High-quality analyses
AltraBio deploys its recognized expertise in bioinformatics, biostatistic and biology to provide services in the analysis and interpretation of all types of omics data (genomics, epigenomics, transcriptomics, proteomics…).
For each project, AltraBio’s team works in interaction with its clients/partners in order to reach their goals.
Expertise in biostatistics and bioinformatics
Prior to performing differential analyses, various methods are implemented to assess the quality of the data and their agreement with the experimental design. We specifically control for outliers and for effects unrelated to the design in order to correct them with the agreement of our client/partner. Thus the relevance of the performed analysis is guaranteed.
Experimental designs may consist of multiple factors (donor, cell type, treatment, dose, timepoints…) and thus can be analyzed from multiple angles. To answer the biological question(s) of the study, AltraBio determines the most suitable statistical model (paired design, batch effect correction, hidden factor estimation, weighting of outliers…).
AltraBio possesses the know-how to integrate different types of data (multi-omics, cytometry, medical data…). Supervised and unsupervised machine learning can be implemented for various applications: biomarker identification, classification, predictive models for diagnostic or response to treatment. Thus our clients benefit from our strong expertise in using up-to-date machine learning algorithms to extract the maximum value from their data.
Expertise in biology
Biological processes and pathways are identified thanks to the implementation of various and complementary methods of functional categories enrichment. These automatic results are then reviewed to assess their relevance with the biological context of the study.
Beyond providing lists of molecules and biological pathways, AltraBio’s role is also to extract meaning. To this end, the interpretation phase takes into account the biological question(s) at the origin of the study and assesses the results while integrating the biological knowledge available in the scientific literature and databases. The goal is to understand the biological mechanisms at play and to formulate new hypotheses to be validated (examples of synthetic diagrams produced by AltraBio in figures S8A and S9A of this article).
Reporting
All of the work carried out is summarized in a complete report transferred to our client/partner and explained during a video conference. This exchange makes it possible to explain the chosen methodological approaches and their results as well as to ensure that our client/partner has the best understanding of their data.
Statistical analysis results are also available in the WikiBioPath web interface which provides our clients/partners a set of visualisation and analysis tools which enables them to continue the exploration of their data. They can easily visualise their volcano plots and generate new heat maps, PCA and enrichment analyses on gene selections.
Our publications in Omics Data Analysis
2014
Idbaih, Ahmed; Mokhtari, Karima; Emile, Jean-François; Galanaud, Damien; Belaid, Hayat; de Bernard, Simon; Benameur, Neila; Barlog, Vlad-Ciprian; Psimaras, Dimitri; Donadieu, Jean; Carpentier, Catherine; Martin-Duverneuil, Nadine; Haroche, Julien; Feuvret, Loic; Zahr, Noel; Delattre, Jean-Yves; Hoang-Xuan, Khê
Dramatic response of a BRAF V600E-mutated primary CNS histiocytic sarcoma to vemurafenib Journal Article
In: Neurology, vol. 83, no. 16, pp. 1478–1480, 2014, ISSN: 1526-632X.
@article{pmid25209580,
title = {Dramatic response of a BRAF V600E-mutated primary CNS histiocytic sarcoma to vemurafenib},
author = {Ahmed Idbaih and Karima Mokhtari and Jean-François Emile and Damien Galanaud and Hayat Belaid and Simon de Bernard and Neila Benameur and Vlad-Ciprian Barlog and Dimitri Psimaras and Jean Donadieu and Catherine Carpentier and Nadine Martin-Duverneuil and Julien Haroche and Loic Feuvret and Noel Zahr and Jean-Yves Delattre and Khê Hoang-Xuan},
doi = {10.1212/WNL.0000000000000880},
issn = {1526-632X},
year = {2014},
date = {2014-10-01},
urldate = {2014-10-01},
journal = {Neurology},
volume = {83},
number = {16},
pages = {1478--1480},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Daussy, Cécile; Faure, Fabrice; Mayol, Katia; Viel, Sébastien; Gasteiger, Georg; Charrier, Emily; Bienvenu, Jacques; Henry, Thomas; Debien, Emilie; Hasan, Uzma A; Marvel, Jacqueline; Yoh, Keigyou; Takahashi, Satoru; Prinz, Immo; de Bernard, Simon; Buffat, Laurent; Walzer, Thierry
T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow Journal Article
In: J Exp Med, vol. 211, no. 3, pp. 563–577, 2014, ISSN: 1540-9538.
