High-quality analyses
AltraBio harnesses its renowned expertise in bioinformatics, biostatistics, and biology to offer services in the analysis and interpretation of various omics data types (genomics, epigenomics, transcriptomics, proteomics, etc.).
Our team collaborates closely with clients and partners for each project to ensure their goals are met.
Expertise in biostatistics and bioinformatics
Before conducting differential analyses, we implement various methods to assess the data quality and its consistency with the experimental design. We specifically address outliers and effects unrelated to the design to correct them in agreement with of our client/partner. This ensures the relevance of the analysis performed.
Experimental designs may involve multiple factors such as donor, cell type, treatment, dose, and timepoints, allowing for analysis from various perspectives. To address the biological question(s) of the study, AltraBio identifies the most appropriate statistical model (paired design, batch effect correction, estimation of hidden factors, outlier weighting, etc.).
AltraBio has the expertise to integrate various types of data (multi-omics, cytometry, medical data, etc.). We employ supervised and unsupervised machine learning for various applications including biomarker identification, classification, predictive models for diagnostics or treatment response. Our clients benefit from our strong proficiency in utilizing state-of-the-art machine learning algorithms to extract maximum value from their data.
Expertise in biology
Biological processes and pathways are identified through the implementation of various complementary methods of functional category enrichment. These automated 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 to extract meaning. In the interpretation phase, we consider the biological question(s) that initiated the study and evaluate the results while integrating biological knowledge available in scientific literature and databases. Our goal is to understand the biological mechanisms at play and formulate new hypotheses for validation. Examples of synthetic diagrams produced by AltraBio can be found in figures S8A and S9A of this article).
Reporting
All the work conducted is summarized in a comprehensive report provided to our client/partner and explained during a video conference. This exchange allows us to clarify the chosen methodological approaches and their results, ensuring that our client/partner has the best understanding of their data.
The results of statistical analysis are also accessible through the WikiBioPath web interface, providing our clients/partners with a set of visualisation and analysis tools to continue exploring their data. They can easily visualize volcano plots, generate new heat maps, perform PCA, and conduct enrichment analyses on gene selections.
Our publications in Omics Data Analysis
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.
@article{pmid25566510,
title = {Granulomatous response to Coxiella burnetii, the agent of Q fever: the lessons from gene expression analysis},
author = {Delphine Faugaret and Amira Ben Amara and Julie Alingrin and Aurélie Daumas and Amélie Delaby and Catherine Lépolard and Didier Raoult and Julien Textoris and Jean-Louis Mège},
doi = {10.3389/fcimb.2014.00172},
issn = {2235-2988},
year = {2014},
date = {2014-01-01},
urldate = {2014-01-01},
journal = {Front Cell Infect Microbiol},
volume = {4},
pages = {172},
abstract = {The formation of granulomas is associated with the resolution of Q fever, a zoonosis due to Coxiella burnetii; however the molecular mechanisms of granuloma formation remain poorly understood. We generated human granulomas with peripheral blood mononuclear cells (PBMCs) and beads coated with C. burnetii, using BCG extracts as controls. A microarray analysis showed dramatic changes in gene expression in granuloma cells of which more than 50% were commonly modulated genes in response to C. burnetii and BCG. They included M1-related genes and genes related to chemotaxis. The inhibition of the chemokines, CCL2 and CCL5, directly interfered with granuloma formation. C. burnetii granulomas also expressed a specific transcriptional profile that was essentially enriched in genes associated with type I interferon response. Our results showed that granuloma formation is associated with a core of transcriptional response based on inflammatory genes. The specific granulomatous response to C. burnetii is characterized by the activation of type 1 interferon pathway.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
@article{pmid23840433,
title = {Differentially expressed androgen-regulated genes in androgen-sensitive tissues reveal potential biomarkers of early prostate cancer},
author = {Dogus Murat Altintas and Nathalie Allioli and Myriam Decaussin and Simon de Bernard and Alain Ruffion and Jacques Samarut and Virginie Vlaeminck-Guillem},
doi = {10.1371/journal.pone.0066278},
issn = {1932-6203},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
journal = {PLoS One},
volume = {8},
number = {6},
pages = {e66278},
abstract = {BACKGROUND: Several data favor androgen receptor implication in prostate cancer initiation through the induction of several gene activation programs. The aim of the study is to identify potential biomarkers for early diagnosis of prostate cancer (PCa) among androgen-regulated genes (ARG) and to evaluate comparative expression of these genes in normal prostate and normal prostate-related androgen-sensitive tissues that do not (or rarely) give rise to cancer.
