Computational analysis of gene expression data:
Saved in:
| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English |
| Published: |
Aachen
Shaker
2004
|
| Series: | Fraunhofer series in information and communication technology
2004,4 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | IV, 164 S. graph. Darst. 23 cm, 260 gr. |
| ISBN: | 3832226060 |
Staff View
MARC
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Record in the Search Index
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|---|---|
| adam_text | Contents
1 Background 1
1.1 Fundamental Molecular Biology 1
1.2 Pharmaceutical Target Finding 3
1.2.1 Experimental Design 4
1.2.2 Measurement of Molecular Data 4
1.2.3 Computational Data Analysis 5
1.2.4 Target Validation 6
1.3 About This Work 6
2 Gene Expression: Measurement, Data and Analysis 9
2.1 Measurement Technology 9
2.1.1 Northern Blotting 10
2.1.2 qPCR (Quantitative Polymerase Chain Reaction) 11
2.1.3 EST (Expressed Sequence Tag) Counting 11
2.1.4 SAGE (Serial Analysis of Gene Expression) 12
2.1.5 MPSS (Massively Parallel Signature Sequencing) 12
2.1.6 Oligonucleotide Fingerprinting 13
2.1.7 Microarrays 14
2.2 Data Sets 15
2.2.1 Human Osteoarthritis Data Sets 16
2.2.2 Yeast Metabolic Shift Data Set 19
2.2.3 Affymetrix Data Sets 19
2.3 Computational Methods for Microarrays 19
2.3.1 Experimental Design 20
2.3.2 Normalization (Preprocessing) 21
2.3.3 Unsupervised (Exploratory) Analysis 22
2.3.4 Supervised (Knowledge Based) Analysis 24
3 Error Model 27
3.1 Background 27
3.2 Investigation of Replicate Measurements 28
3.3 Mathematical Error Model 29
3.3.1 Additive noise 32
3.3.2 Multiplicative noise 34
3.3.3 Final model 36
3.3.4 Replication 38
3.4 Validation 39
i
4 Normalization 41
4.1 Background 41
4.1.1 Review of Existing Methods 42
4.1.2 Desirable Features of a Normalization Method 44
4.2 Methods 44
4.2.1 Implications of Well Behavedness 45
4.2.2 Estimation of Pairwise Relative Scalings 46
4.2.3 Estimation of Most Consistent Sample Scaling Factors 50
4.2.4 Differences to Related Methods 57
4.3 Evaluation 58
4.3.1 Ambiguity of the Housekeeping Method 60
4.3.2 Lack of Robustness of Globalization 60
4.3.3 Lack of Robustness of Other Normalization Methods 62
4.3.4 Normalization of Two Channel Arrays 68
4.4 Discussion 68
5 Required Number of Samples 73
5.1 Background 73
5.2 Mathematical Model and Parameters 75
5.2.1 Technical Variability 76
5.2.2 Biological Variability 77
5.3 Methods 79
5.3.1 Computation of p Value for Rank Sums 81
5.3.2 Required Numbers of Samples and Arrays 83
5.4 Results 84
5.5 Discussion 88
6 Analysis of the OA Data Set 97
6.1 Basic Analysis 97
6.2 Differentially Expressed Genes 98
6.3 Analysis of Time Series 100
6.4 Combination of Data from Different Technology Platforms 1°3
6.5 Clustering and Neighborhood Analyses 104
6.5.1 Distance Function 104
6.5.2 Clustering 106
6.5.3 Neighborhood Analysis 108
6.6 Discussion 108
7 Pathway Scoring 111
7.1 Background Ill
7.2 Data Selection and Generation 113
7.2.1 Gene Expression Data Set H3
7.2.2 Pathways 114
7.3 Scoring Functions 117
7.3.1 Scoring Activation of Expression 119
7.3.2 Scoring Synchronism of Expression 122
7.3.3 Scoring Synchronous Activation of Expression l^3
ii
7.4 Results 123
7.4.1 Comparison to Clustering 125
7.5 Discussion 127
7.5.1 Deficiencies of the Investigated Scoring Functions 128
7.5.2 Deficiencies of Pathway Generation 129
7.5.3 Conclusions 130
8 Discussion and Outlook 133
8.1 General Limitations of Gene Expression
Analysis 133
8.2 Combination with Other Data 135
8.2.1 Biological Networks 136
8.3 Outlook 138
9 Summary 161
10 Zusammenfassung 163
iii
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| id | DE-604.BV019654741 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T20:02:15Z |
| institution | BVB |
| isbn | 3832226060 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-012983301 |
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| physical | IV, 164 S. graph. Darst. 23 cm, 260 gr. |
| publishDate | 2004 |
| publishDateSearch | 2004 |
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| publisher | Shaker |
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| series | Fraunhofer series in information and communication technology |
| series2 | Fraunhofer series in information and communication technology |
| spelling | Zien, Alexander 1971- Verfasser (DE-588)128914521 aut Computational analysis of gene expression data Alexander Zien Aachen Shaker 2004 IV, 164 S. graph. Darst. 23 cm, 260 gr. txt rdacontent n rdamedia nc rdacarrier Fraunhofer series in information and communication technology 2004,4 Zugl.: Bonn, Univ., Diss., 2003 Datenverarbeitung Gene expression Data processing Gene expression Methodology Gene expression Statistical methods Computerunterstütztes Verfahren (DE-588)4139030-1 gnd rswk-swf Datenanalyse (DE-588)4123037-1 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Genexpression (DE-588)4020136-3 s Datenanalyse (DE-588)4123037-1 s Computerunterstütztes Verfahren (DE-588)4139030-1 s DE-604 Fraunhofer series in information and communication technology 2004,4 (DE-604)BV019350332 2004,4 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012983301&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Zien, Alexander 1971- Computational analysis of gene expression data Fraunhofer series in information and communication technology Datenverarbeitung Gene expression Data processing Gene expression Methodology Gene expression Statistical methods Computerunterstütztes Verfahren (DE-588)4139030-1 gnd Datenanalyse (DE-588)4123037-1 gnd Genexpression (DE-588)4020136-3 gnd |
| subject_GND | (DE-588)4139030-1 (DE-588)4123037-1 (DE-588)4020136-3 (DE-588)4113937-9 |
| title | Computational analysis of gene expression data |
| title_auth | Computational analysis of gene expression data |
| title_exact_search | Computational analysis of gene expression data |
| title_full | Computational analysis of gene expression data Alexander Zien |
| title_fullStr | Computational analysis of gene expression data Alexander Zien |
| title_full_unstemmed | Computational analysis of gene expression data Alexander Zien |
| title_short | Computational analysis of gene expression data |
| title_sort | computational analysis of gene expression data |
| topic | Datenverarbeitung Gene expression Data processing Gene expression Methodology Gene expression Statistical methods Computerunterstütztes Verfahren (DE-588)4139030-1 gnd Datenanalyse (DE-588)4123037-1 gnd Genexpression (DE-588)4020136-3 gnd |
| topic_facet | Datenverarbeitung Gene expression Data processing Gene expression Methodology Gene expression Statistical methods Computerunterstütztes Verfahren Datenanalyse Genexpression Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012983301&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV019350332 |
| work_keys_str_mv | AT zienalexander computationalanalysisofgeneexpressiondata |