메뉴 건너뛰기




Volumn 15, Issue 1, 2018, Pages 168-180

Inferring Unknown Biological Function by Integration of GO Annotations and Gene Expression Data

Author keywords

bioinformatics; Clustering; gene ontology; machine learning

Indexed keywords

BIOINFORMATICS; BIOLOGICAL SYSTEMS; COMPUTATIONAL METHODS; GENES; LEARNING SYSTEMS; SEMANTICS;

EID: 85041901722     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2016.2615960     Document Type: Article
Times cited : (12)

References (41)
  • 1
    • 84964654330 scopus 로고    scopus 로고
    • Computational algorithms to predict Gene Ontology annotations
    • P. Pinoli, D. Chicco, M. Masseroli, "Computational algorithms to predict Gene Ontology annotations, " BMC Bioinf., vol. 16, no. Suppl 6, 2015, Art. no. S4.
    • (2015) BMC Bioinf. , vol.16
    • Pinoli, P.1    Chicco, D.2    Masseroli, M.3
  • 3
    • 78650505144 scopus 로고    scopus 로고
    • A novel path-based clustering algorithm using multi-dimensional scaling
    • Berlin, Germany: Springer
    • U. Nguyen, L. A. F. Park, L. Wang, K. Ramamohanarao, "A novel path-based clustering algorithm using multi-dimensional scaling, " in Advances in Artificial Intelligence. Berlin, Germany: Springer, 2009, pp. 280-290.
    • (2009) Advances in Artificial Intelligence , pp. 280-290
    • Nguyen, U.1    Park, L.A.F.2    Wang, L.3    Ramamohanarao, K.4
  • 4
    • 78650792692 scopus 로고    scopus 로고
    • Clustering gene expression data with a penalized graph-based metric
    • A. Baya and P. Granitto, "Clustering gene expression data with a penalized graph-based metric, " BMC Bioinf., vol. 12, no. 1, 2011, Art. no. 2.
    • (2011) BMC Bioinf. , vol.12 , Issue.1
    • Baya, A.1    Granitto, P.2
  • 5
    • 67949110882 scopus 로고    scopus 로고
    • Hoboken, NJ, USA: Wiley
    • R. Xu and D. Wunsch, Clustering, vol. 10. Hoboken, NJ, USA: Wiley, 2008.
    • (2008) Clustering , vol.10
    • Xu, R.1    Wunsch, D.2
  • 6
    • 77957007197 scopus 로고    scopus 로고
    • OmeSOM: A software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants
    • D. Milone, et al., "omeSOM: A software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants, " BMC Bioinf., vol. 11, no. 1, 2010, Art. no. 438.
    • (2010) BMC Bioinf. , vol.11 , Issue.1
    • Milone, D.1
  • 7
    • 84890460044 scopus 로고    scopus 로고
    • Pattern recognition in bioinformatics
    • D. de Ridder and M. Reinders, "Pattern recognition in bioinformatics, " Briefings Bioinf., vol. 14, no. 5, pp. 633-647, 2013.
    • (2013) Briefings Bioinf. , vol.14 , Issue.5 , pp. 633-647
    • De Ridder, D.1    Reinders, M.2
  • 8
    • 84859199364 scopus 로고    scopus 로고
    • A biologically inspired validity measure for comparison of clustering methods over metabolic data sets
    • May/June
    • G. Stegmayer, D. Milone, L. Kamenetzky, M. Lopez, F. Carrari, "A biologically inspired validity measure for comparison of clustering methods over metabolic data sets, " IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 9, no. 3, pp. 706-716, May/June 2012.
    • (2012) IEEE/ACM Trans. Comput. Biol. Bioinf. , vol.9 , Issue.3 , pp. 706-716
    • Stegmayer, G.1    Milone, D.2    Kamenetzky, L.3    Lopez, M.4    Carrari, F.5
  • 9
    • 84882976704 scopus 로고    scopus 로고
    • How many clusters: A validation index for arbitrary-shaped clusters
    • Mar./Apr.
    • A. Baya and P. Granitto, "How many clusters: A validation index for arbitrary-shaped clusters, " IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 10, no. 2, pp. 401-414, Mar./Apr. 2013.
    • (2013) IEEE/ACM Trans. Comput. Biol. Bioinf. , vol.10 , Issue.2 , pp. 401-414
