Course in Multi-omic Integrative Analysis of Gene Expression

Course in Multi-omic Integrative Analysis of Gene Expression, January 23-27 2017. Centro de Investigación Príncipe Felipe, Valencia, Spain

The Genomics of Gene Expression lab presents 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, DNase-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. For this last session, the students can analyze either their own data or the data provided by the organizers.

Where and when?

Príncipe Felipe Research Center

C/Eduardo Primo Yúfera, 3
(Next to the Oceanografic)
46012 Valencia, Spain

23th – 27th of January, 2017     (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:

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

Please note that the following program may be modified according to the profiles of the students finally registered in the course.

  • Introduction to MultiOmics. Review on omics platforms. 
  • NGS: from reads to counts. 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: Quality Control, Normalization, Differential Expression, Functional Enrichment. 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.
  • 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.
  • Methylation: Platforms to measure methylation. Pipeline to process methylation data. Differential methylation. 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. Time-course data. Integrating RNA-seq & DNase-seq from their dynamics changes. Including hands-on session.
  • Integration example 4: Integrating methylation with other omics.
  • Integration example 5: Generalized Linear Models to investigate the multilayer regulation of gene expression. Including hands-on session.
  • Integration example 6: Partial Least Squares related 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. Nuria López Bigas (Institute for Research in Biomedicine, Barcelona) will give a conference on “Tumor genomes shed light into somatic mutational processes and cancer vulnerabilities”.



  • Ana Conesa
  • Sonia Tarazona
  • Lorena de la Fuente
  • Salvador Casaní
  • David Gómez Cabrero




Deadline: 30th of November, 2016

If you wish to pre-register to this course, you must send the following documentation to Sonia Tarazona ( before the 30th of November, 2016:

  • CV
  • Enrollment form, which can downloaded from here here.


Deadline: 22nd December, 2016

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 22nd of December, 2016. 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 Eugenia Flores ( 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 Name: BANKIA
Account Holder: Fundacion de la Comunidad Valenciana Centro de Investigacion Principe Felipe.
Bank Address: C/Doctor Moliner, 2. 46010-VALENCIA
Account: 6000204038
IBAN Code: ES14 2038 9938 4160 0020 4038


Eugenia Flores


Telephone: +34 96 328 96 80

Ext: 3019#