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Raychaudhury S. — Computational text analysis for functional genomics and bioinformatics
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Название: Computational text analysis for functional genomics and bioinformaticsАвтор: 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
Язык: Рубрика: Биология /Статус предметного указателя: Готов указатель с номерами страниц ed2k: ed2k stats Год издания: 2006Количество страниц: 312Добавлена в каталог: 11.12.2007Операции: Положить на полку |
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Munich Information Center for Protein Sequences (MIPS) 7 152 196 Murzin, A.G. Brenner, S.E. et al. 117 Mus musculus see Mouse Mycobacterium tuberculosis, genome size 18 N-gram classifier 241 Naive Bayes text classification scheme 203 204—5 216 Naive Bayes text classification scheme, accuracy 221 222 Naive Bayes text classification scheme, use in gene name recognition 235—6 242—3 Naive Bayes text classification scheme, use in protein-protein interaction identification 262 Name recognition see Gene name recognition National Library of Medicine, assignment of MeSH headings 224 Natural language processing 2 Natural language processing algorithms 83 Nearest neighbor classification 75 Nearest neighbor classification, accuracy 217 218 Nearest neighbor classification, application to text classification 203—4 216 Needleman, S.B. and Wunsch, C.D. 44 Negations 86 Neighbor divergence (ND) 163—4 Neighbor divergence (ND), precision-recall plot 160 Neighbor divergence per gene (NDPG) 152 162 164—6 Neighbor divergence per gene (NDPG) scores, nodes 179 Neighbor divergence per gene (NDPG) scores, random and functional groups 166 Neighbor divergence per gene (NDPG), computational approach 153—5 Neighbor divergence per gene (NDPG), corruption studies 166—7 168 Neighbor divergence per gene (NDPG), data types required 155 Neighbor divergence per gene (NDPG), evaluation across different organisms 184—9 191 Neighbor divergence per gene (NDPG), evaluation of method 155—7 Neighbor divergence per gene (NDPG), precision-recall plot 160 Neighbor divergence per gene (NDPG), scores for functional groups 167 Neighbor divergence per gene (NDPG), screening of gene expression clusters 168—9 173—8 pl Neighbor divergence per gene (NDPG), sensitivity, relationship to annotation quality 179 Neighbor expression information (NEI) scoring 124 130—2 Neighbor expression information (NEI) scoring, application to phosphate metabolism data set 132—6 140 Neighbor expression information (NEI) scoring, application to SAGE and yeast-2-hybrid assays 141 Neighbor expression information (NEI) scoring, low induction genes 138—9 Neighbor expression information (NEI) scoring, scores of individual experiments 136—8 137 Neighborhood words 48 Nelson, D.L., Lehninger, A.L. et al. 17 Networks, genetic 245 246—7 Neural networks 75 Ng, S.K. and Wong, M. 7 Nigam, K., Lafferty, J. et al. 205—6 218 Node selection, dendrograms 179—81 Nodes, pruning 178—81 pl Nodes, states 180 Noise 123 124—6 Noise, management in phosphate metabolism study 129—41 Normal distribution 32 Normal distribution, z-score 35 Novak, J.P., Sladek, R. et al. 124 Nucleosome GO functional group 176 Nucleotide bases 18 19 Nucleotide bases, in RNA 21 Nucleotide bases, pairing 19 20 Nucleotide bases, phosphodiester bond 20 Number, prediction of likelihood of interactions 256 257 258 259 Nylon gene arrays 63 Ohta, Y., Yamamoto, Y. et al. 7 Oligonucleotide arrays 62 Online journals 3 Ono, T., Hishigaki, H. et al. 7 262 Oryza sativa, GO annotated genes 13 Overlap coefficient 87 Overlap, clusters and functional groups 176—7 pl p53 5 Pairwise sequence alignment 44—8 96 PAM250 matrix 44 Parameter weights, maximum entropy classification 209 Parsing sentences 262 Part-of-speech tagging 233—5 241 Part-of-speech, use in identification of protein-protein interactions 262 PATHWAYS database 201 Pearson, W.R. 43 48 Pearson, W.R. and Lipman, D.J. 48 Peer-reviewed literature 2 Peer-reviewed literature, value in genomic data set analysis 8 Peptide bond 24 Performance measures 35—7 