Statistical theory and methods for evolutionary genomics:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2011
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| Ausgabe: | 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XI, 259 S. graph. Darst. |
| ISBN: | 9780199213269 |
Internformat
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| adam_text | IMAGE 1
STATISTICAL THEORY AND METHODS
FOR EVOHITIONARY GENOMICS
XUNGU DEPARTMENT OF GENETICS, DEVELOPMENT AND CELL BIOLOGY, IOWA STATE
UNIVERSITY, USA
OXPORD UNIVERSITY PRESS
IMAGE 2
CONTENTS
1 BASICS IN MOLECULAR EVOLUTION 1
1.1 EVOLUTIONARY DISTANCE OF DNA SEQUENCES 1
1.1.1 JUKES AND CANTOR S MODEL: A TUTORIAL 1
1.1.2 MODELS OF NUCLEOTIDE SUBSTITUTION 3
1.1.3 ONE-PARAMETER METHOD 6
1.1.4 KIMURA S TWO-PARAMETER METHOD 6
1.1.5 THE GENERAL STATIONARY AND TIME-REVERSIBLE MODEL 7
1.1.6 ESTIMATION OF D UNDER VARIABLE RATES 8
1.1.7 THE LOGDET DISTANCE 9
1.2 EVOLUTIONARY DISTANCE BETWEEN PROTEIN-ENCODING SEQUENCES 12 1.2.1
POISSON DISTANCE OF PROTEIN SEQUENCE 12
1.2.2 AMINO ACID SUBSTITUTION MATRIX 12
1.2.3 SYNONYMOUS AND NONSYNONYMOUS DISTANCES 13
1.3 PHYLOGENETICS TREES: AN OVERVIEW 15
1.4 DISTANCE METHOD FOR PHYLOGENETIC INFERENCE 16
1.4.1 PRINCIPLE: MINIMUM-EVOLUTION (ME) 16
1.4.2 ALGORITHM: NEIGHBOR-JOINING (NJ) METHOD 16
1.4.3 FOUR-POINT CONDITION AND NJ ALGORITHM 18
1.4.4 THE (Q-SCORE OF STUDIER AND KEPPLER 19
1.5 PARSIMONY METHODS FOR PHYLOGENETIC INFERENCE 19
1.6 MAXIMUM-LIKELIHOOD (ML) METHODS FOR PHYLOGENETIC INFERENCE 21 1.6.1
LIKELIHOOD FUNCTION 21
1.6.2 TIME-REVERSIBILITY AND THE ROOT PROBLEM 22
1.6.3 SEARCH STRATEGIES FOR ML TREES 22
1.7 BAYESIAN METHODS FOR PHYLOGENETIC INFERENCE 23
1.8 ANCESTRAL SEQUENCE INFERENCE 24
1.8.1 THE MAXIMUM PARSIMONY APPROACH 24
1.8.2 THE PROBABILISTIC (BAYESIAN) APPROACH 25
1.8.3 DELETIONS AND INSERTIONS 27
1.9 RATE VARIATION AMONG SITES 28
1.9.1 NUMBER OF SUBSTITUTIONS AT A SITE 29
1.9.2 ESTIMATION OF A 30
2 BASICS IN BIOINFORMATICS AND STATISTICS 33
2.1 BIOINFORMATIC RESOURCES FOR EVOLUTIONARY GENOMICS 33
2.2 BASIC STATISTICS FOR HOMOLOGOUS SEARCH 36
2.3 SEQUENCE ALIGNMENT 37
2.3.1 PAIRWISE ALIGNMENT 38
2.3.2 MULTIPLE ALIGNMENT WITH A GUIDE TREE: CLUSTAL 39
IMAGE 3
VIII CONTENTS
2.4 MICROARRAYS AND STATISTICS 40
2.4.1 TYPES OF MICROARRAY DATA 40
2.4.2 SOURCES OF NOISES 41
2.4.3 MULTIPLE GENE PROBLEM 41
2.4.4 FALSE DISCOVERY RATE (FDR) 42
2.4.5 ANOVA ANALYSIS OF MANY GENES 44
2.5 MARKOV CHAIN MONTE CARLO (MCMC) 44
