Nonlinear gene cluster analysis with labeling for microarray gene expression data in organ development

BMC Proceedings

Volumn 5, Issue SUPPL. 2, 2011, Pages

  Ehler, Martin ^a,b   Rajapakse, Vinodh N ^b   Zeeberg, Barry R ^c   Brooks, Brian P ^d   Brown, Jacob ^d   Czaja, Wojciech ^b   Bonner, Robert F ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b University of Maryland   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d NATIONAL EYE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; CONFERENCE PAPER; EMBRYO; EYE DEVELOPMENT; GENE CLUSTER; GENE DOSAGE; GENE EXPRESSION; LASER CAPTURE MICRODISSECTED CELL; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RETINA CELL;

MAMMALIA; VERTEBRATA;

EID: 81355144460     PISSN: None     EISSN: 17536561     Source Type: Journal    
DOI: 10.1186/1753-6561-5-S2-S3     Document Type: Conference Paper

References (23)

1. HTRA1 variant confers similar risks to geographic atrophy and neovascular age-related macular degeneration. Mordantameron DJ, Yang Z, Gibbs D, Chen H, Kaminoh Y, Jorgensen A, Zeng J, Luo L, Brinton E, Brinton G, Bernstein PS JMB, Zabriskie NA, Tang S, Constantine R, Tong Z, Zhang K, Cell Cycle 2007 6 9 1122 1125 10.4161/cc.6.9.4157 17426452 (Pubitemid 46708586)
2. A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration. Yang Z, Camp NJ, Sun H, Tong Z, Gibbs D, Cameron DJ, Chen H, Zhao Y, Pearson E, Li X, Chien J, Dewan A, Harmon J, Bernstein PS, Shridhar V, Zabriskie NA, Hoh J, Howes K, Zhang K, Science 2006 314 5801 992 993 10.1126/science.1133811 17053109 (Pubitemid 44749944)
3. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G, Nat. Genet. 2000 25 25 9 10.1038/75556 10802651 (Pubitemid 30257031)
4. The Gene Ontology project in 2008. Gene Ontology Consortium, Nucleic Acids Res 2008 36 440 4 10.1093/nar/gkm883 17984083 (Pubitemid 351149763)
5. Laser capture microdissection: molecular analysis of tissue. Bonner RF, Emmert-Buck M, Cole K, Pohida T, Chuaqui R, Goldstein S, Liotta LA, Science 1997 21 278 1481 1483 10.1126/science.278.5342.1481 (Pubitemid 27509824)
6. Thermal modeling of laser capture microdissection. Goldstein SR, McQueen OG, Bonner RF, Appl. Opt. 1998 37 31 7378 91 10.1364/AO.37.007378 18301572 (Pubitemid 128659484)
7. Laser capture microdissection: a new tool for the study of spermatogenesis. Surez-Quian CA, Goldstein SR, Bonner RF, J. Androl. 2000 21 5 601 8 10975404
8. Expression profiling during ocular development identifies 2 Nlz genes with a critical role in optic fissure closure. Brown JD, Dutta S, Bharti K, Bonner RF, Munson PJ, Dawid IB, Akhtar AL, Onojafe IF, Alur RP, Gross JM, Hejtmancik JF, Jiao X, Chan W, Brooks BP, Proc. Nat. Acad. Sci. USA 2009 106 5 1462 7 10.1073/pnas.0812017106 19171890
9. GoMiner: a resource for biological interpretation of genomic and proteomic data. Zeeberg B, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN, Genome Biol 2003 4 4 28 10.1186/gb-2003-4-4-r28 12702209
10. High-Throughput GoMiner, an industrial-strength integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). Zeeberg B, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN, BMC Bioinformatics 2005 6 168 10.1186/1471-2105-6-168 15998470 (Pubitemid 41372497)
11. Schroedinger Eigenmaps for the analysis of bio-medical data. Czaja W, Ehler M, submitted to IEEE T. Pattern Anal. 2010
12. WGCNA: an R package for weighted correlation network analysis. Langfelder P, Horvath S, BMC Bioinformatics 2008 9 10.1186/1471-2105-9-559 19114008
13. Laplacian eigenmaps and spectral techniques for embedding and clustering. Belkin M, Niyogi P, NIPS 2002 14
14. Laplacian eigenmaps for dimensionality reduction and data representation. Belkin M, Niyogi P, Neural. Comput. 2003 15 6 1373 1396 10.1162/ 089976603321780317 (Pubitemid 37049796)
15. Least-squares quantization in PCM. Lloyd SP, IEEE Trans. Inform. Theory 1982 28 2 129 137 10.1109/TIT.1982.1056489
16. On lines and planes of closest fit to systems of points in space. Pearson K, Philosophical Magazine 1901 2 7-12 559 572
17. Hastie T, Tibshirani R, Friedman J, The Elements of Statistical Learning Springer 2009
18. Clustering Of Gene Expression Data Based On Shape Similarity. Hestilow T, Huang Y, EURASIP J. Bioinform. Syst. Biol. 2009 19404484
19. An information-intensive approach to the molecular pharmacology of cancer. Weinstein JN, Myers TG, OConnor PM, Friend SH, Fornace JAJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johnson GS, Wittes RE, Paull KD, Science 1997 275 5298 343 9 10.1126/science.275.5298. 343 8994024 (Pubitemid 27051604)
20. Genesis: cluster analysis of microarray data. Sturn A, Quackenbush J, Trajanoski Z, Bioinformatics 2002 18 207 8 10.1093/bioinformatics/18.1.207 11836235 (Pubitemid 34145055)
21. Kaufman L, Rousseeuw P, Finding Groups in Data: An Introduction to Cluster Analysis London: John Wiley and Sons 1990
22. The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina. Hum. Reichman S, Kalathur RKR, Lambard S, At-Ali N, Yang Y, Lardenois A, Ripp R, Poch O, Zack DJ, Sahel J, Léveillard T, Mol. Genet. 2010 19 2 250 61
23. Vsx2/Chx10 ensures the correct timing and magnitude of Hedgehog signaling in the mouse retina. Sigulinsky CL, Green ES, Clark AM, Levine EM, Dev. Biol. 2008 317 2 560 75 10.1016/j.ydbio.2008.02.055 18417110