Gene expression data analysis using R:

How to make sense out of your RNA-Seq/microarray data;

Databases & Cytoscape (day 5)

July3-7, 2017

17th edition, organised by MolMed

1vs 170413, some speakers still have to confirm!

Course organizers and website

Program: Dr. Judith Boer

Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital,

Coordination:Dr. Frank van Vliet

MolMed, 010-70 43518/ 06-5474 6408,

Website:

Course website:

Speakers and moderators

  • Judith Boer and Alex Hoogkamer, Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam
  • Marcel Reinders, Information and Communication Theory Group, TU Delft(inv., t.b.c.)
  • Lodewyk Wessels, Bioinformatics and Statistics Group, Netherlands Cancer Institute, Amsterdam(inv., t.b.c.)
  • Renée de Menezes, Department of Epidemiology and Biostatistics, VUmc, Amsterdam
  • Jelle Goeman, Jakub Pecanka, Department of Medical Statistics and Bioinformatics, LUMC(inv., t.b.c.)
  • Maarten van Iterson, Department of Molecular Epidemiology, LUMC Leiden(inv., t.b.c.)
  • …., Department of Urology, Erasmus MC
  • Job van Riet, Cancer Computional Biology Center (CCBC) and Department of Urology, Erasmus MC
  • Andrew Stubbs, Department of Bioinformatics & Alex Hoogkamer, Department of Pedriatrics, Erasmus MC, Rotterdam
  • Henk-Jan van den Ham, Virosciences Department, Erasmus MC, Rotterdam(inv., t.b.c.)
  • Kristina Hettne, Biosemantics Group, LUMC Leiden
  • Peter van Baarlen, Host-Microbe Interactomics Group, Animal Sciences, Wageningen University
  • Course website: Sylvia de Does, Department of Bioinformatics, Erasmus MC(inv., t.b.c.)

Location:Erasmus MC, OWR 22 (Computerroom 22), Education Centre.

Target group

The course is tailored for biological and clinical researchers whose research involves experiments that generate gene expression data by using RNA sequencing or microarrays. The course focuses mostly on the analysis of expression data, and explains general concepts such as experimental design, normalization, testing and interpretation. We do not explain the technologies themselves and we do not cover the mapping of sequence reads. Dedicated courses for next-generation sequencing and RNA-seq covering these topics are available (see Some concepts may be applicable to other types of genomics data. Most of the speakers (and therefore examples) have a biomedical background.

Pre-requisites for participants

Participants need to know what a microarray or RNA sequencing experiment is, and have their own expression profiling data. They have preferably followed an introduction to R course; alternatively they have practiced the "Getting started in R" practical prior to the course. Basic statistical concepts including mean, variance, standard deviation, probability distributions, t-test, p-value, correlation, and linear regression are assumed known. These are typically seen during basic statistics courses.

Please fill in the online registration form (in the free text box at the bottom of the form):

  • do you have basis R knowledge (yes/no); if yes, please indicate how you acquired this knowledge: basic R course/ other…;
  • do you have gene expression data to analyse yes/no, if yes: which platform? Microarrays: Affymetrixmicroarray/ Illumina microarray/ Agilentmicroarray/ othermicroarray: .....

RNA sequencing: tag / transcriptome / other: .....

Format

The course is intensive, and covers the basic concepts and methods required for expression analysis. Presentations are followed by hands-on computer sessions to directly apply and get more insight in the analysis methods. One afternoon is dedicated to the analysis of a new data set, allowing the students to refresh and extend their analysis skill. After the course, the presentations, practicals and test data will remain available for future reference. Software packages used are freeware, including the statistical software R, Bioconductor, Cytoscape and web tools.

Learning objectives

1. The participant has insight in the issues involved in good experimental design ofmicroarray and next-generation sequencing experiments.

2. The participant knows and can perform analysis steps in expression data analysis, visually present and judge the results for:

  • quality control and preprocessing,
  • finding differentially expressed genes,
  • cluster analysis,
  • classification analysis,
  • pathway testing.

3. The participant has insight in the different algorithms and options available to perform an analysis, and can make an informed choice.

4. The participant knows the pitfalls of existing analyses and is able to critically judge the statistical analysis of expression data performed by others.

Registration, deadline, admittance,sponsored places & related courses

The total number of participants is limited to 40. Deadline for registration is 1 week in advance, on Monday 26 June, 9 a.m. When more than 40 students register before this deadline, the organisers will make a selection and admit the students with own data and experience in R. Please note that to this aim you must fill in the online registration form as mentioned above.

MolMed (Erasmus MC) organizesabasic course on R from 18-24 May 2017; see: .

There is also a BioSB Course: Kick start R on April 25 in Amsterdam; see: and register: .

NB: Day 5, Friday July 7: Databases, Pathways and Cytoscape, is also offered as a separate course.

