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Raychaudhury S. — Computational text analysis for functional genomics and bioinformatics
Raychaudhury S. — Computational text analysis for functional genomics and bioinformatics

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Название: Computational text analysis for functional genomics and bioinformatics

Автор: Raychaudhury S.

Аннотация:

This book brings together the two disparate worlds of computational text analysis and biology and presents some of the latest methods and applications to proteomics, sequence analysis and gene expression data. Modern genomics generates large and comprehensive data sets but their
interpretation requires an understanding of a vast number of genes, their complex functions, and interactions. Keeping up with the literature on a single gene is a challenge itself-for thousands of genes it is simply impossible.
Here, Soumya Raychaudhuri presents the techniques and algorithms needed to access and utilize the vast scientific text, i.e. methods that automatically "read" the literature on all the genes. Including background chapters on the necessary biology, statistics and genomics, in addition to practical
examples of interpreting many different types of modern experiments, this book is ideal for students and researchers in computational biology, bioinformatics, genomics, statistics and computer science.


Язык: en

Рубрика: Биология/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2006

Количество страниц: 312

Добавлена в каталог: 11.12.2007

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID
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Предметный указатель
3’ and 5’ untranslated regions      23
Aach, J. and Church, G.M.      67
Abbreviations, use in gene name recognition      228 237—42 238 239 243
Abstract co-occurrences      254—59 256
Abstract co-occurrences, number, prediction of likelihood of interaction      254—59 256 257 258
Accession number (AC), SWISS-PROT      109
Accuracy      36 212
Adenosine      18 19
Affine gap penalty function      43
Affinity precipitation      248
Agglomerative hierarchical clustering      71—2
Alanine      25
Alberts, B., Bray, D. et al.      17
Algorithms, measurement of performance      35—7
Aligned sequences      42
Alignment algorithms      42—4
Alignment, dynamic programming      44—7
Alizadeh, A.A., Eisen, M.B. et al.      62 63 68 78
Alpha helices      25
Alpha helices, hydrogen bonding      pl 2.3
Altman, R.B. and Raychaudhuri, S.      67 86
Altschul, S.F., Gish, W. et al.      48
Altschul, S.F., Madden, T.L. et al.      115
Ambiguity of gene names      229 232
Amino acid sequences, probabilities      30
Amino acids      24—5 25
Amino acids, emission probabilities      59
Amino acids, genetic code      23
Amino acids, secondary structure prediction      56—7
Amino acids, structure      24
Amino acids, substitutions      41 42—3
Amino acids, synthesis      21—2
Amino acids, transition probabilities      59—60
Anchoring enzymes      64
Andrade, M.A. and Valencia, A.      112 113 173
Ank root      237
Annotated genes      see also Functional vocabularies
Annotated genes, use of maximum entropy classifier      221—4
Annotated genes, uses      196—7
Annotation quality, GO      187
Annotation quality, relationship to NDPG sensitivity      179
Appearance of words, use in name recognition      228 232—3 234 241—3 242
Arabidopsis thaliana, GO annotated genes      13
Arbeitman, M.N., Furlong, E.E. et al.      98 193
Arginine      25
Arrays, gene expression profiling      26—7 63 pl
Arrays, noise sources      125
Article indices      227
Ashburner, M., Ball, C.A. et al.      7 90 148 152 196
Asparagine      25
Aspartic acid      25
Average linkage clustering      181 191
Bachrach, C.A. and Charen, T.      213 224
Backward algorithm      60
Bailly, V. et al.      149
Bait proteins      248
Ball, C.A., Awad, I.A. et al.      126
Ball, C.A., Dolinski, K. et al.      212
Base pairing      19 20
Base pairing in RNA      21
Baum — Welsh algorithm      60—1
Bayes' theorem      30 255
Behr, M.A., Wilson, M.A. et al.      63
Ben-Hur, A., Elisseeff, A. et al.      67
Best article score (BAS)      160—2
Best article score (BAS), precision-recall plot      160
Beta sheets      25 26
Beta-GAL      248
Bias in study areas      5 6
Binary vectors, comparison metrics      87
Binding proteins      141
Binomial distribution      31 32 33
Bioinformatics      1 2
Biological function      26—7
Biological function codes      195
Biological function databases      7
Biological function querying      101—4
Biological process terms, Gene Ontology      12 198
Biological similarity, relationship to textual similarity      97—9
BioMed Central      3 9
Biomolecular Interaction Network Database (BIND)      263
Blake, J.A., Richardson, J.E. et al.      9 184 229
Blaschke, C., Andrade, M.A. et al.      7 260—1 265
