Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets:
Gespeichert in:
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2008
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Zsfassung in dt. Sprache |
| Beschreibung: | 169 S. Ill., graph. Darst. |
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Datensatz im Suchindex
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| adam_text | Titel: Assembly of the interactome, characterization of functional modules and novel approaches to the anal
Autor: Dittrich, Marcus
Jahr: 2008
Contents
Abstract 5
Zusammenfassung 7
1 Introduction 9
1.1 Systems Biology 9
1.1.1 Interactomics 10
Interaction Types 11
Interaction Studies 13
Interaction Data Sources 15
1.1.2 Network Analysis 16
1.2 Platelet Omics 19
1.2.1 The Platelet Transcriptome 19
Protein Syntheses in Platelets 19
Expression Profiling in Platelets 20
1.2.2 The Platelet Proteome 22
1.3 Rationale 24
2 Materials and Methods 27
2.1 Databases 27
2.1.1 Proteome and Genome Databases 27
2.1.2 Gene Ontology 28
2.1.3 Interaction Databases 30
2.2 Platelet Preparation and Immunoprecipitation 32
2.3 SAGE Analysis 33
2.3.1 SAGE Technology 33
2.3.2 SAGE Bank Generation 34
2 Contents
2.3.3 PCR Amplification and quantitative RT-PCR 34 :
2.3.4 Transcript Mapping 35 i
2.4 Algorithms 36 i
2.4.1 Sequence Search and Alignment 36 1
2.4.2 UTRAnalysis 38 j
2.4.3 Domain Analysis 38 I
2.4.4 Motif Search 39
2.5 Structural Analyses of the Networks 45
2.6 Software and Computational Implementation 50
3 Results 53 j
3.1 The Platelet Transcriptome 53
3.1.1 Anatomy of the Platelet SAGE Library 53
Comparison to Platelet Microarray Data 54
3.1.2 Purity of the Library 56
Purification of Platelets 57
3.1.3 Functional Characterization of the Platelet Transcriptome 58
3.1.4 Sequence and Structure of Platelet Transcripts 60 j
Structure of Platelet UTRs , 60 i
Specific Sequence Motifs in Platelet UTRs 63 I
3.2 The Platelet Interactome 65 ;
3.2.1 Collation of the Database 65
3.2.2 Construction of the Interactome Network 67 •)
3.2.3 Characterization of the Proteome 71 :
3.3 Global Network Structure 74 j
3.4 Analysis of specific Subnetworks 78 j
3.5 The PlateletWeb Knowledge Base 83
3.6 The Platelet Kinome and Phospho-Interactome 85
3.6.1 The Kinome 85 j
3.6.2 The Phospho-Interactome 85 j
3.6.3 The Platelet Kinase Network 88 j
3.7 Mining the Interactome Network 91 j
3.7.1 Statistics of Scoring Function 91 i
3.7.2 Algorithmic Solution 97 ;
3.7.3 Validation 102 j
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Contents 3
4 Discussion 105
4.1 Platelet SAGE: A comprehensive Mapping 105
4.2 High Purity Preparation of Platelets 107
4.3 Platelet Transcripts: Motifs and Function 108
4.4 A comprehensive Platelet Knowledge Base Ill
4.5 A functional Inventory of the Platelet Proteome 113
4.6 Architecture of the Platelet Interactome 114
4.7 Platelet Kinomics 116
4.8 Characterizing specific Subnetworks 117
4.9 Improved Approaches for functional Network Analysis 119
4.10 Conclusion and Outlook 126
A Additional Material 151
A.1 The platelet transcriptome 151
A.2 The platelet interactome 157
B List of publications 167
B.I Publications related to this work 167
B.2 Further publications 168
B.3 Conference Contributions 169
|
| adam_txt |
Titel: Assembly of the interactome, characterization of functional modules and novel approaches to the anal
Autor: Dittrich, Marcus
Jahr: 2008
Contents
Abstract 5
Zusammenfassung 7
1 Introduction 9
1.1 Systems Biology 9
1.1.1 Interactomics 10
Interaction Types 11
Interaction Studies 13
Interaction Data Sources 15
1.1.2 Network Analysis 16
1.2 Platelet'Omics' 19
1.2.1 The Platelet Transcriptome 19
Protein Syntheses in Platelets 19
Expression Profiling in Platelets 20
1.2.2 The Platelet Proteome 22
1.3 Rationale 24
2 Materials and Methods 27
2.1 Databases 27
2.1.1 Proteome and Genome Databases 27
2.1.2 Gene Ontology 28
2.1.3 Interaction Databases 30