    • Baya, A.1    Granitto, P.2
  • 11
    • 25444476441 scopus 로고    scopus 로고
    • Systematic survey reveals general applicability of " guilt-by-association" within gene coexpression networks
    • C. Wolfe, I. Kohane, A. Butte, "Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks, " BMC Bioinf., vol. 6, no. 1, 2005, Art. no. 227.
    • (2005) BMC Bioinf. , vol.6 , Issue.1
    • Wolfe, C.1    Kohane, I.2    Butte, A.3
  • 12
    • 55949089680 scopus 로고    scopus 로고
    • An introduction to metabolic networks and their structural analysis
    • Oct.-Dec.
    • V. Lacroix, L. Cottret, P. Th-ebault, M.-F. Sagot, "An introduction to metabolic networks and their structural analysis, " IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 5, no. 4, pp. 594-617, Oct.-Dec. 2008.
    • (2008) IEEE/ACM Trans. Comput. Biol. Bioinf. , vol.5 , Issue.4 , pp. 594-617
    • Lacroix, V.1    Cottret, L.2    Thebault, P.3    Sagot, M.-F.4
  • 13
    • 70449115789 scopus 로고    scopus 로고
    • Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
    • B. Usadel, et al., "Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats, " Plant Cell Environment, vol. 32, no. 12, pp. 1633-1651, 2009.
    • (2009) Plant Cell Environment , vol.32 , Issue.12 , pp. 1633-1651
    • Usadel, B.1
  • 15
    • 25144456056 scopus 로고    scopus 로고
    • Computational cluster validation in post-genomic data analysis
    • J. Handl, J. Knowles, D. Kell, "Computational cluster validation in post-genomic data analysis, " Bioinformatics, vol. 21, no. 15, pp. 3201-3212, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.15 , pp. 3201-3212
    • Handl, J.1    Knowles, J.2    Kell, D.3
  • 16
    • 0346801873 scopus 로고    scopus 로고
    • The Gene Ontology (GO) database and informatics resource
    • Jan.
    • G. Consortium, "The Gene Ontology (GO) database and informatics resource, " Nucleic Acids Res., vol. 32, pp. D258-D261, Jan. 2004.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D258-D261
    • Consortium, G.1
  • 17
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the GO: The relationship between sequence and annotation
    • P. Lord, R. Stevens, A. Brass, C. Goble, "Investigating semantic similarity measures across the GO: The relationship between sequence and annotation, " Bioinf., vol. 19, no. 10, pp. 1275-1283, 2003.
    • (2003) Bioinf. , vol.19 , Issue.10 , pp. 1275-1283
    • Lord, P.1    Stevens, R.2    Brass, A.3    Goble, C.4
  • 18
    • 0002016474 scopus 로고    scopus 로고
    • Semantic similarity in a taxonomy: An informationbased measure and its application to problems of ambiguity in natural language
    • P. Resnik, "Semantic similarity in a taxonomy: An informationbased measure and its application to problems of ambiguity in natural language, " J. Artif. Intell. Res., vol. 11, pp. 95-130, 1999.
    • (1999) J. Artif. Intell. Res. , vol.11 , pp. 95-130
    • Resnik, P.1
  • 20
    • 76849109688 scopus 로고    scopus 로고
    • Data-fusion in clustering microarray data: Balancing discovery and interpretability
    • Jan./Feb.
    • R. Kustra and A. Zagdanski, "Data-fusion in clustering microarray data: Balancing discovery and interpretability, " IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 7, no. 1, pp. 50-63, Jan./Feb. 2010.
    • (2010) IEEE/ACM Trans. Comput. Biol. Bioinf. , vol.7 , Issue.1 , pp. 50-63
    • Kustra, R.1    Zagdanski, A.2
  • 21
    • 67649840899 scopus 로고    scopus 로고
    • Seeing the forest for the trees: Using the Gene Ontology to restructure hierarchical clustering
    • Jul.
