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Volumn 6, Issue 1, 2014, Pages

InCHlib - Interactive cluster heatmap for web applications

Author keywords

Big data; Client side scripting; Cluster heatmap; Data clustering; Exploration; JavaScript library; Scientific visualization; Web integration

Indexed keywords


EID: 84908211443     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-014-0044-4     Document Type: Article
Times cited : (51)

References (65)
  • 1
    • 16444383160 scopus 로고    scopus 로고
    • Survey of clustering algorithms
    • Xu R, Wunsch D 2nd: Survey of clustering algorithms. IEEE Trans Neural Netw 2005, 16(3):645-678.
    • (2005) IEEE Trans Neural Netw , vol.16 , Issue.3 , pp. 645-678
    • Xu, R.1    Wunsch 2nd, D.2
  • 3
    • 33645265985 scopus 로고    scopus 로고
    • Clustering methods and their uses in computational chemistry
    • Edited by Lipkowitz KB, Boyd DB. New York: VCH
    • Downs GM, Barnard JM: Clustering methods and their uses in computational chemistry. In Reviews in Computational Chemistry, Volume Volume 18. Edited by Lipkowitz KB, Boyd DB. New York: VCH; 2002:1-40.
    • (2002) Reviews in Computational Chemistry , vol.18 , pp. 1-40
    • Downs, G.M.1    Barnard, J.M.2
  • 4
    • 33751586117 scopus 로고    scopus 로고
    • Using clustering techniques to improve hit selection in high-throughput screening
    • Gagarin A, Makarenkov V, Zentilli P: Using clustering techniques to improve hit selection in high-throughput screening. J Biomol Screen 2006, 11(8):903-914.
    • (2006) J Biomol Screen , vol.11 , Issue.8 , pp. 903-914
    • Gagarin, A.1    Makarenkov, V.2    Zentilli, P.3
  • 6
    • 0032619115 scopus 로고    scopus 로고
    • Application of nearest-neighbor and cluster analyses in pharmaceutical lead discovery
    • Stanton DT, Morris TW, Roychoudhury S, Parker CN: Application of nearest-neighbor and cluster analyses in pharmaceutical lead discovery. J Chem Inf Comput Sci 1999, 39(1):21-27.
    • (1999) J Chem Inf Comput Sci , vol.39 , Issue.1 , pp. 21-27
    • Stanton, D.T.1    Morris, T.W.2    Roychoudhury, S.3    Parker, C.N.4
  • 7
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: A key technique in molecular informatics
    • Bender A, Glen RC: Molecular similarity: a key technique in molecular informatics. Org Biomol Chem 2004, 2(22):3204-3218.
    • (2004) Org Biomol Chem , vol.2 , Issue.22 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 8
    • 14644431061 scopus 로고    scopus 로고
    • Managing molecular diversity
    • Perez JJ: Managing molecular diversity. Chem Soc Rev 2005, 34(2):143-152.
    • (2005) Chem Soc Rev , vol.34 , Issue.2 , pp. 143-152
    • Perez, J.J.1
  • 10
    • 9344242435 scopus 로고    scopus 로고
    • Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections
    • Schuffenhauer A, Popov M, Schopfer U, Acklin P, Stanek J, Jacoby E: Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections. Comb Chem High Throughput Screen 2004, 7(8):771-781.
    • (2004) Comb Chem High Throughput Screen , vol.7 , Issue.8 , pp. 771-781
    • Schuffenhauer, A.1    Popov, M.2    Schopfer, U.3    Acklin, P.4    Stanek, J.5    Jacoby, E.6
  • 12
    • 78650121315 scopus 로고    scopus 로고
    • Clustering algorithms in biomedical research: A review
    • Xu R, Wunsch DC 2nd: Clustering algorithms in biomedical research: a review. IEEE Rev Biomed Eng 2010, 3:120-154.
    • (2010) IEEE Rev Biomed Eng , vol.3 , pp. 120-154
    • Xu, R.1    Wunsch 2nd, D.C.2
  • 14
    • 67449163824 scopus 로고    scopus 로고
    • The history of the cluster heat map
    • Wilkinson L, Friendly M: The history of the cluster heat map. Am Stat 2009, 63(2):179-184.
