Max-Planck-Institut
für molekulare Genetik
Functional Genomics with R
Alena van Bömmel
Max Planck Institute for Molecular Genetics
Software Praktikum, 1.2.2013
Folie 1
Max-Planck-Institut
für molekulare Genetik
Transcriptional Regulation
Software Praktikum, 1.2.2013
Folie 2
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
Software Praktikum, 1.2.2013
Folie 3
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Software Praktikum, 1.2.2013
Folie 4
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Software Praktikum, 1.2.2013
Microarray
Folie 5
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Software Praktikum, 1.2.2013
Microarray
PWM Genome Scan
Folie 6
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Microarray
PWM Genome Scan
Data
analysis
Software Praktikum, 1.2.2013
Folie 7
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Microarray
PWM Genome Scan
Data
analysis
Software Praktikum, 1.2.2013
Folie 8
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Microarray
PWM Genome Scan
Data
analysis
Software Praktikum, 1.2.2013
Folie 9
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Experiments
ChIP-chip, ChIP-seq
Microarray
PWM Genome Scan
Data must be from the same cell line/tissue!
Data
analysis
Software Praktikum, 1.2.2013
Folie 10
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Data
analysis
Software Praktikum, 1.2.2013
Folie 11
Max-Planck-Institut
für molekulare Genetik
Target Genes of a TF
Data
analysis
Comparison
Software Praktikum, 1.2.2013
Folie 12
Max-Planck-Institut
für molekulare Genetik
Some important questions
How do we find the target genes of ChIPseq peaks in enhancers?
• distant location of peaks to genes (>5kb)
• how do we find the target genes?
• additional tools for enhancer-target prediction
In which genomic locations do we predict
the TF-binding?
• promoter region-which exact coordinates?
• do we have an information about open chromatin?
• which additional data can we use?
Software Praktikum, 1.2.2013
Folie 13
Max-Planck-Institut
für molekulare Genetik
Additional analysis
Binding motifs
binding motifs
• are the overrepresented
motifs in the ChIP-peak
regions different?
• do we find any co-factors?
Recommended tool:
RSAT rsat.ulb.ac.be
binding motifs
Software Praktikum, 1.2.2013
binding motifs
Folie 14
Max-Planck-Institut
für molekulare Genetik
Bioinformatics
•
•
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Read mapping
(Bowtie/bwa)
Peak Calling
(MACS/Bioconduct •
or)
•
Peak-Target
Analysis
(Bioconductor)
Microarray data
analysis
(Bioconductor)
Differential Genes
(R)
GSEA
•
•
Software Praktikum, 1.2.2013
•
•
PWM Genome
Scan
(TRAP/MatScan)
Statistics (R)
Data Integration
(R/Python/Perl)
Statistical
Analysis (R)
Folie 15
Max-Planck-Institut
für molekulare Genetik
Bioinformatics tools
READ THE MANUALS!
•
•
•
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Bowtie bowtie-bio.sourceforge.net/manual.shtml
bwa bio-bwa.sourceforge.net/bwa.shtml
MACS github.com/taoliu/MACS/blob/macs_v1/README.rst
TRAP trap.molgen.mpg.de/cgi-bin/home.cgi
matrix-scan http://rsat.ulb.ac.be/
Bioconductor www.bioconductor.org/ (more info in R course)
Databases
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•
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GEO www.ncbi.nlm.nih.gov/geo/
ENCODE genome.ucsc.edu/ENCODE/
SRA www.ncbi.nlm.nih.gov/sra
Software Praktikum, 1.2.2013
Folie 16
Max-Planck-Institut
für molekulare Genetik
Schedule
•
•
11.03. Introduction lecture, R course
19.03. Presentation of the detailed plan of each group
(which TF, cell line, tools, data, data integration, team
work )
• 26.03., 02.04., 09.04., 16.04. progress meetings
• 23.04. Final report deadline, Presentations
• 25.04. Final meeting, discussion of final reports
Software Praktikum, 1.2.2013
Folie 17
Max-Planck-Institut
für molekulare Genetik
Group 1
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•
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Expression data: Lin, Vega et al., PLoS Genet., 2007
ChIP-seq data: Joseph, Orlov, Huss et al., MSB, 2010
PWM database: jaspar.genereg.net
Software Praktikum, 1.2.2013
Folie 18
Max-Planck-Institut
für molekulare Genetik
Group 2
•
Expression data: Cappellen, Schlange, Bauer et al.,
EMBO reports, 2007
• Musgrove et al., PLoS One, 2008
• ChIP-seq data: ENCODE Project
• PWM database: jaspar.genereg.net
Software Praktikum, 1.2.2013
Folie 19
Max-Planck-Institut
für molekulare Genetik
Group 3
•
•
•
Expression data: Lin, Vega et al., PLoS Genet., 2007
ChIP-seq data: Joseph, Orlov, Huss et al., MSB, 2010
PWM database: jaspar.genereg.net
Software Praktikum, 1.2.2013
Folie 20