Day 1 / Monday July 3: Design and Preprocessing
Room: Computer room 22 (Education centre)
Moderator : Judith Boer
9:00 / 9:15 / Welcome coffee and registration
9:15 / 9:30 / Short introduction to data sets and tools / Judith Boer
9:30 / 10:30 / Experimental design: Think before you start / Judith Boer
10:30 / 10:45 / Coffee
10:45 / 11:30 / Normalisation / Judith Boer
11:30 / 12:00 / Introduction to R and Bioconductor / Judith Boer
12:00 / 13:00 / Lunch (in room Ae-406)
13:00 / 14:30 / Practical: Normalization and quality control in R: part 1 / Judith Boer, Alex Hoogkamer, Job van Riet, Henk-Jan van den Ham(inv., t.b.c.)
14:30 / 14:45 / Coffee
14:45 / 17:00 / Practical: Normalization and quality control in R: part 2 / Judith Boer, Alex Hoogkamer, Job van Riet, Henk-Jan van den Ham
Day 2 / Tuesday July 4: Gene testing and Clustering
Room: Computer room 22
Moderator: Marcel Reinders/ Renée de Menezes
8:45 / 9:00 / Welcome coffee
9:00 / 9:45 / Hierarchical and K-means clustering / Marcel Reinders(inv., t.b.c.)
9:45 / 10:00 / Coffee
10:00 / 10:45 / Cluster validation and principal component analysis / Marcel Reinders
10:45 / 12:30 / Practical: Clustering using R / Marcel Reinders, ...(t.b.d.)
12:30 / 13:30 / Lunch (in room Ae-406)
13:30 / 14:15 / Finding differentially expressed genes / Renée de Menezes
14:15 / 14:30 / Coffee
14:30 / 15:00 / Finding differentially expressed genes (cont’d) / Renée de Menezes
15:00 / 17:00 / Practical: Finding differentially expressed genes in Rusing limma / edgeR / Renée de Menezes, Judith Boer, Alex Hoogkamer
Day 3 / Wednesday July 5: Classification and Gene set testing
Room: Computer room 22 (OWR)
Moderators: Lodewijk Wessels/ Jelle Goeman
8:45 / 9:00 / Welcome coffee
9:00 / 9:45 / Classification and PAM / Lodewijk Wessels(inv., t.b.c.)
9:45 / 9:50 / Short break
9;50 / 10:30 / Classification and PAM / Lodewijk Wessels
10:30 / 10:45 / Coffee
10:45 / 12:30 / Practical: Classification using PAM / Lodewijk Wessels, ...
12:30 / 13:30 / Lunch (in room Ae-406)
13:30 / 14:30 / Testing groups of genes / Jelle Goeman(inv., t.b.c.)
14:30 / 14:45 / Coffee
14:45 / 17:00 / Practical: Testing groups of genes / Jelle Goeman (inv., t.b.c.), Jakub Pecanka(t.b.d.)
Day 4 / Thursday July 6: Practical Issues and Practice
Room: Computer room 22 (OWR)
Moderator: Judith Boer
8:45 / 9:00 / Welcome coffee
9:00 / 9:45 / Gene annotation / Maarten van Iterson(inv., t.b.c.)
9:45 / 10:30 / Practical: Gene annotation / Maarten van Iterson, Judith Boer
10:30 / 10:45 / Coffee
10:45 / 11:15 / Batch effects / Judith Boer, Maarten van Iterson
11:15 / 12:00 / Practical: Batch effects / Judith Boer, Maarten van Iterson, Alex Hoogkamer
12:00 / 13:00 / Lunch (in room Ae-406)
13:00 / 14:00 / Gene expression profiling: the cancer transcriptome / ……. (t.b.c.)
14:00 / 14:15 / Coffee
14:15 / 15:45 / Assignment: Data analysis of ALL samples / Judith Boer, Andrew Stubbs,Alex Hoogkamer, Job van Riet
15:45 / 16:00 / Coffee
16:00 / 17:00 / Assignment: Data analysis of ALL samples, continued / Judith Boer, Andrew Stubbs, Alex Hoogkamer, Job van Riet, Henk-Jan van den Ham(inv., t.b.c.)
Day5 / Friday July 7: Databases, Pathways and Cytoscape
Room: Computer room 22 (OWR)
This day is also offered as a separate 1-day course
Moderator: Andrew Stubbs & Peter van Baarlen
8:45 / 9:00 / Welcome coffee
9:00 / 9:45 / Databases and pathway analysis / Andrew Stubbs
9:45 / 10:30 / Interpretation of gene lists / Kristina Hettne, …
10:30 / 10:45 / Coffee
10:45 / 12:15 / Practical: Practical: Interpretation of gene lists with the Anni Web Service and DAVID; Databases and pathway analysis / Kristina Hettne, …
12:15 / 13:15 / Lunch
13:15 / 14:30 / Cytoscape / Peter van Baarlen
14:30 / 14:35 / Short break; coffee
14:35 / 15:30 / Cytoscape (cont’d) / Peter van Baarlen
15:30 / 15:45 / Coffee
15:45 / 17:00 / Practical Cytoscape / Peter van Baarlen
17:00 / End day 5: hand in evaluation form & badge!

Attendance fees

Course tuition for non-commercial participants is € 700. Discounts are handled as followed:

  • Participants from the postgraduate school MolMed get a discount of 100% (tuition = €0).
  • PhD students and Master’s students, regardless of institution, get a discount of 50% (tuition = €350).

The course is considered an entirety, and participants are encouraged to attend all parts of the course. No discounts are given for participants who chose not to participate in a portion of the course.

If these financial requirements pose a problem, please contact Frank van Vliet, managing director of the Erasmus Postgraduate School Mol Med, at: .

Invoices

Fees should only be paid after receipt of an INVOICE. Shortly after your registration you will

receive the INVOICE by mail. Payment should be transferred to account: 43.47.01.408 / Erasmus MC, (IBAN code bank: NL86ANBA0434701408; SWIFT code bank: ABNANL2A), with the invoice number noted. Late registrations may also pay in cash upon arrival.

Cancellations

Cancellation is possible up to one week before the startof the Course. Later cancellation will not be accepted, but you are allowed to send a substitute.

Commercial participants & sponsors

Companies are invited to inquire about commercial participant tuition fees and about sponsoring.

1