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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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Frequency-inverse document frequency weighting 91 Fukuda, K., Tamura, A. et al. 7 233 235 240 Fukuda, T. et al. 151 Function of genes and proteins 26—7 Functional assignment 120 Functional assignment, effectiveness of text classification algorithms 212—21 Functional assignment, value of keywords 123 Functional coherence 147 148—52 171 Functional coherence, assessment see also neighbor divergence per gene (NDPG) Functional coherence, assessment, best article score 160—2 Functional coherence, assessment, computational approach 152—5 Functional coherence, assessment, evaluation of algorithms 155—7 Functional coherence, assessment, neighbor divergence (ND) 163—4 Functional coherence, assessment, screening gene expression clusters 167—9 Functional coherence, assessment, word distribution divergence (WDD) 157—60 Functional coherence, corruption studies 166—7 Functional coherence, relationship to NDPG score 181 Functional coherence, scoring 153—4 157 Functional coherence, scoring, precision-recall plot 160 Functional determination, gene groups 170 Functional gene groups 156 Functional information, use in sequence analysis 107 Functional neighbors, neighbor expression information (NEI) scoring 129—32 Functional vocabularies 90 196—7. Functional vocabularies, Enzyme Commission (EC) 200 201 Functional vocabularies, Kyoto Encyclopedia of Genes and Genomes (KEGG) 200—1 Functions, poorly referenced 188—9 Funk, M.E. and Reid, C.A. 218 G distribution of words 158—9 Gap penalties in multiple alignment 49 Gap penalties in pairwise alignment 42 43—4 45 46 Gavin, A.C., Bosche, M. et al. 248 Gelbart, W.M., Crosby, M. et al. 184 229 GenBank database, growth 37 Gene annotation 104 Gene annotation by maximum entropy, classifier 221—4 Gene deletion identification 63 Gene dictionaries 228—2 Gene duplication identification 63 Gene expression analysis 1 8 14 61—2 65—6 83 171—2 202 pl Gene expression analysis, arrays 26—7 63 pl Gene expression analysis, assignment of keywords 140—5 173 Gene expression analysis, gene groups 172—3 Gene expression analysis, hierarchical clustering 178 183 Gene expression analysis, hierarchical clustering, application to yeast data set 181—3 Gene expression analysis, hierarchical clustering, pruning dendrograms 178—81 Gene expression analysis, SAGE 64—5 pl Gene expression analysis, screening clusters 173—8 Gene expression analysis, sources of noise 125 Gene expression clusters, functional coherence assessment 167—9 Gene expression data, advantage of text-based approach 12 13 Gene expression data, clustering algorithms 66—72 Gene expression data, dimensional reduction 72—4 Gene expression data, matrix organization 65 Gene expression regulation 23—4 Gene expression similarity, relationship to word vector similarity 99 100 Gene expression, relationship to NEI scores 133—5 134 Gene function annotation 195—6 Gene function vocabularies see Functional vocabularies Gene groups 147. see also neighbor divergence per gene (NDPG) Gene groups, best article score (BAS) 160—2 Gene groups, corruption studies 166—7 Gene groups, determination of function 170 Gene groups, evaluation of assessment algorithms 155—7 Gene groups, functional coherence 148—52 Gene groups, in gene expression analysis 172—3 Gene groups, keyword assignment 100 Gene groups, neighbor divergence (ND) 163—4 Gene groups, theoretical distribution of article scores 163—4 Gene groups, word distribution divergence (WDD) 157—60 Gene interactions databases 7 Gene interactions, textual cooccurrences 250—59 Gene name recognition 227—28 Gene name recognition, dictionaries 228—2 Gene name recognition, unified algorithm 240—3 Gene name recognition, use of abbreviations 237—40 238 239 Gene name recognition, use of context 235—7 Gene name recognition, use of morphology 237 Gene name recognition, use of syntax 233—5 Gene name recognition, word structure and appearance 