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| Course Description |
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| Course Name |
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Statistical Analysis of Microarrays |
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| Course Code |
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BT-507 |
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| Course Type |
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Optional |
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| Level of Course |
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Second Cycle |
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| Year of Study |
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1 |
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| Course Semester |
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Fall (16 Weeks) |
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| ECTS |
: |
6 |
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| Name of Lecturer(s) |
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Prof.Dr. ZEYNEL CEBECİ
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| Learning Outcomes of the Course |
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Knows statistical analysis of gene expression, gene clustering and other related methods.
Does statistical analysis of microarray data and interpretes the results of analysis
Uses the bioinformatics databases and other related information repositories on gene/genomic researches
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| Mode of Delivery |
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Face-to-Face |
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| Prerequisites and Co-Prerequisites |
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None |
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| Recommended Optional Programme Components |
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None |
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| Aim(s) of Course |
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This course aims to teach statistical analysis of data from genomics / microarray experiments with a special reference to gene expressions. |
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| Course Contents |
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Topics covered in this course include experimental design for microarrays, normalization, quality control and restoration of microarray images, exploratory analysis, and tests for differential expression. |
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| Language of Instruction |
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Turkish |
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| Work Place |
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Classroom |
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Course Outline /Schedule (Weekly) Planned Learning Activities |
| Week | Subject | Student's Preliminary Work | Learning Activities and Teaching Methods |
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1 |
Introduction to microarrays, basic terms and concepts |
None |
None |
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2 |
Components of microarrays: Arrays, Probs and Estimation |
Searching for microarrays in Internet |
Internet/Computer work |
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3 |
Image processing applications |
Searching for applications of microarray analysis in Internet |
Internet/Computer work |
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4 |
Hybridization, normalization and filtering |
Reading a tutorial about image processing techniques |
Reading |
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5 |
Descriptive statistics |
Downloading and installing R software |
Internet/Computer work |
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6 |
Multiple comparison tests |
Practising a problem on Duncan, Tukey, LSD etc multiple comparison test. |
Exercise |
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7 |
Supervised classification |
Reading a chapter of textbook about classification and clustering methods |
Reading |
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8 |
Midterm exam |
Preparing for midterm exam |
Individual/Group work |
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9 |
Gene clustering |
Reading a textbook chapter about gene clustering |
Reading |
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10 |
Discrimnant analysis |
Reading a textbook chapter about discrimnant analysis |
Reading |
|
11 |
Knowledge and information resources on microarray experiments |
Searching for bioinformatics rsources on Internet |
Internet/Computer work |
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12 |
Project work and presentation - Case study 1 |
Preparing for project presentations |
Internet/Computer work |
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13 |
Project work and presentation - Case study 2 |
Preparing for project presentations |
Internet/Computer work |
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14 |
Project work and presentation - Case study 3 |
Preparing for project presentations |
Internet/Computer work |
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15 |
Final exam preperation |
Yarıyıl sonu sınavına hazırlık |
Individual/Group work |
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16/17 |
Final exam |
Yarıyıl sonu sınavına hazırlık |
Individual/Group work |
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Required Course Resources |
| Resource Type | Resource Name |
| Recommended Course Material(s) |
 J van Helden (2002). Statistical analysis of microarray data. http://www.bigre.ulb.ac.be/Users/jvanheld/web_course_microarrays/
Getting started with microarray analysis in R. http://www.humgen.nl/microarray_analysis_getting_started_with_R.doc
A Pohl, 2003. Microarray Analysis with R. http://classes.soe.ucsc.edu/bme210/Winter03/lectures/Bio210w03-Lect06-R-Biocond-Intro.pdf
Using R to draw a Heatmap from Microarray Data. http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/
DNA microarray data analysis using R / Bioconductor. http://www.csc.fi/english/csc/courses/archive/R2007
Prediction Analysis for Microarrays, for the R package. http://www-stat.stanford.edu/~tibs/PAM/Rdist/index.html
Microarray analysis exercises 1 - with R. http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html
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| |
| Required Course Material(s) |
Statistics in Biotechnology. http://www.intesoft.com/produits/tech/systat/resources/pdf/StatBiotech.pdf
Microarray - How Does It Work? http://www.unsolvedmysteries.oregonstate.edu/microarray_07
The GENSCAN Web Server at MIT. http://genes.mit.edu/GENSCAN.html
Microarray Techniques. http://www.cs.columbia.edu/4761/notes07/chapter5.2-microarray.pdf
Microarrays. The basics. http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Microarray/arrayBasics.pdf
Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397–420. http://www.statsci.org/smyth/pubs/limma-biocbook-reprint.pdf
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Assessment Methods and Assessment Criteria |
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Semester/Year Assessments |
Number |
Contribution Percentage |
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Mid-term Exams (Written, Oral, etc.) |
1 |
40 |
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Homeworks/Projects/Others |
3 |
60 |
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Total |
100 |
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Rate of Semester/Year Assessments to Success |
40 |
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Final Assessments
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100 |
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Rate of Final Assessments to Success
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60 |
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Total |
100 |
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| Contribution of the Course to Key Learning Outcomes |
| # | Key Learning Outcome | Contribution* |
|
1 |
Evaluates and directs his level of learning in the field of knowledge and skills with his expert level critically. |
1 |
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2 |
Transfers current developments in the field of his work, supporting them with quantitative and qualitative data, systematically to the area outside of the field, written, orally and visually. |
2 |
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3 |
Follows national and international publications and attends social interactions and scientific studies in international level, communicates in at least in one foreign language in order to share studies on international base. |
3 |
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4 |
Uses advanced information and communication technologies along with the required level of their computer software. |
5 |
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5 |
Uses the knowledge in his field for problem solving and / or practical skills in interdisciplinary studies. |
4 |
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6 |
Improves common knowledge accumulation concerning the Biotechnology in the frame of basic theory and practices. |
3 |
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7 |
Is aware of scientific, ethical and social values and handles research process with this frame. |
2 |
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8 |
Handles theories, hypothesis, opinions in the field of Biotechnology with an objective sceptic, logical, analytical manner and evaluates them in critical point of view. |
5 |
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9 |
Gains comprehensive information about natural and applied sciences and its limits with modern techniques and methods applied. |
5 |
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10 |
Improves and increases the knowledge to an expert level in the field of biotechnology |
5 |
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11 |
Understands the interdisciplinary interaction associated with biotechnology. |
2 |
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12 |
Integrates and interprets the knowledge from different disciplines by his expertrise in biology and generate new information |
5 |
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13 |
Analizes the problems encountered in the field of research methods. |
2 |
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14 |
Carries out a study requiring expertise in the field independently. |
1 |
|
15 |
Developes new strategic approaches and takes resposibility for analitical solutions for unpredictable complicated problems encountered in applications related to biotechnology. |
4 |
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16 |
Demonstrates leadership in the required environment to solve problems associated with biotechnology. |
1 |
| * Contribution levels are between 0 (not) and 5 (maximum). |
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| Student Workload - ECTS |
| Works | Number | Time (Hour) | Total Workload (Hour) |
| Course Related Works |
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Class Time (Exam weeks are excluded) |
14 |
4 |
56 |
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Out of Class Study (Preliminary Work, Practice) |
14 |
2 |
28 |
| Assesment Related Works |
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Homeworks, Projects, Others |
3 |
10 |
30 |
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Mid-term Exams (Written, Oral, etc.) |
1 |
14 |
14 |
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Final Exam |
1 |
14 |
14 |
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Total Workload: | 142 |
| Total Workload / 25 (h): | 5.68 |
| ECTS Credit: | 6 |
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