Gene regulatory networks: methods and protocols
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
New York [u.a.]
Humana Press
2012
|
| Schriftenreihe: | Methods in molecular biology
786 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben |
| Beschreibung: | XI, 446 S. Ill., graph. Darst. |
| ISBN: | 1617792918 9781617792915 |
Internformat
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Datensatz im Suchindex
| _version_ | 1804148676394745856 |
|---|---|
| adam_text | Titel: Gene regulatory networks
Autor: Deplancke, Bart
Jahr: 2012
Preface.............................................................. v
Contributors.......................................................... ix
Part I Regulatory State Components
1 How Do You Find Transcription Factors? Computational Approaches
to Compile and Annotate Repertoires of Regulators for Any Genome........... 3
Juan M. Vaquerizas, Sarah A. Teichmann, and Nicholas M. Luscombe
2 Expression Pattern Analysis of Regulatory Transcription Factors
in Caenorhabditis elegans............................................ 21
Huiyun Feng, Hannah L. Craig, and Ian A. Hope
3 High-Throughput SELEX Determination of DNA Sequences Bound
by Transcription Factors In Vitro...................................... 51
Nobuo Ogawa and Mark D. Biggin
4 Convenient Determination of Protein-Binding DNA Sequences Using
Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein....... 65
Min-Jeong Kim, Piljoong Chung, Tae-Ho Lee, Tae-Hoon Kim,
Baek Hie Nahm, and Teon-Ki Kim
5 Analysis of Specific Protein-DNA Interactions by Bacterial One-Hybrid Assay .... 79
Marcus B. Noyes
6 MITOMI: A Microfluidic Platform for In Vitro Characterization
of Transcription Factor-DNA Interaction................................ 97
Sylvie Rocket, Marcel Geertz, and Sebastian J. Maerkl
7 Detecting Protein-Protein Interactions with the Split-Ubiquitin Sensor......... 115
Alexander Dunkler, Judith Müller, and Nilsjohnsson
8 Genome-Wide Dissection of Posttranscriptional and Posttranslational
Interactions...................................................... 131
Mukesh Bansal and Andrea Califano
9 Linking Cellular Signalling to Gene Expression Using EXT-Encoded
Reporter Libraries.................................................. 151
Anna Botvinik and Moritz J. Rossner
10 Sample Preparation for Small RNA Massive Parallel Sequencing............... 167
Willemijn M. Gommans and Eugene Berezikov
Part II Genomic Components
11 CAGE (Cap Analysis of Gene Expression): A Protocol for the Detection
of Promoter and Transcriptional Networks............................... 181
Hazuki Takahashi, Sachi Kato, Mitsuyoshi Murata, and Piero Carninci
VII
viii Contents
12 Detecting DNasel-Hypersensitivity Sites with MLPA....................... 201
Thomas Ohnesorg, Stefanie Eggers, and Stefan J. White
13 Detecting Long-Range Chromatin Interactions Using the Chromosome
Conformation Capture Sequencing (4C-seq) Method....................... 211
Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont,
and Alexandre Reymond
Part III Mapping Protein-DNA Interactions
14 Analyzing Transcription Factor Occupancy During Embryo Development
Using ChlP-seq................................................... 229
Tad Ghavi-Helm and Eileen E.M. Furlong
15 Genome-Wide Profiling of DNA-Binding Proteins Using Barcode-Based
Multiplex Solexa Sequencing......................................... 247
Sunil Kumar Raghav and Bart Deplancke
16 Computational Analysis of Protein-DNA Interactions from ChlP-seq Data....... 263
Jacques Rougemont and Felix Naef
17 Using a Yeast Inverse One-Hybrid System to Identify Functional Binding Sites
of Transcription Factors............................................. 275
Jizhou Tan and Shawn M. Burgess
18 Using cisTargetX to Predict Transcriptional Targets and Networks
in Drosophila...................................................... 291
Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez,
Carl Herrmann, and Stein Aerts
19 Proteomic Methodologies to Study Transcription Factor Function............. 315
Harry W.Jarrett
20 A High-throughput Gateway-Compatible Yeast One-Hybrid Screen
to Detect Protein-DNA Interactions.................................... 335
Korneel Hens, Jean-Daniel Feuz, and Bart Deplancke
Part IV Visualization of GRNs
21 BioTapestry: A Tool to Visualize the Dynamic Properties of Gene
Regulatory Networks............................................... 359
William J.R. Longabaugh
Part V Modeling of GRNs
22 Implicit Methods for Qualitative Modeling of Gene Regulatory Networks....... 397
Abhishek Garg, Kartik Mohanram, Giovanni De Micheli,
and Ioannis Xenarios
Index............................................................... 445
|
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| indexdate | 2024-07-10T00:10:55Z |
| institution | BVB |
| isbn | 1617792918 9781617792915 |
| language | English |
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| physical | XI, 446 S. Ill., graph. Darst. |
| publishDate | 2012 |
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| publisher | Humana Press |
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| series | Methods in molecular biology |
| series2 | Methods in molecular biology Springer protocols |
| spelling | Gene regulatory networks methods and protocols ed. by Bart Deplancke ... New York [u.a.] Humana Press 2012 XI, 446 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in molecular biology 786 Springer protocols Literaturangaben Methode (DE-588)4038971-6 gnd rswk-swf Genregulation (DE-588)4122166-7 gnd rswk-swf Netzwerk (DE-588)4171529-9 gnd rswk-swf Genetic regulation. Genetic regulation--Simulation methods. Genetic regulation--Laboratory manuals. (DE-588)4143413-4 Aufsatzsammlung gnd-content Genregulation (DE-588)4122166-7 s Netzwerk (DE-588)4171529-9 s Methode (DE-588)4038971-6 s DE-604 Deplancke, Bart edt Erscheint auch als Online-Ausgabe 978-1-61779-292-2 Methods in molecular biology 786 (DE-604)BV035362695 786 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024624508&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Gene regulatory networks methods and protocols Methods in molecular biology Methode (DE-588)4038971-6 gnd Genregulation (DE-588)4122166-7 gnd Netzwerk (DE-588)4171529-9 gnd |
| subject_GND | (DE-588)4038971-6 (DE-588)4122166-7 (DE-588)4171529-9 (DE-588)4143413-4 |
| title | Gene regulatory networks methods and protocols |
| title_auth | Gene regulatory networks methods and protocols |
| title_exact_search | Gene regulatory networks methods and protocols |
| title_full | Gene regulatory networks methods and protocols ed. by Bart Deplancke ... |
| title_fullStr | Gene regulatory networks methods and protocols ed. by Bart Deplancke ... |
| title_full_unstemmed | Gene regulatory networks methods and protocols ed. by Bart Deplancke ... |
| title_short | Gene regulatory networks |
| title_sort | gene regulatory networks methods and protocols |
| title_sub | methods and protocols |
| topic | Methode (DE-588)4038971-6 gnd Genregulation (DE-588)4122166-7 gnd Netzwerk (DE-588)4171529-9 gnd |
| topic_facet | Methode Genregulation Netzwerk Aufsatzsammlung |
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