatory networks on the one hand, chromosomal localisation and genome architecture on the other hand.

Firstly, we focus on the regulation of gene expression by regulatory proteins; we propose a gene clustering algorithm based on the integration of functional knowledge about genes, which is provided by Gene Ontology annotations. This algorithm provides clusters constituted by genes which have both similar expression profiles and similar functional annotations. The clusters thus constituted are then better candidates for interpretation.

Secondly, we propose to link the study of transcriptomic data to chromosomal localisation in a methodology developed in collaboration with geneticists.

Keywords

transcriptomic data, multidimensional analysis, visualisation, regularisation,
integration of biological knowledge, Gene Ontology, chromosomal localisation

Examination committee

  • Hervé Abdi (University of Texas at Dallas, USA), Rapporteur
  • Philippe Besse (Institut de Mathématiques de Toulouse, France) ,Rapporteur
  • Jean Mosser (CNRS Université de Rennes 1, France), Président
  • Sandrine Lagarrigue (INRA/Agrocampus Ouest, Rennes, France), Examinatrice
  • Jérôme Pagès (Agrocampus Ouest, Rennes, France), Directeur de thèse
  • Sébastien Lê (Agrocampus Ouest, Rennes, France), Directeur de thèse

Manuscript (in french) and Slides (in french)

 

PhD defense video (in french)

 

Qualification

Sections CNU 26: Applied mathematics (mathématiques appliquées et applications des mathématiques)

 

Papers

  • [2016,article] bibtex Go to document
    M. Favennec*, B. Hennart*, M. Verbanck*, M. Pigeyre, R. Caiazzo, V. Raverdy, H. Verkindt, A. Leloire, G. J. Guillemin, L. Yengo, D. Allorge, P. Froguel, F. Pattou, and O. Poulain-Godefroy, Post-Bariatric Surgery Changes in Quinolinic and Xanthurenic Acid Concentrations Are Associated with Glucose Homeostasis, PLOS ONE, vol. 11, iss. 6, p. 0158051, 2016.
    @article{favennec_post-bariatric_2016, title = {Post-{Bariatric} {Surgery} {Changes} in {Quinolinic} and {Xanthurenic} {Acid} {Concentrations} {Are} {Associated} with {Glucose} {Homeostasis}},
      volume = {11},
      issn = {1932-6203},
      url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158051},
      doi = {10.1371/journal.pone.0158051},
      number = {6},
      urldate = {2016-06-22},
      journal = {PLOS ONE},
      author = {Favennec*, Marie and Hennart*, Benjamin and Verbanck*, Marie and Pigeyre, Marie and Caiazzo, Robert and Raverdy, Violeta and Verkindt, Hélène and Leloire, Audrey and Guillemin, Gilles J. and Yengo, Loïc and Allorge, Delphine and Froguel, Philippe and Pattou, François and Poulain-Godefroy, Odile},
      month = jun, year = {2016},
      keywords = {Diabetes mellitus, Digestive system procedures, Glucose metabolism, Obesity, Serotonin, Surgical and invasive medical procedures, Tryptophan, Weight loss},
      pages = {e0158051}
    }
  • [2015,article] bibtex Go to document
    M. Favennec, B. Hennart, R. Caiazzo, A. Leloire, L. Yengo, M. Verbanck, A. Arredouani, M. Marre, M. Pigeyre, A. Bessede, G. J. Guillemin, G. Chinetti, B. Staels, F. Pattou, B. Balkau, D. Allorge, P. Froguel, and O. Poulain-Godefroy, The kynurenine pathway is activated in human obesity and shifted toward kynurenine monooxygenase activation, Obesity (Silver Spring, Md.), 2015.
    @article{favennec_2015, title = {The kynurenine pathway is activated in human obesity and shifted toward kynurenine monooxygenase activation},
      issn = {1930-739X},
      doi = {10.1002/oby.21199},
      language = {ENG},
      journal = {Obesity (Silver Spring, Md.)},
      author = {Favennec, Marie and Hennart, Benjamin and Caiazzo, Robert and Leloire, Audrey and Yengo, Loïc and Verbanck, Marie and Arredouani, Abdelilah and Marre, Michel and Pigeyre, Marie and Bessede, Alban and Guillemin, Gilles J. and Chinetti, Giulia and Staels, Bart and Pattou, François and Balkau, Beverley and Allorge, Delphine and Froguel, Philippe and Poulain-Godefroy, Odile},
      month = sep, year = {2015},
      url = {http://onlinelibrary.wiley.com/doi/10.1002/oby.21199/abstract;jsessionid=63E791E20639D29A1D97142A5D851028.f02t03?systemMessage=Wiley+Online+Library+and+related+systems+will+have+3+hours+of+downtime+on+Saturday+12th+September+2015+from+10%3A00-13%3A00+BST+%2F+05%3A00-08%3A00+EDT+%2F+17%3A00-20%3A00+SGT+for+essential+maintenance.++Apologies+for+the+inconvenience.},
      pmid = {26347385}
    }
  • [2013,article] bibtex Go to document
    M. Verbanck, J. Josse, and F. Husson, Regularised PCA to denoise and visualise data, Statistics and Computing, pp. 1-16, 2013.
    @article{verbanck2013SetC, title = {Regularised {PCA} to denoise and visualise data},
      issn = {0960-3174, 1573-1375},
      doi = {10.1007/s11222-013-9444-y},
      language = {en},
      month = dec, year = {2013},
      journal = {Statistics and Computing},
      author = {Marie Verbanck and Josse, Julie and Husson, François},
      pages = {1--16},
      url = {http://link.springer.com/article/10.1007/s11222-013-9444-y}
    }