Petukhova, G. et al. 149 151 PH011 gene 128 129—30 PH011 gene, expression ratio distribution 131 Phenylalanine 25 Phillips, B., Billin, A.N. et al. 192 Phosphate metabolism study 126—7 Phosphate metabolism study, distribution of NEI scores 133 Phosphate metabolism study, expression log ratios 127 Phosphate metabolism study, keywords 144—5 Phosphate metabolism study, literature-based scoring system 129—30 Phosphate metabolism study, NEI scores 136 Phosphate metabolism study, NEI scores of individual experiments 136—8 137 Phosphate metabolism study, neighbor expression information (NEI) scoring 132—6 Phosphate metabolism study, top fifteen genes 127—9 128 Phosphodiester bond 20 Plasmodium falciparum, genome size 18 Poisson distribution 32 33 163 164 Pollack, J.R., Perou, C.M. et al. 63 Poly-A tail, RNA 21 22 Polyadenylation signal 23 Polymerase proteins 24. see also DNA polymerase; RNA polymerase Poorly referenced areas 108 117 140 184 Poorly referenced areas, functions 188—9 Poorly referenced areas, transference of references 189—92 Poorly referenced areas, use of sequence similarity 111 Poorly referenced areas, worm 187 Population statistics 34—5 Porter, M.F. (Porter’s algorithm) 90 Position specific iterative BLAST (PSI-BLAST) 53—4 115 Position specific iterative BLAST (PSI-BLAST), evaluation 117—20 118 119 Position specific iterative BLAST (PSI-BLAST), modification to include text 116—17 PRECISION 37 212 Precision, PSI-BLAST 118—19 Precision-recall performance, GO codes 222—4 223 Precision-recall plot, functional coherence scoring methods 160 Predefined sets of words 90 Prediction results 36 Predictive algorithms, measures of 35—7 Prey proteins 248 Primary structure, proteins 25 Primary transcript 22 Principal component analysis (PCA) 73—4 92 probability 27—8 Probability density function, multivariate normal distribution 76 Probability distribution functions (pdfs) 31—3 Probability distribution functions (pdfs), statistical parameters 35 Probability, Bayes' theorem 30 Probability, conditional 28—9 Probability, independence of events 29—30 Probability, information theory 33—4 Profile drift 116 Profiles 50 65 Progressive alignment 49 Proline 25 Promoter sites, DNA 21 22 23 Protein binding 141 Protein interaction networks 245 Protein name recognition, use of word appearance 233 234 Protein sequence probabilities, use of Bayes’ theorem 30 Protein-gene interactions 247 Protein-protein interactions 245 247 Protein-protein interactions, affinity precipitation 248 Protein-protein interactions, gene name co-occurrence 250—59 Protein-protein interactions, information extraction strategies 259—2 Protein-protein interactions, statistical textual classifiers 262—68 Protein-protein interactions, yeast-2-hybrid method 247—48 Proteins 24—6 Proteins, Edman degradation 39—40 Proteins, function assignment, role of text analysis 108 Proteins, function assignment, utilization of text and sequence information 120—21 Proteins, functions 18 26 27 Proteins, SCOP database 117—18 Proteins, synthesis 18 21—2 Proteins, tertiary structure pl 2.4 Proteomics methods, introduction 1 Proux, D., Rechenmann, F. et al. 7 233 Pruitt, K.D. and Maglott, D.R. 4 11 Pruning dendrograms 178—81 pl Pruning dendrograms, application to yeast data set 181—4 Pseudo-counts of words, use in naive Bayes classification 204—5 Pseudo-reference assignation 110 PU conditions, phosphate metabolism study 126 Public Library of Science (PLOS) 3 9 PubMed abstracts 2 3 4 9 11 pl PubMed abstracts, use for NDPG 155 PubMed Central 3 9 Purine nucleotide bases 18 19 Pustejovsky, J., Castano, J. et al. 238 Pyrimidine nucleotide bases 18 19 Quality, genomics literature 4 Rain, J.C., Selig, L. et al. 248 Rare words 88 89 91 Ratnaparkhi, A. 205 209 Rattus norvegicus, GO annotated genes 13 Raychaudhuri, S. and Altman, R. B. 184 Raychaudhuri, S., Chang, J.T. et al. 7 8 179 188 Raychaudhuri, S., Schu? tze, H. et al. 152 157 Raychaudhuri, S., Stuart, M. et al. 63 72 Raychaudhuri, S., Sutphin, P.D. et al. 62 RDH54 gene, representation in literature 150 151 Real-values vectors, comparison metrics 87 Recall 37 212 Recall, PSI-BLAST 118 