Course in Multi-omic Integrative Analysis of Gene Expression, March 5-9, 2018. Centro de Investigación Príncipe Felipe, Valencia, Spain
The Genomics of Gene Expression lab presents the second edition of this course that aims to teach the students how to perform an integrative analysis of different omic data types in order to model the regulation of gene expression. To this end, we will first study in depth the pre-processing and statistical analysis of the different omic data types with a special focus on Next Generation Sequencing technologies such as RNA-seq, ChIP-seq, ATAC-seq, DNA-seq and Methyl-seq, but also metabolomics or proteomics. Next, we will study several integration examples to cover different integration strategies. All these lectures will be complemented with hands-on sessions. R programming language will be mostly used. Finally, we will also have a longer practical session to recapitulate all the learned lessons by solving a real integration problem. During this last session, the students can analyze either their own data or the data provided by the organizers.
Where and when?
C/Eduardo Primo Yúfera, 3
(Next to the Oceanografic)
46012 Valencia, Spain
5th – 9th of March, 2018 (40 hours)
Who is the target audience?
The course is targeted to students and researchers with some experience in bioinformatics analysis and R programming language that wish to learn more about the integration of different omic data types.
The course is restricted to a maximum of 25 participants.
The official language of the course will be English.
Requisites: Basic notions of R programming. If students are not familiar with R language, they should complete any of the following (free) courses or materials before coming to the course:
- http://swirlstats.com/students.html with https://github.com/swirldev/swirl_courses#swirl-courses
- https://cran.r-project.org/ → Manuals → An Introduction to R
The students must bring their own computers. The organizers will provide information about the software or R libraries to be installed before the course, as well as the files or data needed for the course.
Program of the course
- Introduction to MultiOmics. Review on omics platforms.
- NGS pipelines. Description of pipelines from library construction to expression quantification or peak calling for RNA-seq, miRNA-seq, ChIP-seq, DNase-seq. Most popular software (pros and cons). Similarities and differences among omics. Which type of output can be obtained?
- NGS analysis. Quality control on quantification data. Biases or technical artifacts in RNA-seq and other omics. Normalization strategies. Detection and correction of batch effects or other unwanted effects from unknown source. Differential expression methods. Functional Enrichment strategies. Including hands-on session.
- Methylation: Platforms to measure methylation. Pipeline to process methylation data. Differential methylation. Including hands-on session.
- Proteomics and metabolomics. Platforms to measure proteomics and metabolomics. Processing pipelines. Normalization and missing value imputation. Including hands-on.
- Overview of omics integration. State of the art in omics integration: methods and software. Considerations on experimental design (sample size) and types of data.
- Matching omics. Methods for linking transcription factor binding sites, miRNA targets, Enhancers and genomic regions to target genes. ID conversion. Including hands-on session.
- Integration example 1. Integrating RNA-seq & ChIP-seq data. Including hands-on session.
- Integration example 2. Paintomics. Visualizing different omic data types on KEGG pathways. Including hands-on session.
- Integration example 3. Integrating DNA-seq with other omics. Including hands-on session.
- Integration example 4: Integrating methylation with other omics. Including hands-on session.
- Integration example 5: Generalized Linear Models to investigate the multilayer regulation of gene expression. Including hands-on session.
- Integration example 6: Multivariate methods to integrate different omics. Including hands-on session.
- Practical session: Recapitulating all that has been learned during the course by applying it on a real multi-omic data set. Work in groups. Results will be presented by the teams at the end of the session.
- Invited speakers: Stefan Götz (BIOBAM) will present Blast2GO software. Ángeles Arzalluz (Centro de Investigación Príncipe Felipe, Valencia) will give a seminar on single cell technologies.
- Ana Conesa
- Sonia Tarazona
- Lorena de la Fuente
- Salvador Casaní
- Manuel Ugidos
- Francisco Pardo
- Teresa Rubio
- David Gómez Cabrero
Deadline: 9th of February, 2018
If you wish to pre-register to this course, you must send the following documentation to Sonia Tarazona (email@example.com) before the 9th of February, 2018:
- Enrollment form, which can downloaded from here.
Deadline: 20th of February, 2018
Price: 500 €. The price includes meals and coffees, as well as the gala dinner.