2.2 Platelet Preparation and Immunoprecipitation 32
2.3 SAGE Analysis 33
2.3.1 SAGE Technology 33
2.3.2 SAGE Bank Generation 34
2 Contents
2.3.3 PCR Amplification and quantitative RT-PCR 34 :
2.3.4 Transcript Mapping 35 i
2.4 Algorithms 36 i
2.4.1 Sequence Search and Alignment 36 1
2.4.2 UTRAnalysis 38 j
2.4.3 Domain Analysis 38 I
2.4.4 Motif Search 39
2.5 Structural Analyses of the Networks 45
2.6 Software and Computational Implementation 50
3 Results 53 j
3.1 The Platelet Transcriptome 53
3.1.1 Anatomy of the Platelet SAGE Library 53
Comparison to Platelet Microarray Data 54
3.1.2 Purity of the Library 56
Purification of Platelets 57
3.1.3 Functional Characterization of the Platelet Transcriptome 58
3.1.4 Sequence and Structure of Platelet Transcripts 60 j
Structure of Platelet UTRs , 60 i
Specific Sequence Motifs in Platelet UTRs 63 I
3.2 The Platelet Interactome 65 ;
3.2.1 Collation of the Database 65 \
3.2.2 Construction of the Interactome Network 67 •)
3.2.3 Characterization of the Proteome 71 :
3.3 Global Network Structure 74 j
3.4 Analysis of specific Subnetworks 78 j
3.5 The PlateletWeb Knowledge Base 83 '
3.6 The Platelet Kinome and Phospho-Interactome 85
3.6.1 The Kinome 85 j
3.6.2 The Phospho-Interactome 85 j
3.6.3 The Platelet Kinase Network 88 j
3.7 Mining the Interactome Network 91 j
3.7.1 Statistics of Scoring Function 91 i
3.7.2 Algorithmic Solution 97 ;
3.7.3 Validation 102 j
I
|
|
j
}
t
I
i
i
Contents 3
4 Discussion 105
4.1 Platelet SAGE: A comprehensive Mapping 105
4.2 High Purity Preparation of Platelets 107
4.3 Platelet Transcripts: Motifs and Function 108
4.4 A comprehensive Platelet Knowledge Base Ill
4.5 A functional Inventory of the Platelet Proteome 113
4.6 Architecture of the Platelet Interactome 114
4.7 Platelet Kinomics 116
4.8 Characterizing specific Subnetworks 117
4.9 Improved Approaches for functional Network Analysis 119
4.10 Conclusion and Outlook 126
A Additional Material 151
A.1 The platelet transcriptome 151
A.2 The platelet interactome 157
B List of publications 167
B.I Publications related to this work 167
B.2 Further publications 168
B.3 Conference Contributions 169 |
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| spelling | Dittrich, Marcus Verfasser aut Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets von Marcus Dittrich 2008 169 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Zsfassung in dt. Sprache Würzburg, Univ., Diss., 2008 Systembiologie (DE-588)4809615-5 gnd rswk-swf Thrombozyt (DE-588)4059964-4 gnd rswk-swf Interaktion (DE-588)4027266-7 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Thrombozyt (DE-588)4059964-4 s Interaktion (DE-588)4027266-7 s Systembiologie (DE-588)4809615-5 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016679659&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| title | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets |
| title_auth | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets |
| title_exact_search | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets |
| title_exact_search_txtP | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets |
| title_full | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets von Marcus Dittrich |
| title_fullStr | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets von Marcus Dittrich |
| title_full_unstemmed | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets von Marcus Dittrich |
| title_short | Assembly of the interactome, characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets |
| title_sort | assembly of the interactome characterization of functional modules and novel approaches to the analysis of signaling networks in human platelets |
| topic | Systembiologie (DE-588)4809615-5 gnd Thrombozyt (DE-588)4059964-4 gnd Interaktion (DE-588)4027266-7 gnd |
| topic_facet | Systembiologie Thrombozyt Interaktion Hochschulschrift |
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