2.5.1 METROPOLIS HASTINGS ALGORITHM 45
2.5.2 CALCULATION OF POSTERIOR DISTRIBUTION 45
3 FUNCTIONAL DIVERGENCE AFTER GENE DUPLICATION: STATISTICAL MODELING 47
3.1 MODELING FUNCTIONAL DIVERGENCE 47
3.2 POISSON MODEL FOR TYPE-I FUNCTIONAL DIVERGENCE 49
3.2.1 TWO-STATE MODEL 49
3.2.2 THE POISSON-GAMMA MODEL FOR PROTEIN SEQUENCE EVOLUTION 50 3.2.3
THE LIKELIHOOD FUNCTION 51
3.2.4 MAXIMUM-LIKELIHOOD ESTIMATION (MLE) 52
3.2.5 PREDICTING CRITICAL AMINO ACID RESIDUES 54
3.2.6 REDUCED RATE CORRELATION BETWEEN DUPLICATE GENES: AN ALTERNATIVE
VIEW OF 6] 57
3.3 MARKOV CHAIN MODEL FOR TYPE-I FUNCTIONAL DIVERGENCE 58
3.3.1 THE MARKOV CHAIN MODEL 58
3.3.2 CASE STUDY: COX (CYCLOOXYGENASE) GENE FAMILY 61
3.3.3 COMPARISONS BETWEEN THE POISSON MODEL AND THE MARKOV CHAIN MODEL
63
3.4 STATISTICAL METHOD FOR TYPE-II FUNCTIONAL DIVERGENCE 63
3.4.1 MODELING TYPE-II FUNCTIONAL DIVERGENCE 63
3.4.2 TWO CLUSTERS BY GENE DUPLICATION 65
3.4.3 POISSON MODEL IN THE LATE-STAGE 65
3.4.4 MAXIMUM-LIKELIHOOD ESTIMATION 66
3.4.5 PREDICTING CRITICAL AMINO ACID RESIDUES: EMPIRICAL BAYESIAN
APPROACH 67
3.5 A UNIFYING MODEL FOR TYPE-I AND -II FUNCTIONAL DIVERGENCES 69
4 FUNCTIONAL DIVERGENCE AFTER GENE DUPLICATION: APPLICATIONS AND OTHERS
73
4.1 DIVERGE-BASED ANALYSIS 73
4.1.1 FUNCTIONAL-STRUCTURAL BASIS OF SHIFTED EVOLUTIONARY RATES BETWEEN
CASPASES 73
4.1.2 PSEUDOKINASE DOMAIN IN JAK PROTEIN KINASE IS FUNCTIONAL 77 4.1.3
PATTERN OF TYPE-II FUNCTIONAL DIVERGENCE 82
4.2 FUNCTIONAL DISTANCE ANALYSIS 84
4.2.1 DISTANCE OF FUNCTIONAL DIVERGENCE 84
4.2.2 THREE-CLUSTER ANALYSIS 86
4.2.3 EXAMPLES: VERTEBRATE DEVELOPMENTAL GENE FAMILIES 87
IMAGE 4
CONTENTS IX
4.3 OTHER METHODS FOR TYPE-I FUNCTIONAL DIVERGENCE 90
4.3.1 KNUDSEN-MIYAMOTO METHOD 90
4.3.2 GAUCHER-MIYAMOTO-BENNER METHOD 91
4.3.3 CODON-BASED METHODS 91
4.3.4 HETEROTACHY MODEL 92
4.3.5 THE ALPHA SHIFT MEASURE (ASM) METHOD 93
4.3.6 NAM ET AL. S METHOD FOR DETECTING FUNCTIONAL DIVERGENCE OF PROTEIN
DOMAINS 93
5 PHYLOGENOMIC EXPRESSION ANALYSIS BETWEEN DUPLICATE GENES 95 5.1
BROWNIAN-RELATED STOCHASTIC MODEL 95
5.1.1 EXPRESSION LIKELIHOOD UNDER PHYLOGENY 95
5.1.2 METHOD OF EXPRESSION DISTANCE 100
5.2 ANCESTRAL GENE EXPRESSION INFERENCE 101
5.3 OAKLEY ET AL. S MODEL 103
5.4 EXPRESSION DIVERGENCE UNDER STABILIZING SELECTION: THE
ORNSTEIN-UHLENBACK (OU) MODEL 105
5.5 LIKELIHOOD AND DISTANCE METHODS UNDER EXPERIMENTAL CORRELATIONS 106
5.6 YEAST GLNS GENE FAMILY: AN EXAMPLE 107
