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Raychaudhury S. — Computational text analysis for functional genomics and bioinformatics
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Íàçâàíèå: Computational text analysis for functional genomics and bioinformaticsÀâòîð: Raychaudhury S. Àííîòàöèÿ: 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
ßçûê: Ðóáðèêà: Áèîëîãèÿ /Ñòàòóñ ïðåäìåòíîãî óêàçàòåëÿ: Ãîòîâ óêàçàòåëü ñ íîìåðàìè ñòðàíèö ed2k: ed2k stats Ãîä èçäàíèÿ: 2006Êîëè÷åñòâî ñòðàíèö: 312Äîáàâëåíà â êàòàëîã: 11.12.2007Îïåðàöèè: Ïîëîæèòü íà ïîëêó |
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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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