Additional file 11: Table S6. of Ancestors’ dietary patterns and environments could drive positive selection in genes involved in micronutrient metabolism—the case of cofactor transporters

Regulome DB annotation. (XLSX 10 kb

Additional file 7: Table S3. of Ancestors’ dietary patterns and environments could drive positive selection in genes involved in micronutrient metabolism—the case of cofactor transporters

SNP functional annotation. (XLSX 194 kb

Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy

<div><p>Although the genetic basis of Duchenne muscular dystrophy has been known for almost thirty years, the cellular and molecular mechanisms characterizing the disease are not completely understood and an efficacious treatment remains to be developed. In this study we analyzed proteomics data obtained with the SomaLogic technology from blood serum of a cohort of patients and matched healthy subjects. We developed a workflow based on biomarker identification and network-based pathway analysis that allowed us to describe different deregulated pathways. In addition to muscle-related functions, we identified other biological processes such as apoptosis, signaling in the immune system and neurotrophin signaling as significantly modulated in patients compared with controls. Moreover, our network-based analysis identified the involvement of FoxO transcription factors as putative regulators of different pathways. On the whole, this study provided a global view of the molecular processes involved in Duchenne muscular dystrophy that are decipherable from serum proteome.</p></div

L'Écho : grand quotidien d'information du Centre Ouest

10 septembre 19381938/09/10 (A67).Appartient à l’ensemble documentaire : PoitouCh

Tissue specificity from Human Protein Atlas.

<p>(a) Bar chart showing the number of proteins in each of the categories defined by Human Protein Atlas to classify the proteins according to their level of tissue-specificity. (b) Bar chart showing the tissues in which the tissue-enriched proteins are expressed. The stars above the columns indicate the significance of enrichment analysis (***Fisher’s exact test p-value < 0.0001; ** Fisher’s exact test p-value < 0.001).</p

Long biomarker panel.

<p>Long biomarker panel.</p

Network-based pathway enrichment analysis.

<p>Network-based pathway enrichment analysis.</p

Age-related changes of biomarker levels in DMD patients and control.

<p>The first chart shows the age distribution in cases and controls while the other charts show the variation in serum protein level for the five proteins showing the most significant age related change. The red dots correspond to the data for DMD patients while the blue ones to the controls. The lines in the corresponding colors show the regression line, while the gray area corresponds to the confidence interval.</p

Short biomarker panel.

<p>Short biomarker panel.</p

Gene-set enrichment analysis.

<p>Gene-set enrichment analysis.</p