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Last update: TAJ143 (03.12.2013)
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Last update: ROZ143 (08.08.2013)
Students will be able to:
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Last update: TAJ143 (02.07.2013)
R: Zvárová J, Mazura I (eds.), Metody molekulární biologie a bioinformatiky, Karolinum, Praha 2013, ISBN: 978-8024621500 A: Tevfik Dorak, M. (ed.), Real-time PCR (Advanced Methods), Taylor & Francis 2006, ISBN: 978-0415377348 A: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (eds.), Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Springer 2005, ISBN: 978-0387251462 |
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Last update: ROZ143 (08.08.2013)
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Last update: ROZ143 (10.06.2013)
Na konci semestru studenti presentují výsledky úkolů a skládají písemnou zkoušku. |
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Last update: ROZ143 (08.08.2013)
1. Introduction. Types of functional genetics data. Aims of the anlyses. 2. RT-qPCR data preprocessing: Primer and probe design. Standard curve. 3. RT-qPCR data preprocessing: Amplification curve. Threshold cycle. Background correction. Data normalization. 4. Transcription chips data preprocessing: Noise removal. Data normalization. Relative and absolute quantification. 5. Transcription chips data preprocessing: Variance stabilization. Summarization of intensity values. 6. High-throughput sequencing: Reading and mapping. 7. Further applications: Analysis of single nucleotide polymorphisms and chromosomal abberations. DNA methylation. 8. Expolratory data analysis: Dimensionality reduction. Clustering. Control points. 9. Linear models. Problem of test multiplicity. 10. Classification methods. 11. Design of experiments and randomization. Replication. 12. Annotation and results archivation: Genomic browsers and expression databases. 13. Biological interpretation: Gene Set Enrichment Analysis (GSEA). Database of signalling pathways. Gene ontologies. 14. Integration with interaction data: Network analysis. Database of interaction data. |
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Last update: ROZ143 (08.08.2013)
Biochemistry, Molecular genetics |
Teaching methods | ||||
Activity | Credits | Hours | ||
Obhajoba individuálního projektu | 0.5 | 14 | ||
Účast na přednáškách | 1 | 28 | ||
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi | 1 | 28 | ||
Práce na individuálním projektu | 0.5 | 14 | ||
Příprava na zkoušku a její absolvování | 1 | 28 | ||
4 / 4 | 112 / 112 |
Coursework assessment | |
Form | Significance |
Defense of an individual project | 30 |
Examination test | 70 |