SGN-6176 Microarray Data Analysis (Period 4, 2010-11)
This course will be lectured on period 4 starting on 8.3. The course consists
of lectures (2-4h per week) on Tuesdays 10-12 (TB223) and Thursdays 14-16
(TB224) and exercises on Fridays 12-14 (except for 25.3. 8-10) in TC407.
The lectures will be given by Juha Kesseli and the exercises by Kirsti
Laurila. The course has a Moodle page, through which the materials for
the course will be distributed. The Moodle page has an access key which will
be given on the first lecture. If you cannot attend, please e-mail the
lecturer and ask for the key.
Lecture schedule:
- 8.3.: Course information. High-throughput measurements.
- 10.3.: Microarrays.
- 15.3.: Microarray data preprocessing. Normalization.
- 17.3.: Differentially expressed genes. SAM.
- 22.3.: Gene ontology analysis. GSEA.
- 24.3.: Clustering.
- 29.3.: Classification.
- 31.3.: Next generation sequencing.
- 5.4.: Alignment methods for NGS. Hash & BWT.
- 12.4.: Promoter analysis. ChIP-seq.
- 19.4.: RNA-seq.
- 28.4.: Concluding remarks.
Exercise schedule:
- 18.3.: Affymetrix microarray quality control and normalization
- 25.3.: Differential gene expression with limma (Illumina microarrays) Note: This class is exceptionally in the morning, 8-10
- 1.4.: Heatmap-visualizations and clustering
- 8.4.: Usage of biomaRT and DAVID analysis
- 15.4.: ChIP-seq peak-finding
- 29.4.: Promoter analysis (transcription factor binding site
prediction)