METHODS: ARG were selected in non-neoplastic adult human prostatic epithelial RWPE-1 cells stably expressing an exogenous human androgen receptor, using RNA-microarrays and validation by qRT-PCR. Expression of 48 preselected genes was quantified in tissue samples (seminal vesicles, prostate transitional zones and prostate cancers, benign prostatic hypertrophy obtained from surgical specimens) using TaqMan® low-density arrays. The diagnostic performances of these potential biomarkers were compared to that of genes known to be associated with PCa (i.e. PCA3 and DLX1).
RESULTS AND DISCUSSION: By crossing expression studies in 26 matched PCa and normal prostate transitional zone samples, and 35 matched seminal vesicle and PCa samples, 14 genes were identified. Similarly, 9 genes were overexpressed in 15 benign prostatic hypertrophy samples, as compared to PCa samples. Overall, we selected 8 genes of interest to evaluate their diagnostic performances in comparison with that of PCA3 and DLX1. Among them, 3 genes: CRYAB, KCNMA1 and SDPR, were overexpressed in all 3 reference non-cancerous tissues. The areas under ROC curves of these genes reached those of PCA3 (0.91) and DLX1 (0.94).
CONCLUSIONS: We identified ARG with reduced expression in PCa and with significant diagnostic values for discriminating between cancerous and non-cancerous prostatic tissues, similar that of PCA3. Given their expression pattern, they could be considered as potentially protective against prostate cancer. Moreover, they could be complementary to known genes overexpressed in PCa and included along with them in multiplex diagnostic tools.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
METHODS: ARG were selected in non-neoplastic adult human prostatic epithelial RWPE-1 cells stably expressing an exogenous human androgen receptor, using RNA-microarrays and validation by qRT-PCR. Expression of 48 preselected genes was quantified in tissue samples (seminal vesicles, prostate transitional zones and prostate cancers, benign prostatic hypertrophy obtained from surgical specimens) using TaqMan® low-density arrays. The diagnostic performances of these potential biomarkers were compared to that of genes known to be associated with PCa (i.e. PCA3 and DLX1).
RESULTS AND DISCUSSION: By crossing expression studies in 26 matched PCa and normal prostate transitional zone samples, and 35 matched seminal vesicle and PCa samples, 14 genes were identified. Similarly, 9 genes were overexpressed in 15 benign prostatic hypertrophy samples, as compared to PCa samples. Overall, we selected 8 genes of interest to evaluate their diagnostic performances in comparison with that of PCA3 and DLX1. Among them, 3 genes: CRYAB, KCNMA1 and SDPR, were overexpressed in all 3 reference non-cancerous tissues. The areas under ROC curves of these genes reached those of PCA3 (0.91) and DLX1 (0.94).
CONCLUSIONS: We identified ARG with reduced expression in PCa and with significant diagnostic values for discriminating between cancerous and non-cancerous prostatic tissues, similar that of PCA3. Given their expression pattern, they could be considered as potentially protective against prostate cancer. Moreover, they could be complementary to known genes overexpressed in PCa and included along with them in multiplex diagnostic tools.
Mahe, Yann F; Perez, Marie-Jesus; Tacheau, Charlotte; Fanchon, Chantal; Martin, Richard; Rousset, Françoise; Seite, Sophie
In: Clin Cosmet Investig Dermatol, vol. 6, pp. 191–196, 2013, ISSN: 1178-7015.
@article{pmid24039440,
title = {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},
author = {Yann F Mahe and Marie-Jesus Perez and Charlotte Tacheau and Chantal Fanchon and Richard Martin and Françoise Rousset and Sophie Seite},
doi = {10.2147/CCID.S47324},
issn = {1178-7015},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
journal = {Clin Cosmet Investig Dermatol},
volume = {6},
pages = {191--196},
abstract = {Vitreoscilla filiformis (VF) biomass (VFB) has been widely used in cosmetic preparations and shown to modulate the major inducible free-radical scavenger mitochondrial superoxide dismutase in skin cells. By adding La Roche-Posay (LRP) thermal spring water to the VF culture medium, we obtained a biomass (LRP-VFB) with a similar mitochondrial superoxide dismutase activation capacity to VF. Also, the new biomass more powerfully stimulated mRNA expression and antimicrobial peptides in reconstructed epidermis. Interestingly, a predictive computer model that analyzed transducing events within skin epidermal cells suggested that this protective activity may involve the Toll-like receptor 2/protein kinase C, zeta transduction pathway. Protein kinase C, zeta inhibition was effectively shown to abolish VFB-induced gene stimulation and confirmed this hypothesis. This thus opens new avenues for investigation into the improvement of skin homeostatic defense in relation to the control of its physiological microbiota and innate immunity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}