Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data:
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2015
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | II, 89 Bl. Ill., graph. Darst. 30 cm |
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Datensatz im Suchindex
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| adam_text | UNRAVELING THE SIGNALING MECHANISMS OF DIFFERENTIATION AND
MIGRATION IN A CELLULAR SYSTEM BASED ON DYNAMIC
TRANSCRIPTOME DATA
INAUGURAL-DISSERTATION
TO OBTAIN THE DOCTORAL DEGREE
FACULTY OF BIOLOGY, ALBERT-LUDWIGS-UNIVERSITAT FREIBURG IM BREISGAU
V
,II
F T. /
-MMC- I %
1
..VCI E,* CSL..
- . /
PRESENTED BY
AM IT SINGH
BORN IN INDIA
FREIBURG IM BREISGAU
JANUARY 2015
HTTP://D-NB.INFO/1071607006
CONTENTS
1. ABSTRACT 1
2. INTRODUCTION 5
2.1. NGF INDUCED PC12 CELL DIFFERENTIATION 5
2.2. HGF-INDUCED KERATINOCYTE MIGRATION 10
3. MATERIALS AND METHODS 13
3.1. TRANSCRIPTOME ANALYSIS - 13
3.1.1. NORMALIZATION 14
3.1.2. PRINCIPAL COMPONENT ANALYSIS 14
3.1.3. GENE SET ENRICHMENT ANALYSIS 15
3.1.4. INGENUITY PATHWAY ANALYSIS 15
3.1.5. REAL TIME POLYMERASE CHAIN REACTION 15
3.2. DISCRETE MODELING 16
3.2.1. MODEL CONSTRUCTION 17
3.2.2. STATE TRANSITIONS 17
3.2.3. MODEL ANALYSIS 19
3.3. MODEL OPTIMIZATION 19
3.3.1. IMPORT OF PRIOR KNOWLEDGE NETWORK AND THE EXPERIMENTAL DATA 19
3.3.2. PREPROCESSING THE PRIOR KNOWLEDGE NETWORK 20
3.3.3. MODEL OPTIMIZATION 20
4. DATA DRIVEN PATHWAYS MODELING OF NGF INDUCED PC12 CELL DIFFERENTI
ATION 22
4.1. TRANSCRIPTOME ANALYSIS 22
4.2. DIMENSIONAL REDUCTION AND VISUALIZATION 22
4.3. FUNCTIONAL ANALYSIS OF GENES 26
4.4. CONSTRUCTION OF PRIOR KNOWLEDGE NETWORK FOR NGF INDUCED PC12 CELL
DIFFERENTIATION 29
4.5. MODEL OPTIMIZATION AND ANALYSIS 31
4.6. CONCLUSIONS AND OUTLOOK 40
5. BOOLEAN APPROACH TO SIGNALING PATHWAY MODELING IN HGF-INDUCED KER
ATINOCYTE MIGRATION 44
5.1. CONSTRUCTION OF THE HGF INDUCED CELL MIGRATION MODEL 44
5.2. THE NHK MIGRATION MODEL AS A DYNAMIC BOOLEAN MODEL 47
I
CONTENTS
5.3. CONCLUSIONS AND OUTLOOK 51
6. CONCLUSIONS 54
A. ABBREVIATIONS 62
B. APPENDIX 64
B.L. CELL CULTURE OF NORMAL HUMAN SKIN KERATINOCYTES 64
B.2. PC12 CELL CULTURE AND IMAGING 64
B.3. SCRATCH ASSAY 64
B.4. CELL MIGRATION ASSAY 65
B.5. WESTERN BLOT 65
B.5.1. HGF INDUCED NHK MIGRATION 65
B.5.2. NGF INDUCED PC12 CELL DIFFERENTIATION 66
B.6. MODEL REFERENCES 67
B.6.1. HGF INDUCED NHK MIGRATION MODEL 67
B.6.2. NGF INDUCED PC12 CELL DIFFERENTIATION MODEL 69
BIBLIOGRAPHY 72
II
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| dewey-ones | 571 - Physiology & related subjects |
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| dewey-search | 571.7436 |
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| language | English |
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| spelling | Singh, Amit Verfasser (DE-588)1071500481 aut Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data presented by Amit Singh 2015 II, 89 Bl. Ill., graph. Darst. 30 cm txt rdacontent n rdamedia nc rdacarrier Freiburg (Breisgau), Univ., Diss., 2015 (DE-588)4113937-9 Hochschulschrift gnd-content DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028240148&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Singh, Amit Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data |
| subject_GND | (DE-588)4113937-9 |
| title | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data |
| title_auth | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data |
| title_exact_search | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data |
| title_full | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data presented by Amit Singh |
| title_fullStr | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data presented by Amit Singh |
| title_full_unstemmed | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data presented by Amit Singh |
| title_short | Unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data |
| title_sort | unraveling the signaling mechanisms of differentiation and migration in a cellular system based on dynamic transcriptome data |
| topic_facet | Hochschulschrift |
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