    • D. Dotan-Cohen, S. Kasif, A. Melkman, "Seeing the forest for the trees: Using the Gene Ontology to restructure hierarchical clustering, " Bioinf., vol. 25, no. 14, pp. 1789-95, Jul. 2009.
    • (2009) Bioinf. , vol.25 , Issue.14 , pp. 1789-1795
    • Dotan-Cohen, D.1    Kasif, S.2    Melkman, A.3
  • 23
    • 84874663959 scopus 로고    scopus 로고
    • A large-scale evaluation of computational protein function prediction
    • P. Radivojac, et al., "A large-scale evaluation of computational protein function prediction, " Nature Methods, vol. 10, no. 3, pp. 221-227, 2013.
    • (2013) Nature Methods , vol.10 , Issue.3 , pp. 221-227
    • Radivojac, P.1
  • 24
    • 45549107329 scopus 로고    scopus 로고
    • Use and misuse of the Gene Ontology annotations
    • S. Rhee, V. Wood, K. Dolinski, S. Draghici, "Use and misuse of the Gene Ontology annotations, " Nature Rev. Genetics, vol. 9, no. 7, pp. 509-515, 2008.
    • (2008) Nature Rev. Genetics , vol.9 , Issue.7 , pp. 509-515
    • Rhee, S.1    Wood, V.2    Dolinski, K.3    Draghici, S.4
  • 25
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Jan.
    • D. Huang, B. Sherman, R. Lempicki, "Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists, " Nucleic Acids Res., vol. 37, no. 1, pp. 1-13, Jan. 2009.
    • (2009) Nucleic Acids Res. , vol.37 , Issue.1 , pp. 1-13
    • Huang, D.1    Sherman, B.2    Lempicki, R.3
  • 26
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • M. Eisen, P. Spellman, P. Brown, D. Botstein, "Cluster analysis and display of genome-wide expression patterns, " in Proc. Nat. Academy Sci. USA, vol. 95, no. 25, pp. 14863-14868, 1998.
    • (1998) Proc. Nat. Academy Sci. USA , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.1    Spellman, P.2    Brown, P.3    Botstein, D.4
  • 27
    • 71549114836 scopus 로고    scopus 로고
    • A problem with the correlation coefficient as a measure of gene expression divergence
    • Dec.
    • V. Pereira, D. Waxman, A. Eyre-Walker, "A problem with the correlation coefficient as a measure of gene expression divergence, " Genetics, vol. 183, no. 4, pp. 1597-1600, Dec. 2009.
    • (2009) Genetics , vol.183 , Issue.4 , pp. 1597-1600
    • Pereira, V.1    Waxman, D.2    Eyre-Walker, A.3
  • 28
    • 0036798238 scopus 로고    scopus 로고
    • Judging the quality of gene expressionbased clustering methods using gene annotation
    • F. Gibbons and F. Roth, "Judging the quality of gene expressionbased clustering methods using gene annotation, " Genome Res., vol. 12, no. 10, pp. 1574-1581, 2002.
    • (2002) Genome Res. , vol.12 , Issue.10 , pp. 1574-1581
    • Gibbons, F.1    Roth, F.2
  • 29
    • 84874253819 scopus 로고    scopus 로고
    • Gene Ontology annotations and resources
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium, "Gene Ontology annotations and resources, " Nucleic Acids Res., vol. 41, pp. D530-D535, 2013.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D530-D535
  • 30
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on Gene Ontology
    • Jan.
    • A. Schlicker, F. Domingues, J. Rahnenfuhrer, T. Lengauer, "A new measure for functional similarity of gene products based on Gene Ontology, " BMC Bioinf., vol. 7, Jan. 2006, Art. no. 302.
    • (2006) BMC Bioinf. , vol.7
    • Schlicker, A.1    Domingues, F.2    Rahnenfuhrer, J.3    Lengauer, T.4
  • 31
    • 85041916211 scopus 로고    scopus 로고
    • A novel clustering approach for biological data using a new distance based on Gene Ontology
    • G. Leale, D. Milone, A. Baya, P. Granitto, G. Stegmayer, "A novel clustering approach for biological data using a new distance based on Gene Ontology, " in Proc. Arg. Symp. Artif. Intell., 2013, pp. 85-96.
    • (2013) Proc. Arg. Symp. Artif. Intell. , pp. 85-96