R code Readme

  • [2013,article] bibtex Go to document
    M. Verbanck, S. Lê, and J. Pagès, A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data, BMC Bioinformatics, vol. 14, iss. 1, p. 42, 2013.
    @article{verbanck2013bmc, title = {A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data},
      volume = {14},
      url = {http://www.biomedcentral.com/1471-2105/14/42/abstract},
      language = {en},
      number = {1},
      journal = {{BMC} Bioinformatics},
      author = {Verbanck, Marie and Lê, Sébastien and Pagès, Jérôme},
      month = feb, year = {2013},
      pages = {42},
      }

Open AccessHighly Accessed

InteGO package

Conferences

  • [2012,conference] bibtex
    M. Verbanck, J. Josse, and F. Husson, PCA visualization improved by regularization, , Oviedo, Spain, 2012.
    @conference{verbanck2012ercim,
      author = {Verbanck, Marie and Josse, Julie and Husson, François},
      title = {PCA visualization improved by regularization},
      organization = {ERCIM},
      address = {Oviedo, Spain},
      month = {December 1-3},
      year = {2012}
    }
  • [2012,conference] bibtex
    M. Verbanck, S. Lê, and J. Pagès, Revealing new relationships among genes by combining external biological knowledge with expression data in an exploratory framework, , Florence, Italy, 2012.
    @conference{verbanck2012slds,
      author = {Verbanck, M. and Lê, S. and Pagès, J.},
      title = {Revealing new relationships among genes by combining external biological knowledge with expression data in an exploratory framework},
      organization = {Symposium on Learning and Data Sciences (SLDS)},
      address = {Florence, Italy},
      month = {May 7-9},
      year = {2012}
    }
  • [2011,conference] bibtex
    M. Verbanck, S. Lê, and J. Pagès, Towards the integration of biological knowledge with canonical correspondence analysis when analyzing Xomic data in an exploratory framework, , Rennes, France, 2011.
    @conference{verbanck2011carme,
      author = {Verbanck, M. and Lê, S. and Pagès, J.},
      title = {Towards the integration of biological knowledge with canonical correspondence analysis when analyzing Xomic data in an exploratory framework},
      organization = {Correspondance Analysis and Related MEthods (CARME)},
      address = {Rennes, France},
      month = {February 8-11},
      year = {2011}
    }
  • [2011,conference] bibtex
    M. Verbanck, S. Lê, and J. Pagès, Towards the integration of external information combining biological knowledge and coexpression when interpreting Xomic data in an exploratory framework, , Paris, France, 2011.
    @conference{verbanck2011smpgd,
      author = {Verbanck, M. and Lê, S. and Pagès, J.},
      title = {Towards the integration of external information combining biological knowledge and coexpression when interpreting Xomic data in an exploratory framework},
      organization = {Statistical Methods for Post Genomic Data (SMPGD)},
      address = {Paris, France},
      month = {January 27-28},
      year = {2011}
    }
  • [2010,conference] bibtex
    M. Verbanck, S. Lê, and J. Pagès, Integrating biological knowledge related to coexpression when analysing Xomic data, , Paris, France, 2010.
    @conference{verbanck2010,
      author = {Verbanck, M. and Lê, S. and Pagès, J.},
      title = {Integrating biological knowledge related to coexpression when analysing Xomic data},
      organization = {19th International Conference on Computational Statistics.},
      address = {Paris, France},
      month = {August 22-27},
      year = {2010}
    }

 

Seminars

  • [2013,misc] bibtex
    M. Verbanck, J. Josse, and F. Husson, Visualisation de données par ACP régulariséeParis, France: , 2013.
    @MISC{verbanck2013cnam,
      author = {Verbanck, Marie and Josse, Julie and Husson, François},
      title = {Visualisation de données par ACP régularisée},
      organization = {Séminaire de statistique du CNAM},
      address = {Paris, France},
      month = {16 janvier},
      year = {2013}
    }

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