232—3 Gene names, synonyms 228—29 230 231 Gene networks 245 246—7 Gene networks, roles of scientific text 249 Gene networks, roles of scientific text, co-occurring genes 249—50 Gene Ontology 7 11—12 13 90 152 184 196 197—198 Gene Ontology, evidence codes 198 199—200 Gene Ontology, functional groups, yeast 175—6 Gene Ontology, functional groups, yeast, correlation with NDPG score of nodes 181 182 Gene Ontology, precision-recall performance of codes 222—4 223 Gene Ontology, quality of annotations 188 Gene references, skewed distribution 174 Gene-protein interactions 247 General Repository for Interaction Datasets (GRID) 250 251 261 266 267 Generalized iterative scaling (GIS) 209—10 Genes 22—4 GENES database 201 Genes, defining textual profiles 94—6 Genes, functional assignment 120 Genes, functions 26—7 Genes, homology 40 Genes, querying for biological function 101—4 Genes, structure 22 genetic code 22 23 Genome databases 9—11 Genome sequence information 125—6 Genome sizes 18 Genomic data analysis 7—8 pl Genomics era 1 Genomics literature 2—4 Genomics literature, diversity 5 Genomics literature, quality 4 Genomics literature, relevance 4—5 Giot, L., Bader, J.S. et al. 248 Glenisson, P., Coessons, B. et al. 90 95 99 Glutamic acid 25 Glutamine 25 Glycine 25 Glycogenin 192 Glycolysis genes 150 gold standards 116—17 184 197 222 Golub, T. R, Slonim, D.K. et al. 78 Gotoh, O. 47 Groups of genes see Gene groups Guanine 18 19 Guzder, S.N. et al. 149 Haber, J.E. 151 Hairpin loops, RNA 21 Halushka, M.K., Fan, J.B. et al. 63 Heartless gene 97 98 Heartless gene, synonyms 229 230 Heat shock protein GO functional group 176 Hermeking, H. 64 Hersh, W. 86 Hersh, W., Bhuporaju, R.T. et al. 195 Heyer, L.J., Kruglyak, S. et al. 67 Hidden Markov models (HMM) 54—61 57 Hidden Markov models (HMM), use in gene name recognition 237 Hierarchical clustering 70—2 86 pl Hierarchical clustering, fly gene expression data et 191—4 Hierarchical clustering, gene expression analysis 178—84 Hierarchical organization, Gene Ontology 12 197 198 High entropy models 206 High-Wire press 3 9 Hill, D.P., Davis, A.P. et al. 187—88 Histidine 25 Ho, Y., Gruhler, A. et al. 248 Homayouni, R., Heinrich, K. et al. 92 Homologous genes, recognition 108 114—15 190 Homologous sequences 111 Homology 40—2 117 Homology, remote 114—15 Hughes, T.R., Marton, M.J. et al. 63 Human genes, bias in areas studied 5 6 Human genome project 1 Human genome size 18 Humphreys, K., Demetriou, G. et al. 7 Hutchinson, D. 3 Hvidsten, T.R., Komorowski, J. et al. 187—88 Hydrogen bonding, nucleotide bases 19 20 Hydrogen bonding, proteins 25 26 pl IDA (inferred from direct assay) 188 Incoherent gene groups, article scores 163 164 Inconsistencies in classification of documents 218 Independence assumption 29—30 Independence assumption, naive Bayes classification 204 205 218 Independence of events 29—30 Inferred from Electronic Annotation (IEA) evidence code 189 198 200 Inferred from Reviewed Computational Analysis (RCA), evidence code 198 200 Inferred from Sequence Similarity (ISS), evidence code 189 198 199 Information extraction 259—2 Information retrieval 86 Information retrieval, latent semantic indexing 92 104 Information theory 33—4 Inter-gene difference calculation 181 Interaction verbs 260—1 interactions 245 Introns 21 22 23 Inverse document frequency weighted word vectors 91 161 Isoleucine 25 Iterative sequence similarity searches modification to include text 115—17. see also Position specific iterative BLAST (PSI-BLAST) Ito, T., Chiba, T. et al. 248 Jacard coefficient 87 Jenssen, T.K., Laegreid, A. et al. 8 152 250 Journals relevant to genomics 3 Journals, online 3 K-means clustering 68 173 177 pl Kanehisa, M., Goto, S. et al. 200 Kegg Orthology (KO) numbers 201 Kellis, M. et al. 151 Kerr, M.K. and Churchill, G.A. 67 Key articles, recognition 153 Keyword queries 101—4 102 103 Keywords field (KW), SWISS-PROT 109 Keywords, assignment 100 141—5 173 Keywords, assistance in functional assignment 123 Keywords, breathless and heartless genes 