Francisco García García, fgarcia@cipf.es

1. General overview of the sessions. Studies of genomic variation. Prioritization of variants and genes. Introduction.
2. CSVS (Collaborative Spanish Variant Server). This database provides information about the variability of the Spanish population. It is very useful for filtering polymorphisms and local variations when prioritizing candidate disease genes. CSVS exercises.
3. Prioritization of genes and functional profiling **: *PANTHER:** Protein ANalysis THrough Evolutionary Relationships. Functional profiling tool. Exercises.
   • STRING: functional protein association networks. Exercises.
   • g:Profiler. Functional profiling web tool.
   • Endeavour web tool. How to prioritize from Endeavour?. Exercises: 2 cases + 4 more activities
4. More interesting web tools:
   • Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Scientific Reports 2021.

/*

1. BiERapp. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies. BiERapp exercises.
2. TEAM (Targeted Enrichment Analysis and Management). Management of panels of genes for targeted enrichment and massive sequencing for diagnostic applications. How to design panels of genes. TEAM exercises.

*/

Marta Hidalgo Garcia, mhidalgo@cipf.es

Introduction to Babelomics 5 (from Mozilla Firefox browser)

• RNA-Seq Data Analysis. transcriptomics_upv_mbb.pdf
• Practical exercises:
  1. Normalization exercise
  2. Differential expression exercise
  3. Single Enrichment exercise
  4. Clustering exercise

/*

• Pipeline exercise:
  • Expression file: kirc_demo_counts_4babelomics.txt
  • Experimental design file: kirc_demo_ed.txt

babelomics_practicas.zip diff_exp16.pdf

*/

• hiPathia. High-throughput pathway inference analysis. hipathia_upv_mbb.pdf

/* * PathAct. Actionable pathway workshop. pathact_2018jan.pdf

*/

• Babelomics 5.0: functional interpretation for new generations of genomic data. Alonso R, Salavert F, Garcia-Garcia F, et al. Nucleic Acids Res. 2015;43:W117-W121.
• High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J. Oncotarget. 2017 Jan 17;8(3):5160-5178. doi: 10.18632/oncotarget.14107.
• A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W88-W93.
• A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Alemán A, Garcia-Garcia F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W83-W87.
• ** Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.** Salavert F, Hidalgo MR, Amadoz A, Çubuk C, Medina I, Crespo D, Carbonell-Caballero J, Dopazo J, Nucleic Acids Res. 2016 May 2. DOI 10.1093/nar/gkw369.
• PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. Paul D. Thomas, Michael J. Campbell, Anish Kejariwal, Huaiyu Mi, Brian Karlak, Robin Daverman, Karen Diemer, Anushya Muruganujan, and Apurva Narechania.Genome Res. 2003. 13: 2129-2141.
• CSVS, a crowdsourcing database of the Spanish population genetic variability. Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, Lopez-Lopez D, Loucera C, Fernandez-Rueda JL, Gallego A, García-Garcia F, González-Neira A, Pita G, Núñez-Torres R, Santoyo-López J, Ayuso C, Minguez P, Avila-Fernandez A, Corton M, Moreno-Pelayo MÁ, Morin M, Gallego-Martinez A, Lopez-Escamez JA, Borrego S, Antiñolo G, Amigo J, Salgado-Garrido J, Pasalodos-Sanchez S, Morte B; Spanish Exome Crowdsourcing Consortium, Carracedo Á, Alonso Á, Dopazo J. Nucleic Acids Res. 2021 Jan 8;49(D1):D1130-D1137. doi: 10.1093/nar/gkaa794. PMID: 32990755; PMCID: PMC7778906.
• More publications.

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