5.7 ESTIMATING EXPRESSION DIVERGENCE BASED ON MASSIVELY PARALLEL
SEQUENCING TECHNOLOGY 109
5.7.1 THE POISSON-LOGNORMAL MODEL 109
5.7.2 [/-DISTANCE FOR EXPRESSION DIVERGENCE 110
6 EXPRESSION BETWEEN DUPLICATE GENES: GENOME-WIDE ANALYSIS 113 6.1
CODING SEQUENCE DIVERGENCE VS EXPRESSION DIVERGENCE 113
6.2 REGULATORY MOTIF DIVERGENCE VS EXPRESSION DIVERGENCE BETWEEN
DUPLICATES 114
6.3 GENE DUPLICATION AND EXPRESSION DIVERSIFICATION 115
6.4 EXPRESSION DIVERGENCE AND RETENTION OF DUPLICATE GENES 116
6.5 EVOLUTIONARY, DISTANCE OF EXPRESSION DIVERGENCE 118
6.6 RATE OF EXPRESSION DIVERGENCE BETWEEN YEAST DUPLICATE GENES 120 6.7
ASYMMETRIC EXPRESSION EVOLUTION AFTER GENE DUPLICATIONS 123
6.8 CONCLUDING REMARKS 125
7 TISSUE-DRIVEN HYPOTHESIS OF GENOMIC EVOLUTION 127
7.1 TISSUE-DRIVEN HYPOTHESIS OF GENOMIC EVOLUTION 127
7.1.1 EXPRESSION DIVERGENCE UNDER STABILIZING MODEL 127
7.1.2 TISSUE-DEPENDENT RATE OF PROTEIN EVOLUTION 129
7.1.3 TISSUE-DRIVEN HYPOTHESIS 130
7.2 TESTING THE TISSUE-DRIVEN HYPOTHESIS 132
7.2.1 ESTIMATION OF GENOMIC DISTANCES 132
7.2.2 TISSUE EXPRESSION DIVERGENCE BETWEEN HUMAN AND MOUSE 133 7.2.3
CORRELATION (E T I - D TL ) BETWEEN TISSUE EXPRESSION AND SEQUENCE
DIVERGENCE 134
IMAGE 5
X CONTENTS
7.2.4 TISSUE CORRELATION (EN - DA) BETWEEN INTER-SPECIES AND DUPLICATE
EXPRESSION DIVERGENCE 135
7.2.5 EVOLUTIONARY TATE OF PROTEIN SEQUENCE UNDER MULTIPLE TISSUE
CONSTRAINTS 135
7.2.6 SOME COMMENTS 136
7.3 COMPOUND-POISSON MODEL OF EXPRESSION EVOLUTION 137
7.4 EXPRESSION SHIFTS IN THE HUMAN BRAIN 138
7.4.1 EVOLUTION OF THE HUMAN BRAIN 138
7.4.2 ENARD ET AL. S ANALYSIS 138
7.4.3 GU AND GU S ANALYSIS 138
7.4.4 CONCLUDING COMMENTS 141
8 GENE PLEIOTROPY AND EVOLUTION OF PROTEIN SEQUENCE 143
8.1 MODEL FOR PROTEIN SEQUENCE EVOLUTION 143
8.1.1 FISHER S MODEL AND MOLECULAR PHENOTYPES 143
8.1.2 STABILIZING SELECTION 146
8.1.3 MICRO-ADAPTATION 146
8.1.4 DISTRIBUTION OF MUTATIONAL EFFECTS 147
. 8.1.5 5-DISTRIBUTION 148
8.2 SELECTION INTENSITY AND MODEL CLASSIFICATION 148
8.2.1 MEAN OF SELECTION INTENSITY 148
8.2.2 MODEL CLASSIFICATION 150
8.3 EVOLUTIONARY RATE OF PROTEIN SEQUENCES 151
8.3.1 GENERAL FORMULA 151
8.3.2 K-MODE AND .B-MODE FOR THE RATE OF PROTEIN EVOLUTION 153 8.3.3
EFFECT OF .^-VARIATION ON THE EVOLUTIONARY RATE 154
8.4 ESTIMATION OF GENE PLEIOTROPY AND SELECTION INTENSITY 155
8.4.1 THE SECOND-MOMENT OF EVOLUTIONARY RATE 155
8.4.2 EFFECTIVE GENE PLEIOTROPY (K E ) 155
8.4.3 ESTIMATION PIPELINE 157
8.4.4 EFFECTIVE SELECTION INTENSITY 157