    • Leale, G.1    Milone, D.2    Baya, A.3    Granitto, P.4    Stegmayer, G.5
  • 33
    • 84861793773 scopus 로고    scopus 로고
    • Gene set enrichment analysis: Performance evaluation and usage guidelines
    • May
    • J. Hung, T. Yang, Z. Hu, Z. Weng, C. DeLisi, "Gene set enrichment analysis: Performance evaluation and usage guidelines, " Briefings Bioinf., vol. 13, no. 3, pp. 281-91, May 2012.
    • (2012) Briefings Bioinf. , vol.13 , Issue.3 , pp. 281-291
    • Hung, J.1    Yang, T.2    Hu, Z.3    Weng, Z.4    DeLisi, C.5
  • 34
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, open problems
    • P. Khatri and S. Draghici, "Ontological analysis of gene expression data: Current tools, limitations, open problems, " Bioinf., vol. 21, no. 18, pp. 3587-3595, 2005.
    • (2005) Bioinf. , vol.21 , Issue.18 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 35
    • 78649592081 scopus 로고    scopus 로고
    • Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in arabidopsis
    • C. Espinoza, et al., "Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in arabidopsis, " PloS One, vol. 5, no. 11, 2010, Art. no. e14101.
    • (2010) PloS One , vol.5 , Issue.11
    • Espinoza, C.1
  • 36
    • 33749428430 scopus 로고    scopus 로고
    • Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
    • S. Datta and S. Datta, "Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes, " BMC Bioinf., vol. 7, no. 1, 2006, Art. no. 397.
    • (2006) BMC Bioinf. , vol.7 , Issue.1
    • Datta, S.1    Datta, S.2
  • 37
    • 84945923591 scopus 로고
    • A method for comparing two hierarchical clusterings
    • E. Fowlkes and C. Mallows, "A method for comparing two hierarchical clusterings, " J. Amer. Statist. Assoc., vol. 78, no. 383, pp. 553-569, 1983.
    • (1983) J. Amer. Statist. Assoc. , vol.78 , Issue.383 , pp. 553-569
    • Fowlkes, E.1    Mallows, C.2
  • 38
    • 0035532141 scopus 로고    scopus 로고
    • Estimating the number of clusters in a data set via the gap statistic
    • R. Tibshirani, G. Walther, T. Hastie, "Estimating the number of clusters in a data set via the gap statistic, " J. Roy. Stat. Soc. Series B, vol. 63, no. 2, pp. 411-423, 2001.
    • (2001) J. Roy. Stat. Soc. Series B , vol.63 , Issue.2 , pp. 411-423
    • Tibshirani, R.1    Walther, G.2    Hastie, T.3
  • 39
    • 33847663266 scopus 로고    scopus 로고
    • Co-clustering and visualization of gene expression data and Gene Ontology terms for saccharomyces cerevisiae using self-organizing maps
    • M. Brameier and C. Wiuf, "Co-clustering and visualization of gene expression data and Gene Ontology terms for saccharomyces cerevisiae using self-organizing maps, " J. Biomed. Informat., vol. 40, no. 2, pp. 160-173, 2007.
    • (2007) J. Biomed. Informat. , vol.40 , Issue.2 , pp. 160-173
    • Brameier, M.1    Wiuf, C.2
  • 40
    • 79959923522 scopus 로고    scopus 로고
    • G: Profiler-a Web server for functional interpretation of gene lists (2011 update)
    • J. Reimand, T. Arak, J. Vilo, "G: Profiler-a Web server for functional interpretation of gene lists (2011 update), " Nucleic Acids Res., vol. 39, no. suppl 2, pp. W307-W315, 2011.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W307-W315
    • Reimand, J.1    Arak, T.2    Vilo, J.3
  • 41
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • A. Subramanian, et al., "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, " in Proc. Nat. Academy Sci. USA, vol. 102, no. 43, pp. 15545-15550, 2005.
    • (2005) In Proc. Nat. Academy Sci. USA , vol.102 , Issue.43 , pp. 15545-15550
    • Subramanian, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.