bioinformatics wp sp-hpp november 5th and 6th, 2013 alberto pascual-montano
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Bioinformatics WPsp-HPP
November 5th and 6th, 2013
Alberto Pascual-Montano
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1616
1. Bioinformatic analysis of Chromosome 16.2. Cell type(s) selection. Trascriptomic and Proteomic detailed analysis.3. Expression, purification and characterization of proteins encoded by
chromosome 16 that have not been described so far.4. Development of MRM methods for the quantification of the most
abundant protein species encoded by each of the chromosome 16 genes.
5. Identification, characterization and quantification of protein variants from chromosome 16 genes.
6. Definition of SOPs7. Development of bioinformatic environment.8. Biobanking.9. Configuration of the B-D pilar for the Spanish HPP consortium.
Chromosome 16 general aims
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32 research units organized in 5 WG:WG1. Protein expression and purification. Peptides. Transcriptomics.WG2. Development of quantitative S/MRM assays.WG3. Shotgun proteomics. Molecular profiles and PTMs.WG4. BioinformaticsWG5. Biology and disease. Neurodegenerative, cardiovascular, infectious, cancer, obesity, Rheumatic disorders.
AIMS• Chromosome 16 annotation.• Selection of 3 cell lines based on published transcriptomic profiles for maximum
chromosome 16 coverage• Transcriptomic analysis of the selected cell lines.• Shotgun proteomic analysis of the selected cell lines.• Development of SRM methods for 200 proteins/year.• Expression of missing proteins and development of SRM methods.
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Plataforma de Recursos Biomoleculares y Bioinformáticos
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WG 4.-Bioinformatics Team
RU4aJP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid
Chair: Alberto Pascual Co-chair: Alberto Medina
RU4bFJ. CorralesCIMA-UNProteoRed-ISCIII, Pamplona
RU4cJ. AbianIIBB-CSIC ProteoRed-ISCIII, Barcelona
RU4dC. GilPCM-UCMProteoRed-ISCIII, Madrid
RU4eJM. ArizmendiUPV/EHUProteoRed-ISCIII, Bilbao
RU4gA. PascualCNB-CSIC, Madrid
Scientific Researchers:
M-Bartolomé S. Medina A.
Scientific Researchers:Guruceaga E. Segura V.
Scientific Researchers:
Gallardo O.
Scientific Researchers:
Vialás V.
Scientific Researchers:Fullaondo A. Prieto G.
Scientific Researchers:
Nogales R.Tabas D.Martínez D.Cruceiro J.
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WG 4.-Bioinformatics Team
RU4aJP. AlbarCNB-CSIC, ProteoRed-ISCIII, Madrid
Chair: Alberto Pascual Co-chair: Alberto Medina
RU4bFJ. CorralesCIMA-UNProteoRed-ISCIII, Pamplona
RU4cJ. AbianIIBB-CSIC ProteoRed-ISCIII, Barcelona
RU4dC. GilPCM-UCMProteoRed-ISCIII, Madrid
RU4eJM. ArizmendiUPV/EHUProteoRed-ISCIII, Bilbao
RU4gA. PascualCNB-CSIC, Madrid
Scientific Researchers:
M-Bartolomé S. Medina A.
Scientific Researchers:Braga M. Guruceaga E. Segura V.
Scientific Researchers:
Gallardo O.
Scientific Researchers:
Vialás V.
Scientific Researchers:Fullaondo A. Prieto G.
Scientific Researchers:Cruceiro J.Martínez D.Nogales R.Tabas D.
RU2hE. SabidóCRG/UPF Barcelona
Scientific Researchers:
Mancuso F.
SpHPP Meeting, La Cristalera, Nov 2013
Scientific Researchers:
?
RU2iJ. VázquezCNIC
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Objetivos hasta Dic. 2013
• Unificar y estandarizar el flujo de análisis Shotgun.
• Incorporar la reunión de datos. Protein Grouping.
• Proteogenomics: integración gene expression (microarrays, RNA-seq) y Shotgun
• Implementar sistema de información MRM.• Página Web.
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Grado de consecución de los objetivos Dic. 2013
• Se ha definido un pipeline de análisis de datos shotgun basado en MASCOT, agrupamiento de proteínas (protein grouping) y de publicación de resultados. PMWTK & MiapeExtractor. Aunque se ha probado Sequest no se ha conseguido integrar plenamente.
• Se ha implementado un sistema apoyado en BD para la inserción y validación de datos MRM. No permite una consulta exhaustiva de los datos.
• Se ha implementado flujos para integración microarrays y RNA-seq y Shutgun
• Se ha implementado flujos para búquedas de proteínas en BDs de RNA-seq
• Página Web, FTP y DropBox.
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Nueva estructura del WP4 (Bioinformática)
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Shotgun MS/MSQue tenemos y que no tenemos
• Envío desde el cliente y almacenamiento MS/MS. • Plataforma “casi-automática” para analizar
experimentos Shotgun. (basado en MASCOT)• Generación de metafile para envío de datos a PX• Envío desatendido de datos a BD• Análisis local y abierto de datos MS/MS• Actualización automática e incremental de
datos MS/MS• Envío totalmente automático a PX.
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MRMQue tenemos y que no tenemos
• Almacenamiento mínimo de experimentos MRM. • Consultas básicas de detección MRM.• Validación cruzada experimentos MRM.• Envío masivo de datos MRM.• Conexión con datos MS/MS.• Consultas complejas MRM.• Exportación de datos en formato estandar y
envío a PX (Passel).
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PTMQue tenemos y que no tenemos
• Caracterización de las PTM Chr 16
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ProteogenomicsQue tenemos y que no tenemos
• Anotación de las missing proteins empleando neXtProt (versión Ensembl v73)
• Cuantificación y anotación de los 16 tejidos del HBM (sólo muestras SE)
• Integración de datos HBM y shotgun (Jurkat, MCF7, CCD18, Ramos) chr16
• Búsqueda de missing proteins en datos RNA-seq HBM chr16• Análisis de todos los datos del HBM• Extensión del estudio a todos los cromosomas• Generación de bases de datos para búsquedas de proteínas en
base al HBM• Incluir datos públicos de shotgun
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System BiologyQue tenemos y que no tenemos
• Algoritmo de cuantificación de expresión génica mediante RNA-seq
• Análisis de 3 líneas celulares de ENCODE• Análisis de todas líneas celulares de ENCODE• Análisis de todos los cromosomas• Dashboard para compartir resultados• Análisis funcional y de regulación• Pathways y conexión con B/D
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InfrastuctureQue tenemos y que no tenemos
• Web: http://hpp-sp.com/• Dropbox• FTP• Recursos computacionales propios
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Our main deliverable: create a proteo-genomics dashboard for spHPP and HPP:
RNA-seqMicroarraysShutgun proteomicsNAPPAMRM
Others?
Cell lines and Tissues
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Consideraciones generales I:
• Se crea un comité de decisión para acciones bioinformáticas que estará compuesto por Victor Segura, Alberto Medina y Alberto Pascual-Montano. Este comité consultará cualquier decisión que afecte los flujos y análisis bionformáticos del consorcio.
• Se creará un documento descriptivo de los análisis bioinformáticos que estén haciendo cada uno de los miembros del consorcio. Este documento será compartido y es responsabilidad de cada grupo su actualización.
• Este comité deberá ser informado siempre por parte del resto de IPs del consorcio de cualquier cambio en criterios por parte de HUPO, o de cualquier decisión importante que afecte el desarrollo bioinformático del proyecto
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Consideraciones generales II:
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Gracias!