Summarizing biological networks:
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Electronic eBook |
| Language: | English |
| Published: |
Cham
Springer
[2017]
|
| Series: | Computational Biology
24 |
| Subjects: | |
| Online Access: | BTU01 FHA01 FHI01 FHM01 FHN01 FHR01 FKE01 FLA01 FRO01 FWS01 FWS02 HTW01 UBG01 UBM01 UBR01 UBT01 UBW01 UBY01 UER01 UPA01 Volltext Inhaltsverzeichnis |
| Physical Description: | 1 Online-Ressource (XV, 146 Seiten, 54 illus., 31 illus. in color) |
| ISBN: | 9783319546216 |
| ISSN: | 1568-2684 |
| DOI: | 10.1007/978-3-319-54621-6 |
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Record in the Search Index
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| adam_text | Contents
1 Introduction 1
1 1 Challenges 4
1 2 Overview of This Book 5
References 7
2 Background 9
2 1 Proteins: The Building Block of Life 9
2 2 Protein-Protein Interaction (PPI) 11
2 3 Methods to Analyze Protein-Protein Interactions 12
231 Yeast Two-Hybrid (Y2H) 12
232 Tandem Affinity Purification (TAP) 13
233 Bimolecular Fluorescence Complementation (BIFC) 13
234 Noise in High-Throughput Screening Methods 14
2 4 Protein-Protein Interaction Databases 15
2 5 Annotating the Roles of Proteins and Their Interactions 16
251 The Structure of Gene Ontology 17
2 6 Summary 19
References 19
3 Clustering PPI Networks 23
3 1 PPI Network Clustering Problem 24
311 Problem Definition 25
312 Challenges 25
313 Representative Clustering Measures 27
314 Overview 29
3 2 PPI Network Clustering Techniques 32
321 Heuristic-Based Algorithms 32
322 Flow-Based Algorithms 36
323 Complete Enumeration Algorithms 38
324 Random Walks and Message Passing Algorithms 40
xiii
XIV
Contents
325 Graph-Cut and Hierarchical Clustering Algorithms 42
326 Multiple Clustering-Based Algorithms 46
327 Genomic Data-Driven Clustering Algorithms 48
3 3 Cluster Validation Measures 49
331 Functional Homogeneity-Based Validation 50
332 MIPS-based Validation 51
333 Other Measures 52
3 4 Comparative Summary 52
3 5 Conclusions 54
References 55
4 Functional Summarization 59
4 1 Motivation 59
4 2 Limitations of PPI Clustering Techniques 60
4 3 Overview 63
4 4 Related Work 63
4 5 The Functional Summarization Problem 65
451 Functional Summary of PPI 65
452 Problem Statement 69
4 6 The Algorithm FUSE 71
4 7 Experimental Results 74
471 Evaluation Metrics 75
472 FUSE Versus Graph Clustering Methods 76
473 Effects of Different Parameters 82
474 Runtime and Scalability 87
4 8 Case Study on AD Network 88
4 9 Inferring Functional Cluster Hubs 90
4 10 Conclusions 92
References 92
5 Multi-faceted Functional Decomposition 95
5 1 Motivation 95
5 2 Related Work 97
5 3 Problem Statement 97
531 Terminology 97
532 Multi-faceted Functional Decomposition Problem 98
533 Problem Definition 101
5 4 FACETS Algorithm 101
541 The Initialization Phase 101
542 The Iteration Phase 102
5 5 Experimental Study 105
551 Experiment Settings 105
552 Results 106
5 6 Case Study: Human Autophagy System 113
Contents
xv
5 7 Conclusions 115
References 115
6 Differential Functional Summarization 117
6 1 Background 117
6 2 Motivation and Overview 119
6 3 Functional Subgraphs in a Differential Network 120
631 Constructing Differential Networks 120
632 Functional Subgraphs 123
6 4 Differential Summarization Problem 125
6 5 The DiffNet Algorithm 127
6 6 Experimental Study 128
661 Functional Analysis of MMS-treated/untreated
dE-MAP Network 129
662 Comparison with Graph Clustering Algorithms 130
663 Effect of Various Parameters 132
664 Running Times 133
665 Effect of Interaction Noise 135
666 Effect of Annotation Loss 136
6 7 Conclusions 137
References 137
7 The Road Ahead 139
7 1 Summary 139
7 2 Future Research 140
References 142
Index
|
| any_adam_object | 1 |
| author | Bhowmick, Sourav S. Seah, Boon-Siew |
| author_facet | Bhowmick, Sourav S. Seah, Boon-Siew |
| author_role | aut aut |
| author_sort | Bhowmick, Sourav S. |
| author_variant | s s b ss ssb b s s bss |
| building | Verbundindex |
| bvnumber | BV044291191 |
| collection | ZDB-2-SCS |
| ctrlnum | (ZDB-2-SCS)9783319546216 (OCoLC)985991192 (DE-599)BVBBV044291191 |
| dewey-full | 570.285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology |
| dewey-raw | 570.285 |
| dewey-search | 570.285 |
| dewey-sort | 3570.285 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik |
| doi_str_mv | 10.1007/978-3-319-54621-6 |
| format | Electronic eBook |
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| issn | 1568-2684 |
| language | English |
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| psigel | ZDB-2-SCS ZDB-2-SCS_2017 |
| publishDate | 2017 |
| publishDateSearch | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| record_format | marc |
| series | Computational Biology |
| series2 | Computational biology |
| spellingShingle | Bhowmick, Sourav S. Seah, Boon-Siew Summarizing biological networks Computational Biology Computer science Data mining Bioinformatics Systems biology Computer Science Computational Biology/Bioinformatics Data Mining and Knowledge Discovery Systems Biology Informatik |
| title | Summarizing biological networks |
| title_auth | Summarizing biological networks |
| title_exact_search | Summarizing biological networks |
| title_full | Summarizing biological networks Sourav S. Bhowmick, Boon-Siew Seah |
| title_fullStr | Summarizing biological networks Sourav S. Bhowmick, Boon-Siew Seah |
| title_full_unstemmed | Summarizing biological networks Sourav S. Bhowmick, Boon-Siew Seah |
| title_short | Summarizing biological networks |
| title_sort | summarizing biological networks |
| topic | Computer science Data mining Bioinformatics Systems biology Computer Science Computational Biology/Bioinformatics Data Mining and Knowledge Discovery Systems Biology Informatik |
| topic_facet | Computer science Data mining Bioinformatics Systems biology Computer Science Computational Biology/Bioinformatics Data Mining and Knowledge Discovery Systems Biology Informatik |
| url | https://doi.org/10.1007/978-3-319-54621-6 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029695293&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV044435637 |
| work_keys_str_mv | AT bhowmicksouravs summarizingbiologicalnetworks AT seahboonsiew summarizingbiologicalnetworks |