    • (2009) Am Stat , vol.63 , Issue.2 , pp. 179-184
    • Wilkinson, L.1    Friendly, M.2
  • 16
    • 79951480123 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for statistical computing
    • Team. RDC: R: a language and environment for statistical computing. Vienna, Austria: R Foundation for statistical computing; 2010. http://www.gbif.org/resources/2585.
    • (2010) R: A Language and Environment for Statistical Computing
  • 18
    • 84894581705 scopus 로고    scopus 로고
    • CIMminer. http://discover.nci.nih.gov/cimminer/home.do.
    • CIMminer
  • 20
    • 84908158169 scopus 로고    scopus 로고
    • TreeView. http://rana.lbl.gov/EisenSoftware.htm.
    • TreeView
  • 22
    • 0037336331 scopus 로고    scopus 로고
    • Open source software for the analysis of microarray data
    • Dudoit S, Gentleman RC, Quackenbush J: Open source software for the analysis of microarray data. Biotechniques 2003, 34(Supp):45-51. http://www.biotechniques.com/multimedia/archive/00072/Mar03Dudoit-72037a.pdf.
    • (2003) Biotechniques , vol.34 , pp. 45-51
    • Dudoit, S.1    Gentleman, R.C.2    Quackenbush, J.3
  • 23
    • 9444225935 scopus 로고    scopus 로고
    • Java Treeview-extensible visualization of microarray data
    • Saldanha AJ: Java Treeview-extensible visualization of microarray data. Bioinformatics 2004, 20(17):3246-3248.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3246-3248
    • Saldanha, A.J.1
  • 26
    • 0036169031 scopus 로고    scopus 로고
    • Genesis: Cluster analysis of microarray data
    • Sturn A, Quackenbush J, Trajanoski Z: Genesis: cluster analysis of microarray data. Bioinformatics 2002, 18(1):207-208.
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 207-208
    • Sturn, A.1    Quackenbush, J.2    Trajanoski, Z.3
  • 28
    • 77954519381 scopus 로고    scopus 로고
    • geWorkbench: An open source platform for integrative genomics
    • Floratos A, Smith K, Ji Z, Watkinson J, Califano A: geWorkbench: an open source platform for integrative genomics. Bioinformatics 2010, 26(14):1779-1780.
    • (2010) Bioinformatics , vol.26 , Issue.14 , pp. 1779-1780
    • Floratos, A.1    Smith, K.2    Ji, Z.3    Watkinson, J.4    Califano, A.5
  • 30
    • 84908206663 scopus 로고    scopus 로고
    • GENE-E. http://www.broadinstitute.org/cancer/software/GENE-E/.
    • GENE-E
  • 31
    • 84908176734 scopus 로고    scopus 로고
    • QCanvas: An advanced tool for data clustering and visualization of genomics data
    • Kim N, Park H, He N, Lee HY, Yoon S: QCanvas: an advanced tool for data clustering and visualization of genomics data. Genomics Inform 2012, 10(4):263-265.
    • (2012) Genomics Inform , vol.10 , Issue.4 , pp. 263-265
    • Kim, N.1    Park, H.2    He, N.3    Lee, H.Y.4    Yoon, S.5
  • 32
    • 79955934629 scopus 로고    scopus 로고
    • Gitools: Analysis and visualisation of genomic data using interactive heat-maps
    • Perez-Llamas C, Lopez-Bigas N: Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One 2011, 6(5):e19541.
    • (2011) PLoS One , vol.6 , Issue.5 , pp. e19541
    • Perez-Llamas, C.1    Lopez-Bigas, N.2
  • 38
    • 84900376656 scopus 로고    scopus 로고
    • INVEX-a web-based tool for integrative visualization of expression data
    • Xia J, Lyle NH, Mayer ML, Pena OM, Hancock RE: INVEX-a web-based tool for integrative visualization of expression data. Bioinformatics 2013, 29(24):3232-3234.
