Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters:
Gespeichert in:
| Beteilige Person: | |
|---|---|
| Format: | Hochschulschrift/Dissertation Buch |
| Sprache: | Englisch |
| Veröffentlicht: |
2012
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| Schlagwörter: | |
| Links: | http://edoc.ub.uni-muenchen.de/15076/ https://nbn-resolving.org/urn:nbn:de:bvb:19-150764 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025493433&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| Umfang: | XX, 115 S. Ill., graph. Darst. |
Internformat
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| 245 | 1 | 0 | |a Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters |c Holger Hartmann |
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Datensatz im Suchindex
| DE-BY-TUM_katkey | 1905274 |
|---|---|
| _version_ | 1821935086017183745 |
| adam_text | IMAGE 1
CONTENTS
ACKNOWLEDGMENTS VII
SUMMARY IX
I. XXMOTIF - P-VALUE BASED MOTIF IDENTIFICATION 1
1. INTRODUCTION T O MOTIF FINDING 3
1.1. MOTIF FINDING PROBLEM 4
1.2. MOTIF MODELS 5
1.2.1. CONSENSUS STRING 5
1.2.2. POSITION WEIGHT MATRIX (PWM) 6
1.3. APPROACHES TO SOLVE THE MOTIF FINDING PROBLEM 7
1.3.1. ENUMERATIVE APPROACH 7
1.3.2. ITERATIVE APPROACH 7
2. MATERIALS AND METHODS 9
2.1. AVAILABILITY 9
2.2. STATISTICAL FRAMEWORK 9
2.2.1. CALCULATING THE SIGNIFICANCE OF AN Z-MER - BACKGROUND MODEL . . .
. 9
2.2.2. CALCULATING THE SIGNIFICANCE OF A BINDING SITE GIVEN A PWM 11
2.2.3. CALCULATE THE SIGNIFICANCE OF A SET OF BINDING SITES 14
2.2.4. CORRECTING P-VALUES FOR MULTIPLE TESTING 15
2.2.5. CALCULATING CONSERVATION P-VALUES 16
2.2.6. WEIGHTED COMBINATION OF P-VALUES 17
2.2.7. CALCULATING POSITIONAL P-VALUES 17
2.3. WORKFLOW OF XXMOTIF 24
2.3.1. XXMASKER 24
2.3.2. SEEDS PHASE 25
2.3.3. EXTENSION PHASE 25
2.3.4. MERGING PHASE 28
2.3.5. REFINEMENT PHASE 29
XI
HTTP://D-NB.INFO/1031896996
IMAGE 2
2.4. OVERVIEW OF THE USED PUBLISHED MOTIF FINDERS 30
2.4.1. PRIORITY 30
2.4.2. MEME 31
2.4.3. WEEDER 33
2.4.4. ERMIT 33
2.4.5. AMADEUS 34
3. XXMOTIF WEB SERVER 35
3.1. OVERVIEW OF WEB SERVERS 35
3.2. INPUT 36
3.3. OUTPUT 36
3.4. DOCUMENTATION 39
3.5. IMPLEMENTATION 40
3.6. CONCLUSION 40
II. ANALYSIS OF TRANSCRIPTION FACTORS AND CORE PROMOTERS 41
4. TRANSCRIPTION FACTORS 4 3
4.1. OVERVIEW 43
4.2. FAMILIES OF DNA-BINDING DOMAINS 45
4.2.1. HELIX-TURN-HELIX MOTIF 45
4.2.2. HOMEODOMAIN 46
4.2.3. C2H2 ZINC FINGER 46
4.2.4. C6-ZINC CLUSTER FAMILY 47
4.3. EXPERIMENTAL TECHNIQUES FOR IN VITRO ANALYSIS OF TFBSS 48
4.3.1. PROTEIN-BINDING MICROARRAYS 49
4.3.2. HT-SELEX 49
4.3.3. HITS-FLIP 50
4.4. EXPERIMENTAL TECHNIQUES FOR IN VIVO ANALYSIS OF TFBSS 50
4.4.1. DNASE I HYPERSENSITIVE SITES 51
4.4.2. CHROMATIN IMMUNOPRECIPITATION (CHIP) . 51
5. PERFORMANCE OF XXMOTIF ON TFBSS 53
5.1. BENCHMARKS 53
5.1.1. DRABL0S BENCHMARK 53
5.1.2. MOTIF SENSITIVITY BENCHMARK 55
5.1.3. PWM QUALITY BENCHMARK 58
5.1.4. METAZOAN BENCHMARK 62
5.2. REGULATORY MOTIFS FOR EARLY EMBRYO SEGMENTATION IN FLIES 64
5.3. HUMAN CORE PROMOTER MOTIFS 66
XII
IMAGE 3
5.4. DISCUSSION 69
6. ANALYSIS OF THE MOTIF ARCHITECTURE WITHIN FLY CORE PROMOTERS 73
6.1. INTRODUCTION TO CORE PROMOTERS IN D. MELANOGASTER 73
6.2. DROSOPHILA CORE PROMOTERS FALL INTO FOUR CLASSES 75
6.2.1. TSS CLUSTER WIDTH 75
6.2.2. GENE SETS 76
6.2.3. IDENTIFICATION OF CORE PROMOTER ELEMENTS 78
6.2.4. CORE PROMOTER ELEMENTS ALLOW FOR THE PREDICTION OF GENE
PROPERTIES . 82
6.2.5. CORE PROMOTER ELEMENTS BELONG TO SPECIFIC ARCHITECTURES 84
6.2.6. EACH CLASS OF CORE PROMOTERS HAS DEFINED PHYSICAL PROPERTIES 85
6.3. SUMMARY 87
6.4. MATERIALS AND METHODS 88
6.4.1. TAG CLUSTERING 88
6.4.2. OPTIMIZATION OF MINIMAL SCORE THRESHOLDS 88
6.4.3. CONSERVATION SCORES 88
III. APPENDIX 89
A. DETAILED PERFORMANCE OF XXMOTIF 91
A.L. DRABL0S BENCHMARK 91
A.2. MOTIF SENSITIVITY BENCHMARK 92
A.3. PWM QUALITY BENCHMARK 93
A.4. METAZOAN BENCHMARK 94
A. 5. REGULATORY MOTIFS FOR EARLY EMBRYO SEGMENTATION IN FLIES 95
B. DROSOPHILA CORE PROMOTERS 97
B.L. TSS CLUSTER WIDTH 97
B.2. MOTIF CONSERVATION 98
B.3. CORE PROMOTER ELEMENTS VS. DEVELOPMENTAL STAGES 102
B.4. CLASS 4 CORE PROMOTER ELEMENTS 103
BIBLIOGRAPHY 105
CURRICULUM VITAE 116
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| language | English |
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| physical | XX, 115 S. Ill., graph. Darst. |
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| spellingShingle | Hartmann, Holger Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters |
| subject_GND | (DE-588)4113937-9 |
| title | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters |
| title_auth | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters |
| title_exact_search | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters |
| title_full | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters Holger Hartmann |
| title_fullStr | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters Holger Hartmann |
| title_full_unstemmed | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters Holger Hartmann |
| title_short | Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters |
| title_sort | regulatory motif discovery using pwms and the architecture of eukaryotic core promoters |
| topic_facet | Hochschulschrift |
| url | http://edoc.ub.uni-muenchen.de/15076/ https://nbn-resolving.org/urn:nbn:de:bvb:19-150764 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025493433&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT hartmannholger regulatorymotifdiscoveryusingpwmsandthearchitectureofeukaryoticcorepromoters |