@article{pmid24516120,
title = {T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow},
author = {Cécile Daussy and Fabrice Faure and Katia Mayol and Sébastien Viel and Georg Gasteiger and Emily Charrier and Jacques Bienvenu and Thomas Henry and Emilie Debien and Uzma A Hasan and Jacqueline Marvel and Keigyou Yoh and Satoru Takahashi and Immo Prinz and Simon de Bernard and Laurent Buffat and Thierry Walzer},
doi = {10.1084/jem.20131560},
issn = {1540-9538},
year = {2014},
date = {2014-03-01},
urldate = {2014-03-01},
journal = {J Exp Med},
volume = {211},
number = {3},
pages = {563--577},
abstract = {Trail(+)DX5(-)Eomes(-) natural killer (NK) cells arise in the mouse fetal liver and persist in the adult liver. Their relationships with Trail(-)DX5(+) NK cells remain controversial. We generated a novel Eomes-GFP reporter murine model to address this question. We found that Eomes(-) NK cells are not precursors of classical Eomes(+) NK cells but rather constitute a distinct lineage of innate lymphoid cells. Eomes(-) NK cells are strictly dependent on both T-bet and IL-15, similarly to NKT cells. We observed that, in the liver, expression of T-bet in progenitors represses Eomes expression and the development of Eomes(+) NK cells. Reciprocally, the bone marrow (BM) microenvironment restricts T-bet expression in developing NK cells. Ectopic expression of T-bet forces the development of Eomes(-) NK cells, demonstrating that repression of T-bet is essential for the development of Eomes(+) NK cells. Gene profile analyses show that Eomes(-) NK cells share part of their transcriptional program with NKT cells, including genes involved in liver homing and NK cell receptors. Moreover, Eomes(-) NK cells produce a broad range of cytokines, including IL-2 and TNF in vitro and in vivo, during immune responses against vaccinia virus. Thus, mutually exclusive expression of T-bet and Eomes drives the development of different NK cell lineages with complementary functions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Samarut, Eric; Gaudin, Cyril; Hughes, Sandrine; Gillet, Benjamin; de Bernard, Simon; Jouve, Pierre-Emmanuel; Buffat, Laurent; Allot, Alexis; Lecompte, Odile; Berekelya, Liubov; Rochette-Egly, Cécile; Laudet, Vincent
Retinoic acid receptor subtype-specific transcriptotypes in the early zebrafish embryo Journal Article
In: Mol Endocrinol, vol. 28, no. 2, pp. 260–272, 2014, ISSN: 1944-9917.
@article{pmid24422634,
title = {Retinoic acid receptor subtype-specific transcriptotypes in the early zebrafish embryo},
author = {Eric Samarut and Cyril Gaudin and Sandrine Hughes and Benjamin Gillet and Simon de Bernard and Pierre-Emmanuel Jouve and Laurent Buffat and Alexis Allot and Odile Lecompte and Liubov Berekelya and Cécile Rochette-Egly and Vincent Laudet},
doi = {10.1210/me.2013-1358},
issn = {1944-9917},
year = {2014},
date = {2014-02-01},
urldate = {2014-02-01},
journal = {Mol Endocrinol},
volume = {28},
number = {2},
pages = {260--272},
abstract = {Retinoic acid (RA) controls many aspects of embryonic development by binding to specific receptors (retinoic acid receptors [RARs]) that regulate complex transcriptional networks. Three different RAR subtypes are present in vertebrates and play both common and specific roles in transducing RA signaling. Specific activities of each receptor subtype can be correlated with its exclusive expression pattern, whereas shared activities between different subtypes are generally assimilated to functional redundancy. However, the question remains whether some subtype-specific activity still exists in regions or organs coexpressing multiple RAR subtypes. We tackled this issue at the transcriptional level using early zebrafish embryo as a model. Using morpholino knockdown, we specifically invalidated the zebrafish endogenous RAR subtypes in an in vivo context. After building up a list of RA-responsive genes in the zebrafish gastrula through a whole-transcriptome analysis, we compared this panel of genes with those that still respond to RA in embryos lacking one or another RAR subtype. Our work reveals that RAR subtypes do not have fully redundant functions at the transcriptional level but can transduce RA signal in a subtype-specific fashion. As a result, we define RAR subtype-specific transcriptotypes that correspond to repertoires of genes activated by different RAR subtypes. Finally, we found genes of the RA pathway (cyp26a1, raraa) the regulation of which by RA is highly robust and can even resist the knockdown of all RARs. This suggests that RA-responsive genes are differentially sensitive to alterations in the RA pathway and, in particular, cyp26a1 and raraa are under a high pressure to maintain signaling integrity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}