PhenUMA Course

The CIBER of Rare Diseases organized the course: "Introduction to the Analysis of Phenotypic and Functional Networks in Rare Diseases" the next 13 and June 14 in Malaga. This course will be taught by Unit 741 researchers, led by Dr. Francisca Sanchez-Jimenez, with the support of the Research Program of Hereditary Metabolic Medicine.

The main objective is to introduce researchers in the use of the platform PhenUMA ( www.phenuma.uma.es) developed by CIBERER 741 unit. The course is organized in a day of theoretical sessions and practical sessions with other use cases.

This course is aimed at researchers without previous experience in the study of biomedical networks.

Practical Session I: PhenUMA Introduction

• In this session we have included an introduction to the type of indentifiers used as input of the application. Additionally, we have included a short introduction to the most relevant public databases (OMIM, Orphanet, NCBI, ect) to search the indentifier of a gene, diseases or phenotype.
• Introduction to all type of relationships stored in the PhenUMA Database: Known, Inferred and using Semantic Similarity (Funtional and Phenotipic)
• Funtionalities: Working with networks, options and how to extract the information.



• Resources:

  	Donwload slides in PDF
  	Demo: Inputs
  	Demo: PhenExplorer
  	Demo: Handling the interface
  	Demo: Outputs

Sessions II amd III: use cases and examples

• Exercises and examples
• Introduction to Cytoscape



• Resources:

  	Download slides of sessions II and III in PDF
  	Demo: Download an create subnetworks
  	Demo: Visualizing networks using Cytoscape
  	Resources for the practices

• Links to public databases:
  • NCBI: http://www.ncbi.nlm.nih.gov/
  • Ensembl: http://www.ensembl.org/index.html
  • HGNC: http://www.genenames.org/
  • OMIM: http://omim.org/
  • Orphanet: http://www.orpha.net/consor/cgi-bin/index.php


• Other interesting databases:
  • GeneCards http://www.genecards.org/
  • STRING - Known and Predicted Protein-Protein Interactions http://string-db.org/
  • Gene Ontology http://www.geneontology.org/


• References:

  • Armando Reyes-Palomares, Rocio Rodríguez-López, Juan Antonio Ranea, Francisca Sánchez-Jiménez, Miguel Ángel Medina. Global analysis of the human pathophenotypic similarity gene network merges disease module components. PLoS One. 2013;8(2):e56653. doi:10.1371/journal.pone.0056653. Epub 2013 Feb 21

  • Kwang-Il Goh, Michael E. Cusick, David Valle , Barton Childs, Marc Vidal and Albert-László Barabási The human disease network doi: 10.1073/pnas.0701361104 PNAS May 22, 2007 vol. 104 no. 21 8685-8690

  • Hiroaki Kitano Systems Biology: A Brief Overview Science 295, 1662 (2002); DOI: 10.1126/science.1069492

Interesting talk of Albert-László Barabási in TEDMED 2012.