8.4.5 BIAS-CORRECTED ESTIMATION OF EFFECTIVELY GENE PLEIOTROPY 158 8.5
PRELIMINARY ANALYSIS OF GENE PLEIOTROPY 159
8.5.1 EXTENT OF GENE PLEIOTROPY 160
8.5.2 BIOLOGICAL RELEVANCE 160
8.6 COMMENTS ON GENE PLEIOTROPY 165
9 MODELING THE GENOMIC EVOLUTION OF GENE CONTENTS 167
9.1 THE BIRTH-DEATH MODEL OF GENE CONTENT EVOLUTION 167
9.1.1 JOINT SIZE DISTRIBUTION OF GENE FAMILIES 167
9.1.2 GENOME DISTANCES AND GENE CONTENT INFORMATION 169
9.1.3 EXTENDED GENE CONTENT AND GENOME DISTANCE ESTIMATION 170 9.1.4
SIMULATIONS AND CASE STUDY 172
9.2 LIKELIHOOD OF FOUR GENOMES UNDER SIMPLE GENE CONTENTS 174
9.2.1 LIKELIHOOD FUNCTION: CASE A 175
IMAGE 6
CONTENTS XI
9.2.2 LIKELIHOOD FUNCTION: CASE B 179
9.2.3 LIKELIHOOD FUNCTION 180
9.3 BIRTH-DEATH MODEL WITH LATERAL GENE TRANSFER 182
9.3.1 GENERAL BIRTH-DEATH PROCESS CONSIDERING LGT 182
9.3.2 EXTENDED GENE CONTENT UNDER LGT 183
9.3.3 SIMPLE GENE CONTENT AND LGT 184
9.3.4 COMMENTS 185
9.4 OTHER MODELS 185
9.4.1 BLOCKS MODEL 185
9.4.2 EQUAL BIRTH-DEATH RATE MODEL 186
9.4.3 CONSTANT-BIRTH, PROPORTIONAL-DEATH MODEL 186
10 ADVANCED TOPICS IN SYSTEMS BIOLOGY AND NETWORK EVOLUTION 187 10.1 GC
MUTATIONAL BIAS RATHER THAN ADAPTATION DRIVING TYROSINE LOSS IN METAZOAN
GENOME EVOLUTION 188
10.2 CONTRIBUTION OF DUPLICATE GENES TO GENETIC ROBUSTNESS 190
10.2.1 FUNCTIONAL COMPENSATION BETWEEN DUPLICATE GENES 191 10.2.2 WHEN
AN ESSENTIAL GENE IS DUPLICATED 191
10.2.3 WHEN A DISPENSABLE GENE IS DUPLICATED 194
10.2.4 HYPOTHESIS: DUPLICATION OF DISPENSABLE GENES TO MAINTAIN GENETIC
BUFFERING 194
10.3 EVOLUTION OF GENE-GENE INTERACTIONS 196
10.3.1 P- VALUE REPRESENTATION OF GENE-GENE INTERACTION 196 10.3.2
GENERAL FRAMEWORK 197
10.3.3 ESTIMATION OF 7N, 710, 701, AND 700 198
10.3.4 COMMENTS 199
10.4 ORIGIN OF MODULARITY AND COMPLEXITY 200
10.4.1 SOME BACKGROUNDS 200
10.4.2 SCALE-FREE NETWORK AND MODULARITY 201
10.4.3 ORIGIN OF MODULARITY IN A SCALE-FREE NETWORK 203
10.4.4 PROTEIN-PROTEIN INTERACTION DATA ANALYSIS 207
10.4.5 HYPOTHESIS: RANDOM LOSS OF INTERACTIONS MAY SHAPE MODULARITY IN A
COMPLEX GENE NETWORK 208
10.5 NETWORK MOTIF ANALYSIS AND YEAST GENOME DUPLICATION 211
10.6 EVOLUTIONARY KINETIC (EK) ANALYSIS OF DUPLICATE GENES 216
10.6.1 REPROGRAMMING IN DUPLICATE BACKUP CIRCUITS 216
10.6.2 RESPONSIVE BACKUP CIRCUITS (RBC) AND REGULATORY DESIGNS 217
10.6.3 EXPRESSION-TRIGGERED BACKUP CIRCUIT HYPOTHESIS 219 REFERENCES 223
INDEX 251
|
| any_adam_object | 1 |
| author | Gu, Xun |
| author_GND | (DE-588)142906999 |