Reference indices 95 152 185 188 Reference indices, genome databases 9—11 Reference matrix (R) 142 References, in SWISS-PROT 109 Relevance, literature sources 4—5 Replicates, value in recognition of false positives 138 Reporter genes 248 Restriction enzymes 64 Ribonucleic acid see RNA Ribonucleotides 21 Ribose 19 Ribosomal RNAs (rRNA) 21 Riley, M. 196 Rindflesch, T.C., Tanabe, L. et al. 236 Ripley, B.D. 67 75 RNA 18 20—2 RNA polymerase 18 21 RNA, binding by proteins 25 26 RNA, nucleotide bases 19 RNA, yeast transfer RNA structure pl 2.2 Roberts, R.J. 3 Roots of gene names 237 241—2 Rosenfeld, R. 83 197 218 Ross, D.T., Scherf, U. et al. 67 Saccharomyces cerevisiae see Yeast Saccharomyces Genome Database (SGD) 9 11 127 174 180 184 212 221 251 SAGE (Serial Analysis of Gene Expression) 62 64—5 pl SAGE (Serial Analysis of Gene Expression), use with NEI scores 141 Saldanha, A.J., Brauer, M. et al. 126 Sample preparation, sources of variability 125 Sanger dideoxy method 39 pl Sanger dideoxy sequencing method 39 pl Schena, M., Shalon, D. et al. 63 Schug, J., Diskin, S. et al. 188 Scope of functionally coherent gene groups 150 Score matrix, dynamic programming 45 Score step, gene name finding algorithm 241 Scoring functions in multiple alignment 48—9 Scoring functions in pairwise alignment 42 Scoring of functional coherence 153—4 157 Secondary structure prediction, hidden Markov models 56 57 Sekimizu, T., Park, H.S. et al. 7 262 Selected state of nodes 180 Self-hybridization, mRNA 21 Self-organizing maps 69—70 173 pl.7.1 Self-organizing maps, yeast gene expression data 70 174 Semantic neighbors 153 Semantic neighbors, number, relationship to performance of NDPG 165 Sensitivity 36 37 Sensitivity of NDPG 187 Sentence co-occurrences 251 252 253 254 Sequence alignment 42—4 Sequence alignment, BLAST 48 Sequence alignment, dynamic programming 44—7 Sequence alignment, multiple 48—61 Sequence analysis, use of text 107—9 Sequence comparison 40—2 Sequence contamination 54 Sequence hits, description by keywords 112—14 Sequence hits, organization by textual profiles 114 Sequence hits, sequence information, combination with textual information 120—21 Sequence similarity, relationship to word vector similarity (breathless) 99 Sequence similarity, use to extend literature references 111—12 Sequences, comparison to profiles 50—3 sequencing 8 14 38 Sequencing, Edman degradation of proteins 39—40 Serine 25 Sharff, A. and Jhoti, H. 1 Shatkay, H. and Feldman, R. 2 7 Shatkay, H., Edwards, S. et al. 8 95 112 Sherlock, G. 67 Shinohara, M. et al. 151 Shor, E. et al. 151 Shotgun assembly strategy 39 Signon, L. et al. 151 Single expression series, keyword assignment 141—5 Single expression series, lack of context 123 Single expression series, noise 124—6 Single expression series, phosphate metabolism study 126—30 132—40 Single nucleotide polymorphism, detection, introduction 1 Single nucleotide polymorphism, identification 63 Smarr, J. and Manning, C. 241 Sources of noise 125 Specificity 36 Spellman, P.T., Sherlock, G. et al. 63 78 Splicing, primary transcript 22 Spotted DNA microarrays 62 63 Standard deviation 34 35 Standardized gene names 228—29 Stanford Microarray Database (SMD) 126 Stapley, B.J. , Kelley, L.A. et al. 120 Statistical machine learning 262—68 Statistical parameters 34—5 Statistical parameters, gene reference indices 174 Stein, L., Sternberg, P. et al. 9 184 229 Stemming 90 Stephens, M., Palakal, M. et al. 7 Stop lists 89 90 stopwords 216 String matching strategy 40—1 Structural Classification of Proteins Database (SCOP) 117—18 Structural proteins 24 Stryer, L. 17 39 Study areas, bias 5 Subsequence alignment 45 Substitution matrices 43 44 Substitution of amino acids 41 42—3 Sum of pairs scoring system 49 Sung, P. et al. 151 Supervised machine learning algorithms 66 74—9 202 Support vector machine classifiers 242 243 263 SWISS-PROT database 3 11 11 108 109—11 115 118 189 pl Symington, L.S. 151 Synonym lists 229 Synonyms for genes 230—1 232 Syntax, use in recognition of gene names 228 233—5 241 Tag sequences 64 Tagging enzyme 64
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