96 97 Keywords, definition for proteins 107 Keywords, expression values pl 5.1 Keywords, in identification of protein-protein interactions 260 Keywords, MeSH headings 9 Keywords, phosphate metabolism study 144—5 Keywords, use in recognition of gene names 233 235 236 Keywords, use to summarize sequence hits 112—14 Klein, H.L. 151 Krauthammer, M., Rzhetsky, A. et al. 232 Krogh, A., Brown, M. et al. 54 Kullback — Liebler (KL) distance 34 131—2 Kullback — Liebler (KL) distance in ND 163 Kullback — Liebler (KL) distance in NDPG 154 Kullback — Liebler (KL) distance in WDD 159 Kwok, P.Y. and Chen, X. 1 Kyoto Encyclopedia of Genes and Genomes (KEGG) 200—1 Latent dimension, relationship to variance 94 Latent semantic indexing (LSI) 92—4 93 104 140 Lee, M.L., Kuo, F.C. et al. 124 Lee, S.E. et al. 151 Lesk, A.M. 1 Leucine 25 Linear discriminant analysis (LDA) 75—9 76 pl Linear discriminant analysis (LDA), applications 78 Linear time algorithms 48 Literature 2—4 Literature index 185 186 Literature index, comparison between organisms 185—6 Literature similarity constraint, modified PSI-BLAST 117 120 Literature, diversity 5 Literature, quality 4 Literature, relevance 4—5 LocusLink 3—4 5 6 11 11 Logistic regression 75 Logistic regression classification 239—40 Low entropy models 206 Low induction false positives, recognition 138 Low induction genes, NEI scores 139 Lu, Z., Szafron, D. et al. 120 Lymphoma, gene expression profiles 62 Lysine 25 MacCallum, R.M., Kelley, L.A. et al. 8 107 115 Machine learning algorithms, combination of sequence and textual information 120—21 Machine learning algorithms, supervised 66 74—9 Machine learning algorithms, unsupervised see Clustering algorithms Manning, C.M. and Schutze, H. 2 84 86 89 202 204 Mantovani, R. 50 Marcotte, E.M., Xenarios, I. et al. 7 262 Mass spectroscopy 248 Masys, D.R., Welsh, J.B. et al. 112 Matching coefficient 87 Matrices, reference matrix (R) 142 Matrices, text matrix (T) 143 Matrices, weighted word-document matrix (W) 91 Matrices, word covariance matrix 92—4 Matrices, word-document matrix (A) 85 Matrix organization, gene expression data 65 Maximum entropy modeling 195—6 203 205—10 207 Maximum entropy modeling, accuracy 217 218 219 220 Maximum entropy modeling, annotation of genes 221—4 Maximum entropy modeling, in identification of protein-protein interactions 263—68 264—5 266 267 Maximum entropy modeling, use in gene name recognition 236 242 243 McCallum, J. and Ganesh, S. 107 114 Mean 34—5 Meaning of text 86 Median 34 35 Medline database, abbreviations 240 Medline database, format 9 10 Merging articles, disadvantages 157 MeSH headings 9 213 MeSH headings, assignment by National Library of Medicine 224 MeSH headings, consistency of assignment 218 Messenger RNA (mRNA) 18 21 Messenger RNA (mRNA), measurement in gene expression arrays 63 Metabolism genes 150 Methionine 25 Mewes, H.W., Frishman, D. et al. 7 78 152 169 196 Michaels, G.S., Carr, D.B. et al. 67 Microarrays see Arrays Mitchell, A.P. 78 Miyagawa, K. et al. 151 Molecular biology, biological function 26—7 Molecular biology, central dogma 18 pl Molecular biology, deoxyribonucleic acid (DNA) 18—20 Molecular biology, genes 22—4 Molecular biology, proteins 24—6 Molecular biology, ribonucleic acid (RNA) 20—2 Molecular function terms, Gene Ontology 11—12 197—198 Morgan, A.A., Hirschman, L. et al. 232 237 240 Morphological variants 242 Morphology, use in gene name recognition 228 Mouse genes, ank root 237 Mouse Genome Database (MGD) 9 11 184 Mouse Genome Database (MGD), synonym lists 229 Mouse, assembly of functional groups 185—9 Mouse, GO annotated genes 13 Mouse, literature index 185 186 Mouse, sensitivity of NDPG 187 Mouse, tricarboxylic acid cycle (TCA) functional group 189 Multiple functions of genes 150 Multiple sequence alignment 48—9 83 Multiple sequence alignment, hidden Markov models 54—61 57 Multiple sequence alignment, position specific iterative BLAST (PSI-BLAST) 53—4 Multivariate normal distribution 76
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