| author_facet | Gu, Xun |
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| ctrlnum | (OCoLC)812182997 (DE-599)BVBBV025607041 |
| discipline | Biologie |
| edition | 1. publ. |
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| id | DE-604.BV025607041 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:37:23Z |
| institution | BVB |
| isbn | 9780199213269 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020202094 |
| oclc_num | 812182997 |
| open_access_boolean | |
| owner | DE-11 DE-91G DE-BY-TUM DE-20 DE-83 |
| owner_facet | DE-11 DE-91G DE-BY-TUM DE-20 DE-83 |
| physical | XI, 259 S. graph. Darst. |
| publishDate | 2011 |
| publishDateSearch | 2011 |
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| publisher | Oxford Univ. Press |
| record_format | marc |
| spelling | Gu, Xun Verfasser (DE-588)142906999 aut Statistical theory and methods for evolutionary genomics Xun Gu 1. publ. Oxford [u.a.] Oxford Univ. Press 2011 XI, 259 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Populationsgenetik (DE-588)4046804-5 gnd rswk-swf Biostatistik (DE-588)4729990-3 gnd rswk-swf Populationsgenetik (DE-588)4046804-5 s Biostatistik (DE-588)4729990-3 s DE-604 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020202094&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Gu, Xun Statistical theory and methods for evolutionary genomics Populationsgenetik (DE-588)4046804-5 gnd Biostatistik (DE-588)4729990-3 gnd |
| subject_GND | (DE-588)4046804-5 (DE-588)4729990-3 |
| title | Statistical theory and methods for evolutionary genomics |
| title_auth | Statistical theory and methods for evolutionary genomics |
| title_exact_search | Statistical theory and methods for evolutionary genomics |
| title_full | Statistical theory and methods for evolutionary genomics Xun Gu |
| title_fullStr | Statistical theory and methods for evolutionary genomics Xun Gu |
| title_full_unstemmed | Statistical theory and methods for evolutionary genomics Xun Gu |
| title_short | Statistical theory and methods for evolutionary genomics |
| title_sort | statistical theory and methods for evolutionary genomics |
| topic | Populationsgenetik (DE-588)4046804-5 gnd Biostatistik (DE-588)4729990-3 gnd |
| topic_facet | Populationsgenetik Biostatistik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020202094&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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