If you are selected to join the course, you will be notified by e-mail and will have to formalize the payment before 20th of February, 2018. The payment (500 €) must be done by bank transfer to the bank account below (transfers from outside Spain will need SWITF or IBAN codes).
The transference confirmation must be sent by e-mail to Laura Galisteo (firstname.lastname@example.org). Please, follow these instructions:
- E-mail subject must be “Name Person +MIAGE course registration”.
- Attach the transference confirmation.
- If you need an invoice, you must include in the e-mail the information for invoicing: Name or Institution, Address, and VAT/CIF registration number.
- If you have any special dietary requirements or food allergies, let us know.
BANK ACCOUNT INFORMATION
|Account Holder:||Fundacion de la Comunidad Valenciana Centro de Investigacion Principe Felipe.|
|Bank Address:||C/Doctor Moliner, 2. 46010-VALENCIA|
|IBAN Code:||ES14 2038 9938 4160 0020 4038|
|Concept:||MIAGE + YOUR NAME|
Telephone: +34 96 328 96 80
These are some of the courses we have organized or participated in the past:
|Specific Multi-Omics Analysis Pipelines||5th-9th December 2017||Karolinska Institutet (Stockholm)||Ana Conesa & Salvador Casaní & Jorge Ferrer & Santosh Atanur & Oscar Yanes & Jordi Capellades & Axel Imhof & Andreas Schmidt|
|DEANN workshop in multiomic data integration and technology transfer||November 13th – 17th, 2017||Instituto Nacional de Medicina Genómica (INMEGEN), Mexico D.F.||Ana Conesa & Sonia Tarazona & Claudia Rangel||+ info|
|Genomics-oriented Biostatistics||5th - 7th April 2017||Centro de Investigación Príncipe Felipe (Valencia, Spain)||Ana Conesa & Sonia Tarazona & Salvador Casaní|
|Multi-omic Integrative Analysis of Gene Expression||January 23-27 2017||Centro de Investigación Príncipe Felipe (Valencia, Spain)||Ana Conesa & Sonia Tarazona & Lorena de la Fuente & Salvador Casaní & David Gómez Cabrero||MIAGE 2017|
|Introduction to programming||19th-22nd December 2016||Josep Carreras Leukaemia Research Institute (IJC) (Spain)||Ana Conesa & Salvador Casaní|
|Técnicas Estadísticas en Informática||7th October, 2016||Universidad de Sevilla (Sevilla, Spain)||Sonia Tarazona|
|STATegra Summer School in Omics Data Integration||7th-11th September, 2015||Benicàssim (Castellón, Spain)||STATegra consortium||STATegra Summer School|
|The Genomics of Gene Expression RNA-Seq course||March, 2015||Centro de Investigación Príncipe Felipe, Valencia (Spain)||Genomics of Gene Expression group|
|The Genomics of Gene Expression RNA-Seq course||September, 2014||Centro de Investigación Príncipe Felipe, Valencia (Spain)||Genomics of Gene Expression group|
|The Genomics of Gene Expression RNA-Seq course||March, 2014||Centro de Investigación Príncipe Felipe, Valencia (Spain)||Genomics of Gene Expression group|
|Course in Automated Functional Annotation and Data Mining||January, 2014||La Paz (Mexico)||Ana Conesa & Stefan Göetz|
|Course in RNA-seq and Functional Annotation||November, 2013||Buenos Aires (Argentina)||Ana Conesa|
|Course in Automated Functional Annotation and Data Mining||November, 2013||Sao Paulo (Brasil)||Ana Conesa & Stefan Göetz|
|Course in Automated Functional Annotation and Data Mining||October, 2013||Centro de Investigación Príncipe Felipe, Valencia (Spain)||Ana Conesa & Stefan Göetz|
|Course in Automated Functional Annotation and Data Mining||March, 2013||Oeiras (Portugal)||Ana Conesa & Stefan Göetz|
|Course in Automated Functional Annotation and Data Mining||January, 2013||Brisbane (Autralia)||Ana Conesa & Stefan Göetz|
|Análisis de RNA-seq y ChIP-seq||2012||IDIBAPS (Barcelona, Spain)||Sonia Tarazona & Javier Santoyo|
|Data analysis workshop for massive sequencing data||2011||Universidad de Granada (Spain)||Sonia Tarazona|