How to Make Sense out of Your RNA-Seq/Microarray Data;

Gene expression data analysis using R: How to make sense out of your RNA-Seq/microarray data; Databases & Cytoscape (day 5)

July 3-7, 2017 17th edition, organised by MolMed Final vs 170421

Course organizers and website Program: Dr. Judith Boer Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, [email protected] Coordination: Dr. Frank van Vliet MolMed, 010-70 43518/ 06-5474 6408, [email protected] Website: www.molmed.nl Course website: http://molmed-expression.erasmusmc.nl/

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  Lodewyk Wessels, Bioinformatics and Statistics Group, Netherlands Cancer Institute, Amsterdam (inv., t.b.c.)  Renée de Menezes, Department of Epidemiology and Biostatistics, VUmc, Amsterdam  Mitra Ebrahimpoor, Department of Medical Statistics and Bioinformatics, LUMC  Maarten van Iterson, Department of Molecular Epidemiology, LUMC Leiden  Maarten Fornerod, Dept’s of Pediatric Oncology & Cell Biology, 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  Kristina Hettne, Biosemantics Group, LUMC Leiden  Peter van Baarlen, Guido Hooiveld (t.b.c.), 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 http://biosb.nl). Some concepts may be applicable to other types of genomics data. Most of the speakers (and therefore examples) have a biomedical background.

1 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: Affymetrix microarray/ Illumina microarray/ Agilent microarray/ other microarray: ..... 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 of microarray 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) organizes a basic course on R from 18-24 May 2017; see: www.molmed.nl. There is also a BioSB Course: Kick start R on May 19th in Amsterdam; see: http://biosb.nl/education/course-portfolio/course-kick-start-r/ and register: http://biosb.nl/education/course-portfolio/course-kick-start-r/enrollment-kick-start-r-course- 4th-edition/ .

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

2 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 Judith Boer, Alex Hoogkamer, Job R: part 1 van Riet, Henk-Jan van den Ham 14:30 14:45 Coffee 14:45 17:00 Practical: Normalization and quality control in Judith Boer, Alex Hoogkamer, Job R: part 2 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 9:45 10:00 Coffee 10:00 10:45 Cluster validation and principal component Marcel Reinders analysis 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 Renée de Menezes (cont’d) 15:00 17:00 Practical: Finding differentially expressed Renée de Menezes, Judith Boer, genes in R using limma / edgeR Alex Hoogkamer, Henk-Jan van den Ham

Day 3 Wednesday July 5: Classification and Gene set testing Room: Computer room 22 (OWR) Moderators: Lodewyk Wessels / Mitra Ebrahimpoor 8:45 9:00 Welcome coffee 9:00 9:45 Gene annotation Maarten van Iterson, LUMC 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 Practical: Batch effects Judith Boer, Maarten van Iterson, 11:15 12:00 Alex Hoogkamer 12:00 12:30 Remaining questions, discussion Judith Boer, Maarten van Iterson 12:30 13:30 Lunch (in room Ae-406) 13:30 14:30 Testing groups of genes Mitra Ebrahimpoor, LUMC 14:30 14:45 Coffee 14:45 17:00 Practical: Testing groups of genes Mitra Ebrahimpoor, assistant …. (t.b.d.)

3 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 Classification and PAM Lodewyk Wessels 9:45 9:50 Short break 9;50 10:30 Classification and PAM Lodewyk Wessels 10:30 10:45 Coffee 10:45 12:30 Practical: Classification using PAM Lodewyk Wessels, ... 12:30 13:30 Lunch (in room Ae-406) 13:30 14:15 Exploring a genomic landscape Maarten Fornerod, Dept’s of Pediatric Oncology & Cell Biology 14:15 14:30 Coffee 14:30 17:00 Assignment: Data analysis of ALL samples Judith Boer, Andrew Stubbs, Alex Hoogkamer, Job van Riet

Day 5 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 Kristina Hettne, … lists with the Anni Web Service and DAVID; Databases and pathway analysis 12:15 13:15 Lunch 13:15 14:30 Cytoscape Peter van Baarlen, Guido Hooiveld (t.b.c.) 14:30 14:35 Short break; coffee 14:35 15:30 Cytoscape (cont’d) Peter van Baarlen, Guido Hooiveld 15:30 15:45 Coffee 15:45 17:00 Practical Cytoscape Peter van Baarlen, Guido Hooiveld 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: [email protected].

4 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 start of 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.