BLAST (Basic Linear Alignment Search Tool)      39 48 83 107
BLAST, comparison of breathless protein with other proteins      97 98.
Boeckmann, B., Bairoch, A. et al.      3 109
Breathless      228
Breathless, abbreviations      237—38
Breathless, gene literature study      96—9
Breathless, SWISS-PROT record      109 pl
Breathless, synonyms      229 231
Breitkreutz, B.J., Stark, C. et al.      250
Brill, E.      234
Brown, P.O. and Bostein, D.      1
Caenorhabditis elegans, assembly of functional groups      185—9
Caenorhabditis elegans, Candida albicans, GO annotated genes      13
Caenorhabditis elegans, GO annotated genes      13
Caenorhabditis elegans, literature index      185 186
Caenorhabditis elegans, sensitivity of NDPG      187
Calculation of mean      35
Candidate gene identification      8
Carbohydrate metabolism genes      150
Catlett, M.G. and Forsburg, S.L.      151
CCAAT promoter      50
Cellular compartment terms, Gene Ontology      198
Central dogma of molecular biology      18 pl
Centred correlation metric      181
Chang, J.T., Raychaudhuri, S. et al.      8 107 117 118
Chang, J.T., Schutze, H. et al.      233 235 238—40
Chang, J.T., Schutze, H. et al., unified gene name finding algorithm      240—3
Chaperones      24
Chaussabel, D. and Sher, A.      95
Chee, M., Yang, R. et al.      63
Chen, J.J., Wu, R. et al.      63
Cherry, J.M., Adler, C. et al.      9 155 174 181 184 212 229
Chi-square testing, feature selection      210—12 211 216 218
Chips, sources of noise      125
Cho, R.J., Campbell, M.J. et al.      63
Chu, S. and Herskowitz, I.      78
Chu, S., DeRisi, J.L. et al.      78
Classification methods      66 74—9
Classification of documents, inconsistencies      218
Clustal Walgorithm      48 49
Cluster boundary optimization      178—84 192—3
Cluster identification      192—3
Cluster software      86 181
Clustering algorithms      66—72 172
Clustering algorithms, k-means clustering      pl 2.8
Clustering, hierarchical      178—84
Clustering, NDPG scoring      173—8
Clustering, use in organizing sequence hits      114
Co-occurring gene names      249—50
Co-occurring gene names, assessment of efficacy      250—4
Co-occurring gene names, interaction verbs      260—1
Co-occurring gene names, number, prediction of likelihood of interaction      254—59
Coded messages, information theory      33—4
Codons      21—2
Codons, genetic code      23
Coherence of gene groups      147. See also Functional coherence of gene groups
Coin tossing, hidden Markov models      55—6
Coin tossing, probabilities      28 29
Collection frequency      85—6
Comments field (CC), SWISS-PROT      109
Comprehensive Yeast Genome Database (CYGD)      169
Concordance      see Overlap clusters
Conditional probability      28—9
Conditional probability, Bayes’ theorem      30
Conditions, in expression analysis      65
Confidence scores of maximum entropy classifier      220—21
Consensus sequences      50
Conserved substitutions      41
Context, use in recognition of gene names      228 235—7 242
Continuous probability distribution functions      31 32 33
Core terms, in name finding algorithm      233 234
Correlation coefficient      67
Corruption studies, gene groups      166—7
Cosine metric      87
Cosine metric, comparison of breathless with other genes      96—7
Cosine metric, comparison of gene expression profiles      98
Cosine metric, neighborhood expression information scoring      130—1 203
Covariance matrices, linear discriminant analysis      77 pl
Covariance matrices, principal component analysis      73
Craven, M. and Kalian, J.      7
Credibility, genomics literature      4
Cross-referencing, assessment of functional coherence of gene groups      152
Cysteine      25
Cytochrome P450 genes, appearance      232—3
Cytosine      18 19
Danio rerio, GO annotated genes      13
Data analysis      65—6
Data analysis, clustering algorithms      66—72
Data analysis, dimensional reduction      72—4
Data interpretation      66 68 74 77 pl pl
Data interpretation problems      1—2
Data, statistical parameters      34—5
Database building      5 7
Database of Interacting Proteins (DIP)      7 262
databases      3—4 7 9—11.
Databases, Biomolecular Interaction Network Database (BIND)      263
Databases, Comprehensive Yeast Genome Database (CYGD)      169
Databases, electronic text      9
Databases, GenBank database, growth      37
Databases, GENES database      201
Databases, PATHWAYS database      201
Databases, SCOP database      117—18
Databases, Stanford Microarray Database (SMD)      126
Dendrograms, hierarchical clustering      71 178
Deoxyribonucleic acid      see DNA
Deoxyribonucleotides      18 19
Deoxyribose      18 19
DeRisi, J.L., Iyer, V.R. et al.      66 78
Dice coefficient      87
Dictionary strategy, gene name identification      228—2 240 251
Dictyostelium discoideum, GO annotated genes      13