    • (2013) Bioinformatics , vol.29 , Issue.24 , pp. 3232-3234
    • Xia, J.1    Lyle, N.H.2    Mayer, M.L.3    Pena, O.M.4    Hancock, R.E.5
  • 39
  • 41
    • 84908194090 scopus 로고    scopus 로고
    • CanvasXpress. http://www.canvasxpress.org/.
  • 42
    • 84908194089 scopus 로고    scopus 로고
    • KineticJS. http://kineticjs.com/.
  • 43
    • 84908194088 scopus 로고    scopus 로고
    • jQuery. http://jquery.com.
  • 44
    • 84908194087 scopus 로고    scopus 로고
    • JSON (JavaScript Object Notation). http://json.org/.
  • 45
    • 84878460994 scopus 로고    scopus 로고
    • Fastcluster: Fast hierarchical, agglomerative clustering routines for r and python
    • Müllner D: Fastcluster: fast hierarchical, agglomerative clustering routines for r and python. J Stat Softw 2013, 53(9):1-18.
    • (2013) J Stat Softw , vol.53 , Issue.9 , pp. 1-18
    • Müllner, D.1
  • 46
    • 0000521616 scopus 로고    scopus 로고
    • Superparamagnetic clustering of data
    • Blatt M, Wiseman S, Domany E: Superparamagnetic clustering of data. Phys Rev Lett 1996, 76(18):3251-3254.
    • (1996) Phys Rev Lett , vol.76 , Issue.18 , pp. 3251-3254
    • Blatt, M.1    Wiseman, S.2    Domany, E.3
  • 49
    • 0030199294 scopus 로고    scopus 로고
    • Nuclear hormone receptors: Ligand-activated regulators of transcription and diverse cell responses
    • Katzenellenbogen JA, Katzenellenbogen BS: Nuclear hormone receptors: ligand-activated regulators of transcription and diverse cell responses. Chem Biol 1996, 3(7):529-536.
    • (1996) Chem Biol , vol.3 , Issue.7 , pp. 529-536
    • Katzenellenbogen, J.A.1    Katzenellenbogen, B.S.2
  • 50
    • 0033253070 scopus 로고    scopus 로고
    • Steroid hormone receptors: Evolution, ligands, and molecular basis of biologic function
    • Whitfield GK, Jurutka PW, Haussler CA, Haussler MR: Steroid hormone receptors: evolution, ligands, and molecular basis of biologic function. J Cell Biochem 1999, 33(Suppl 32):110-122.
    • (1999) J Cell Biochem , vol.33 , pp. 110-122
    • Whitfield, G.K.1    Jurutka, P.W.2    Haussler, C.A.3    Haussler, M.R.4
  • 51
    • 0034485142 scopus 로고    scopus 로고
    • Estrogen receptor alpha in human breast cancer: Occurrence and significance
    • Ali S, Coombes RC: Estrogen receptor alpha in human breast cancer: occurrence and significance. J Mammary Gland Biol Neoplasia 2000, 5(3):271-281.
    • (2000) J Mammary Gland Biol Neoplasia , vol.5 , Issue.3 , pp. 271-281
    • Ali, S.1    Coombes, R.C.2
  • 55
    • 0029894013 scopus 로고    scopus 로고
    • The properties of known drugs. 1. Molecular frameworks
    • Bemis GW, Murcko MA: The properties of known drugs. 1. Molecular frameworks. J Med Chem 1996, 39(15):2887-2893.
    • (1996) J Med Chem , vol.39 , Issue.15 , pp. 2887-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 56
    • 33646242741 scopus 로고    scopus 로고
    • Assessing the scaffold diversity of screening libraries
    • Krier M, Bret G, Rognan D: Assessing the scaffold diversity of screening libraries. J Chem Inf Model 2006, 46(2):512-524.
