Data integration in microbial genomics ... - Jacobs University

More documents

Recommendations

Info

CHAPTER 6 DOMAINS OF UNKNOWN FUNCTION Ecological perspectives on domains of unknown function: a marine point of view Authors: Pier Luigi Buttigieg, Wolfgang Hankeln, Melissa Beth Duhaime, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner Submitted to: ISME Journal, January 2011 Personal Contribution: Helped to analyse the data after HMM calculations by generating network graphs together with Pier Luigi Buttigieg. Relevance: Generating hypothesis about the possible functions of protein domains in silico, based on their co-occurrence patterns and environmental gradients. 6.1 Abstract Metagenomic datasets from environmental samples offer attractive opportunities to characterize genomic elements of unknown function. We employed graph-theoretic approaches to visualize correlations between protein domains of unknown function detected in the Global Ocean Sampling metagenomes. Functional hypotheses for groups of these domains were generated based on network topology and existing putative functional assignments. Environmental contextualization of one such hypothesis was carried out using indirect gradient analysis.
Page 1:
Max Planck Institute for Marine Mic
Page 4 and 5:
List of abbreviations BLAST Basic L
Page 6 and 7:
Thesis abstract Deoxyribonucleic ac
Page 8 and 9:
4.2 Introduction . . . . . . . . .
Page 10 and 11:
2 1. Introduction syntax: data leve
Page 12 and 13:
4 1. Introduction used to derive ne
Page 14 and 15:
6 1. Introduction croorganisms thri
Page 16 and 17:
8 1. Introduction the middle at the
Page 18 and 19:
10 1. Introduction marker genes hel
Page 20 and 21:
12 1. Introduction what kind and wh
Page 22 and 23:
14 1. Introduction possibilities li
Page 24 and 25:
16 1. Introduction tual data acquis
Page 26 and 27:
18 1. Introduction Doug Wendel, Owe
Page 29 and 30:
CHAPTER 2 METABAR A tool for consis
Page 31 and 32:
2.2. Background 23 molecular sequen
Page 33 and 34:
2.2. Background 25 printing of data
Page 35 and 36: 2.4. Results 27 KML export function
Page 37 and 38: 2.4. Results 29 Figure 2.3: Screens
Page 39 and 40: 2.5. Discussion 31 taking samples i
Page 41 and 42: 2.5. Discussion 33 Handlebar MetaBa
Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
Page 45: 2.6. Conclusion 37 RK advised progr
Page 48 and 49: 40 3. CDinFusion Genomic Standards
Page 50 and 51: 42 3. CDinFusion sortium (GSC), an
Page 52 and 53: 44 3. CDinFusion tiFASTA file with
Page 54 and 55: 46 3. CDinFusion offered the option
Page 56 and 57: 48 3. CDinFusion AMD Opteron TM pro
Page 58 and 59: 50 3. CDinFusion able separately an
Page 60 and 61: 52 3. CDinFusion and upload it with
Page 63 and 64: CHAPTER 4 MIMARKS The Minimum infor
Page 65 and 66: 4.2. Introduction 57 edge generatio
Page 67 and 68: 4.3. Development of MIMARKS 59 in t
Page 69 and 70: 4.4. Survey of published parameters
Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
Page 73 and 74: 4.6. Conclusions and call for actio
Page 75 and 76: CHAPTER 5 MEGX.NET Integrated datab
Page 77 and 78: 5.3. New database structure and con
Page 79 and 80: 5.3. New database structure and con
Page 81 and 82: 5.4. User Access 73 5.4 User Access
Page 83 and 84: 5.4. User Access 75 tal context, co
Page 85: 5.5. Summary 77 access charge: Max
Page 89 and 90: 6.4. Results 81 bations are grouped
Page 91 and 92: 6.4. Results 83 employed indirect g
Page 93: 6.5. Conclusion 85 dients and accom
Page 96 and 97: 88 7. Summary and discussion for a
Page 98 and 99: 90 7. Summary and discussion and de
Page 100 and 101: 92 7. Summary and discussion http:/
Page 102 and 103: 94 7. Summary and discussion tive f
Page 105 and 106: CHAPTER 8 CONCLUSION AND OUTLOOK
Page 107 and 108: 8.3. A contextual data utopia 99 mi
Page 109 and 110: Bibliography [Ackoff, 1989] Ackoff,
Page 111 and 112: BIBLIOGRAPHY 103 throughput communi
Page 113 and 114: BIBLIOGRAPHY 105 [Floridi, 2003] Fl
Page 115 and 116: BIBLIOGRAPHY 107 [Hewson and Fuhrma
Page 117 and 118: BIBLIOGRAPHY 109 [Ludwig and Schlei
Page 119 and 120: BIBLIOGRAPHY 111 [Norvig, 2009] Nor
Page 121 and 122: BIBLIOGRAPHY 113 Hoffman, J. M., Re
Page 123 and 124: BIBLIOGRAPHY 115 [van der Staay et
Page 125: BIBLIOGRAPHY 117 [Zehr and Kudela,
show all

Data integration in microbial genomics ... - Jacobs University

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?