Nutrient - Gene - Disease correlation through the understandings of ‘omics’

Transcript

1. Nutrient - Gene - Disease correlation through the understandings of ‘omics’ Authors: Miodrag Cekikj Slobodan Kalajdzhiski - 14th International Conference on Informatics and Information Technologies -
2. Agenda 2  Industrial “REVOLUTION” through FOOD “production”  Reference research point – DATA systematization  Nutrient – Gene interactions  Gene – Gene associations  Gene – Disease dependencies  Conclusion and further guidance
3. 1. Industrial “REVOLUTION” through FOOD “production” 3  Food Revolution vs. Food Industrialization  Original Food vs. Healthy Food
4. 1. Industrial “REVOLUTION” through FOOD “production” 4  What to EAT, or NOT to EAT, that is the question?  A growing proportion of the world population is obsessed with healthy food and choice of nutrients that maintain physical and mental health
5. 1. Industrial “REVOLUTION” through FOOD “production” 5  Ayurveda medicine - 'ayus' (life) and 'ved‘ (knowledge)  Complete system of medicine with Indian historical roots  Provides a guide to diet and lifestyle of the people in order to stay healthy as well as people that can improve their health
6. 1. Industrial “REVOLUTION” through FOOD “production” 6  Gregor Mendel (1822 - 1884) laid the foundations of classical genetics which enables fertile ground for scientific research in the context of the characteristics and development of generations, or descendants
7. 2. Reference research point – DATA systematization 7  The Nielsen Co (2012) – Social networks “BOOM” Confidential sources EVOLUTION Versatile sources Classic EMAIL TRANSFORMATION SOCIAL NETWORKS
8. 2. Reference research point – DATA systematization 8  The impact of network communication in the preservation of ethnographic and anthropological food characteristics
9. 2. Reference research point – DATA systematization 9 RAW DATA Ingredients/Nutrition values Preparation ??! Recipes Initial Data Set (100.000,00 recipes) NLP libraries Web Crawler (custom implementation) Python Programming Language Web sites APIs
10. 3. Nutrient – Gene interactions 10 Internal organism factors  The expression of genetic information can be highly dependent on, and regulated by, nutrients, micronutrients, and phytochemicals found in food.
11. 3. Nutrient – Gene interactions 11  Genomics - study of the genome, more specific an approach of mapping, sequencing, and analysis of all genes present in the genome  Functional genomics - a field that tries to understand the pattern of gene expression, especially across different environmental conditions Frederick Sanger (1918 - 2013) Sanger Sequencing (complete genome of a virus and of a mitochondrion)
12. 3. Nutrient – Gene interactions 12 Nutrients from our food are funneled into a biochemical pathway that extracts methyl groups and then attaches them to our DNA.
13. 3. Nutrient – Gene interactions 13
14. 3. Nutrient – Gene interactions 14  A big set of dietary components can alter organism`s genetic properties and thereby influence human health. RAW Data (NUTRIENTS) GENES/ GENOME DISEASES Preparation, Circumstances, Amount… ?!
15. 4. Gene – Gene associations 15  Which of the multitude of genetic variants are useful for predicting who is at risk for common diseases?  All techniques/tools are based on well - known knowledge databases created to support the processes of identifying specific gene - gene interactions and their influence in different environment conditional systems.
16. 4. Gene – Gene associations 16  GeneMANIA - finds other genes that are related to a set of input genes, using a very large set of functional association data  Association data include protein and genetic interactions, pathways, co- expression, co - localization and protein domain similarity.
17. 4. Gene – Gene associations 17  STRING - database of known and predicted protein - protein interactions  The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms and from interactions aggregated from other (primary) databases.
18. 4. Gene – Gene associations 18  Gene - gene and gene - disease interactions underlay on common concepts and goals, to understand the relation between genes properties and disease activation.  A lot of researchers work on ideas where main hypothesis is that the most central genes in an interaction network for a disease are likely to be related to the disease.
19. 5. Gene – Disease dependencies 19  Online Mendelian Inheritance in Man (OMIM, 2007) - An Online Catalog of Human Genes and Genetic Disorders  In light of scientific developments, one of the most well - known databases that stores gene - disease associations
20. 5. Gene – Disease dependencies 20  DisGeNET - a discovery platform integrating information on gene-disease associations  The platform provides a score in order to rank the associations based on the supporting evidence.  DisGeNET can be queried through Search and Browse functionalities available from this web interface
21. 5. Gene – Disease dependencies 21  Mala Cards - an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human gene  The database is organized into "disease cards", each integrating prioritized information, and listing numerous known aliases for each disease, along with a variety of annotations, as well as inter - disease connections, empowered by the GeneCards relational database, searches, and GeneAnalytics set-analyses.
22. 6. Conclusion and further guidance 22  Nutrients as probably the most important external environment factor that is in direct correlation with genes processes.  Various disciplines that solve relevant complex issues and conditions which are very closely related to the human health and further human survival.
23. 6. Conclusion and further guidance 23  Detailed analysis of nutrient - gene, gene - gene and gene - disease interactions and different techniques and approaches for data mining, visualization, processing and correlation in order to get understanding and better knowledge for nutrient - disease relationship and dependencies.