Dimensional reduction      66 67 72—4
Dimensional reduction, feature selection      88—90
Dimensional reduction, latent semantic indexing      92—4
Dimensional reduction, weighting words      90—1
Dirichlet priors      159
Discrete probability distribution functions      31 32 33
Discriminant line, linear discriminant analysis      76
Distance metrics, clustering algorithms      67
Distribution functions      see Probability
Distribution functions (pdfs)      0
Distributions of words, WDD      157—60
Divergence value, WDD      15
Diversity, genomics literature      5 141 150 195
DNA (deoxyribonucleic acid)      18—20
DNA (deoxyribonucleic acid), binding by proteins      25 26
DNA (deoxyribonucleic acid), Sanger dideoxy sequencing method      39 pl
DNA (deoxyribonucleic acid), transcription      21 22 245 247
DNA polymerase      18
DNA polymerase, use in Sanger dideoxy sequencing method      39
DNA-dependent ATPase genes, yeast      148—50 149
Document classification      see Text classification
Document frequency      85 88 89 91
Document gene indices      95. see also Databases
Document similarity assessment      83—4
Document similarity assessment, comparison metrics      86—7
Document similarity assessment, word values      88
Document vectors      84—6 85
Document vectors, latent semantic indexing      92—3
Document vectors, vocabulary building      88—90
Document vectors, weighting words      90—1
Donaldson, I., Martin, J. et al.      7 263
Dossenbach, C. Roch, S. et al.      96
Dot plots      41—2
Drosophila melanogaster, assembly of functional groups      185—9
Drosophila melanogaster, breathless gene literature search      96—9
Drosophila melanogaster, breathless gene literature search, BLAST hits      pl 5.1
Drosophila melanogaster, breathless gene literature search, BLAST hits, keywords      112 113
Drosophila melanogaster, gene name detection      232
Drosophila melanogaster, genome size      18
Drosophila melanogaster, GO annotated genes      13
Drosophila melanogaster, keyword queries      101—4 103 104
Drosophila melanogaster, latent semantic indexing      94
Drosophila melanogaster, literature      183
Drosophila melanogaster, literature index      185 186
Drosophila melanogaster, literature, document frequencies of words      88 89
Drosophila melanogaster, sensitivity of NDPG      187
Durbin, R., Eddy, S. et al.      40
Dwight, S.S., Harris, M.A. et al.      187
Dynamic programming      44—7 83
Dynamic programming score matrix      45
Dynamic programming, forward algorithm      59
Dynamic programming, multiple alignment      49
Dynamic programming, tracing back      47
Dynamic programming, use in gene name recognition      238—40
Dynamic programming, Viterbi algorithm      57—9 58
Edman degradation of proteins      39—40
Eisen, M.B., Spellman, P.T. et al.      67 70 78 86 168—9 172 174 180
Electronic publishers      2—3
Electronic text resources      9
Emission probabilities, amino acids      59
Empirical distribution, article scores      164
Enhancers      23—4
Entrez Gene      11
Entropy models      206. see also Maximum entropy modeling
Entropy of a distribution      34
Enzyme Commission (EC) classification scheme      200 201
Enzymes      24
Epstein Barr virus, genome size      18
Error sources, gene expression analysis      125
Escherichia. coli, genome size      18
Eskin, E. and Agichtein, E.      107 120 121
Euclidean metric      67 87
Events, conditional probability      28—9
Events, independence      29—30
Events, probability      27—8
Evidence codes      188 189 198 199—200
Exons      21 22
Exponential distributions      32
Exponential distributions, expression value of words      142—3 pl
Exponential distributions, maximum entropy probability distribution      208
Extend step, gene name recognition algorithm      243
Faculty of 1000      4
False negatives      36
False positives      36
False positives in single gene expression series      124
False positives in single gene expression series, recognition      135 137—8
Fbgn0023184      192
Fbgn0029196      192
Fbgn0034603 (glycogenin)      192
Feature selection      88—90
Feature selection, text classification algorithms      210—12
Feature terms in name finding algorithm      233 234
Features, in expression analysis      65
Features, in maximum entropy classification      206
Feng, Z.P.      120
Fields, S. and Song, O.      141
Filtering, gene name detection      232 241
Fly functional clusters      193 pl
Fly gene expression data et, hierarchical pruning      189—2
FlyBase      9 11 88 95 109 184 190
FlyBase, lists of synonyms      229 230
FlyBase, standardized names      228
FORWARD ALGORITHM      59
Fractional reference (fr) parameter, WDD      158
Fractional references for documents, best article score system      160—1
Frequency of words      see Document frequency
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