    • (2006) J Chem Inf Model , vol.46 , Issue.2 , pp. 512-524
    • Krier, M.1    Bret, G.2    Rognan, D.3
  • 57
    • 76049086854 scopus 로고    scopus 로고
    • Scaffold diversity analysis of compound daft sets using an entropy-based measure
    • Medina-Franco JL, Martinez-Mayorga K, Bender A, Scior T: Scaffold diversity analysis of compound daft sets using an entropy-based measure. Qsar Comb Sci 2009, 28(11-12):1551-1560.
    • (2009) Qsar Comb Sci , vol.28 , Issue.11-12 , pp. 1551-1560
    • Medina-Franco, J.L.1    Martinez-Mayorga, K.2    Bender, A.3    Scior, T.4
  • 58
    • 75749154412 scopus 로고    scopus 로고
    • Scaffold distributions in bioactive molecules, clinical trials compounds, and drugs
    • Hu Y, Bajorath J: Scaffold distributions in bioactive molecules, clinical trials compounds, and drugs. ChemMedChem 2010, 5(2):187-190.
    • (2010) ChemMedChem , vol.5 , Issue.2 , pp. 187-190
    • Hu, Y.1    Bajorath, J.2
  • 59
    • 79960743954 scopus 로고    scopus 로고
    • Mining for bioactive scaffolds with scaffold networks: Improved compound set enrichment from primary screening data
    • Varin T, Schuffenhauer A, Ertl P, Renner S: Mining for bioactive scaffolds with scaffold networks: improved compound set enrichment from primary screening data. J Chem Inf Model 2011, 51(7):1528-1538.
    • (2011) J Chem Inf Model , vol.51 , Issue.7 , pp. 1528-1538
    • Varin, T.1    Schuffenhauer, A.2    Ertl, P.3    Renner, S.4
  • 60
    • 52649134945 scopus 로고    scopus 로고
    • Scaffold diversity of natural products: Inspiration for combinatorial library design
    • Grabowski K, Baringhaus KH, Schneider G: Scaffold diversity of natural products: inspiration for combinatorial library design. Nat Prod Rep 2008, 25(5):892-904.
    • (2008) Nat Prod Rep , vol.25 , Issue.5 , pp. 892-904
    • Grabowski, K.1    Baringhaus, K.H.2    Schneider, G.3
  • 61
    • 0035347869 scopus 로고    scopus 로고
    • Scaffold architecture and pharmacophoric properties of natural products and trade drugs: Application in the design of natural product-based combinatorial libraries
    • Lee ML, Schneider G: Scaffold architecture and pharmacophoric properties of natural products and trade drugs: application in the design of natural product-based combinatorial libraries. J Comb Chem 2001, 3(3):284-289.
    • (2001) J Comb Chem , vol.3 , Issue.3 , pp. 284-289
    • Lee, M.L.1    Schneider, G.2
  • 62
    • 77957665087 scopus 로고    scopus 로고
    • Structural and potency relationships between scaffolds of compounds active against human targets
    • Hu Y, Bajorath J: Structural and potency relationships between scaffolds of compounds active against human targets. ChemMedChem 2010, 5(10):1681-1685.
    • (2010) ChemMedChem , vol.5 , Issue.10 , pp. 1681-1685
    • Hu, Y.1    Bajorath, J.2
  • 63
    • 84874420780 scopus 로고    scopus 로고
    • Systematic identification of scaffolds representing compounds active against individual targets and single or multiple target families
    • Hu Y, Bajorath J: Systematic identification of scaffolds representing compounds active against individual targets and single or multiple target families. J Chem Inf Model 2013, 53(2):312-326.
    • (2013) J Chem Inf Model , vol.53 , Issue.2 , pp. 312-326
    • Hu, Y.1    Bajorath, J.2
  • 64
    • 84895557543 scopus 로고    scopus 로고
    • Many drugs contain unique scaffolds with varying structural relationships to scaffolds of currently available bioactive compounds
    • Hu Y, Bajorath J: Many drugs contain unique scaffolds with varying structural relationships to scaffolds of currently available bioactive compounds. Eur J Med Chem 2014, 76:427-434.
    • (2014) Eur J Med Chem , vol.76 , pp. 427-434
    • Hu, Y.1    Bajorath, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.