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

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2014

Faugaret, Delphine; Amara, Amira Ben; Alingrin, Julie; Daumas, Aurélie; Delaby, Amélie; Lépolard, Catherine; Raoult, Didier; Textoris, Julien; Mège, Jean-Louis

Granulomatous response to Coxiella burnetii, the agent of Q fever: the lessons from gene expression analysis Journal Article

In: Front Cell Infect Microbiol, vol. 4, pp. 172, 2014, ISSN: 2235-2988.

Abstract | Links | BibTeX

2013

Altintas, Dogus Murat; Allioli, Nathalie; Decaussin, Myriam; de Bernard, Simon; Ruffion, Alain; Samarut, Jacques; Vlaeminck-Guillem, Virginie

Differentially expressed androgen-regulated genes in androgen-sensitive tissues reveal potential biomarkers of early prostate cancer Journal Article

In: PLoS One, vol. 8, no. 6, pp. e66278, 2013, ISSN: 1932-6203.

Abstract | Links | BibTeX

Mahe, Yann F; Perez, Marie-Jesus; Tacheau, Charlotte; Fanchon, Chantal; Martin, Richard; Rousset, Françoise; Seite, Sophie

A new Vitreoscilla filiformis extract grown on spa water-enriched medium activates endogenous cutaneous antioxidant and antimicrobial defenses through a potential Toll-like receptor 2/protein kinase C, zeta transduction pathway Journal Article

In: Clin Cosmet Investig Dermatol, vol. 6, pp. 191–196, 2013, ISSN: 1178-7015.

Abstract | Links | BibTeX

34 entries « 11 of 12 »