Bioinformatics

Untargeted methods of omics generate massive amounts of data that need to be processed and interpreted. We have understood that this data processing, beyond the biostatistical and bioinformatic methods that we have developed, must go as far as the expression of the phenomena observed in terms of biology.

We propose the analysis of eukaryotic proteomes or transcriptomes with the CORAVALID pipeline and the analysis of the metaproteome with the HolXplore pipeline.

CORAVALID: Complementary analysis of relative quantification data in the comparison of two proteomic conditions.

LEVEL 1: Enrichment Analysis

The basic version of CORAVALID is a complementary analysis of the data, highlighting the biological processes, molecular functions, cellular components and metabolic and signal pathways related to proteins or genes significantly regulated in a quantitative comparison in high resolution proteomics or in genomics (" biochips ").

The associations are validated by statistical tests and manual curation.

LEVEL 2: Synthesis and interpretation

The standard version of CORAVALID Level 2 synthesizes and interprets these results and the information associated with each protein, to highlight the phenomena and mechanisms at work distinguishing the two samples compared. This synthesis makes it possible to highlight the major biological functions impacted.

Contextualization and / or follow-up meeting if desired

LEVEL 3: Biological Meanings - Proposed Claims

A selection of the major impacted biological functions is performed to determine if they are positively or negatively regulated. This choice takes place during the contextualization and / or follow-up meeting. In the absence of a meeting, a selection of the most important biological functions will be carried out. The in-depth analysis of this selection will make it possible to determine the biological significance of the results obtained (to determine if the major biological functions impacted are positively or negatively regulated and to deduce the associated consequences), to determine phenotypes, and to propose claims.

HolXplore: Global analysis of the human proteome and metaproteome of the associated microbiota.

HolXplore is a complementary analysis of data from metaproteomic experiments, highlighting the biological effects related to the results:

LEVEL 1 Taxonomic analyzes.

- Analysis of the diversity of the microbiota associated with the 2 conditions tested.

- Evaluation of a potential change in microbiota structure at different taxonomic levels, validation by statistical analysis.

- Dispersion of samples according to the diversity of their microbiota.

LEVEL 2 Functional Analyzes

The following analyzes will be carried out in parallel for the taxa 1) Bacteria, 2) Fungiet 3) Homo sapiens:

• Research of orthologues and functional categories and associated general COG processes.
• Determination of potential significant evolutions at different functional levels (terms, functional categories, general processes).
• Involvement of protein orthologs in KEGG pathways.
• Dispersion of samples according to the bacterial, fungal or human proteome.

LEVEL 3 Correlations / Claims

• Dispersion of samples according to bacterial, fungal and human proteomes.
• Calculation of correlation coefficients between different functions.
• Calculation of correlation coefficients between different functions and taxonomic groups.
• Involvement of orthologs of bacterial, fungal and human proteins in KEGG pathways.
• Claims / Biological effects possible on the collection of the host and its microbiota.