Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation

Journal of Biomedicine and Biotechnology

Volumn 2010, Issue , 2010, Pages

  Garbe, John R ^a   Elsik, Christine G ^b,c   Antoniou, Eric ^d   Reecy, James M ^e   Clark, Karl J ^a   Venkatraman, Anand ^c   Kim, Jae Woo ^d   Schnabel, Robert D ^d   Michael Dickens, C ^c   Wolfinger, Russell D ^f   Fahrenkrug, Scott C ^a   Taylor, Jeremy F ^d  

^a UNIVERSITY OF MINNESOTA   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

^d UNIVERSITY OF MISSOURI   (United States)

^e IOWA STATE UNIVERSITY   (United States)

^f SAS INSTITUTE INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; MESSENGER RNA;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; COW; DNA MICROARRAY; FEMALE; GENE SEQUENCE; GENE TARGETING; GENETIC TRANSCRIPTION; MULTIGENE FAMILY; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYLOGENOMICS; SENSITIVITY AND SPECIFICITY; SWINE; ANIMAL; ANTIBODY SPECIFICITY; BIOLOGY; CATTLE; CHEMISTRY; CLUSTER ANALYSIS; EXPRESSED SEQUENCE TAG; GENE; GENE EXPRESSION PROFILING; GENOME; HUMAN; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; SIGNAL PROCESSING; SIGNAL TRANSDUCTION;

BOVINAE; SUIDAE; SUS; VERTEBRATA;

ANIMALS; CATTLE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENES; GENOME; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; ORGAN SPECIFICITY; PRINCIPAL COMPONENT ANALYSIS; RNA, MESSENGER; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING, COMPUTER-ASSISTED; SIGNAL TRANSDUCTION; SWINE;

EID: 79251562825     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2010/453638     Document Type: Article

References (35)

1. Kumar S., Hedges S. B., A molecular timescale for vertebrate evolution Nature 1998 392 6679 917 920
2. Suchyta S. P., Sipkovsky S., Kruska R., Jeffers A., McNulty A., Coussens M. J., Tempelman R. J., Halgren R. G., Saama P. M., Bauman D. E., Boisclair Y. R., Burton J. L., Collier R. J., DePeters E. J., Ferris T. A., Lucy M. C., McGuire M. A., Medrano J. F., Overton T. R., Smith T. P., Smith G. W., Sonstegard T. S., Spain J. N., Spiers D. E., Yao J., Coussens P. M., Development and testing of a high-density cDNA microarray resource for cattle Physiological Genomics 2004 15 2 158 164
3. Zhao S. H., Recknor J., Lunney J. K., Nettleton D., Kuhar D., Orley S., Tuggle C. K., Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig Genomics 2005 86 5 618 625
4. Li X., He Z., Zhou J., Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation Nucleic Acids Research 2005 33 19 6114 6123
5. Liu Y., Qin X., Song X. Z. H., Jiang H., Shen Y., Durbin K. J., Lien S., Kent M. P., Sodeland M., Ren Y., Zhang L., Sodergren E., Havlak P., Worley K. C., Weinstock G. M., Gibbs R. A., Bos taurus genome assembly BMC Genomics 2009 10, article 180
6. Steibel J. P., Wysocki M., Lunney J. K., Ramos A. M., Hu Z. L., Rothschild M. F., Ernst C. W., Assessment of the swine protein-annotated oligonucleotide microarray Animal Genetics 2009 40 6 883 893
7. Boguski M. S., Lowe T. M. J., Tolstoshev C. M., dbESTdatabase for 'expressed sequence tags' Nature Genetics 1993 4 4 332 333
8. Morgulis A., Gertz E. M., Schffer A. A., Agarwala R., A fast and symmetric DUST implementation to mask low-complexity DNA sequences Journal of Computational Biology 2006 13 5 1028 1040
9. Jurka J., Kapitonov V. V., Pavlicek A., Klonowski P., Kohany O., Walichiewicz J., Repbase Update, a database of eukaryotic repetitive elements Cytogenetic and Genome Research 2005 110 14 462 467
10. Hubbard T., Andrews D., Caccamo M., Cameron G., Chen Y., Clamp M., Clarke L., Coates G., Cox T., Cunningham F., Curwen V., Cutts T., Down T., Durbin R., Fernandez-Suarez X. M., Gilbert J., Hammond M., Herrero J., Hotz H., Howe K., Iyer V., Jekosch K., Kahari A., Kasprzyk A., Keefe D., Keenan S., Kokocinsci F., London D., Longden I., McVicker G., Melsopp C., Meidl P., Potter S., Proctor G., Rae M., Rios D., Schuster M., Searle S., Severin J., Slater G., Smedley D., Smith J., Spooner W., Stabenau A., Stalker J., Storey R., Trevanion S., Ureta-Vidal A., Vogel J., White S., Woodwark C., Birney E., Ensembl 2005 Nucleic Acids Research 2005 33 supplement 1 D447 D453
11. Wootton J. C., Federhen S., Analysis of compositionally biased regions in sequence databases Methods in Enzymology 1996 266 554 571
12. Pearson W. R., Lipman D. J., Improved tools for biological sequence comparison Proceedings of the National Academy of Sciences of the United States of America 1988 85 8 2444 2448
13. Pearson W. R., Wood T., Zhang Z., Miller W., Comparison of DNA sequences with protein sequences Genomics 1997 46 1 24 36
14. Pertea G., Huang X., Liang F., Antonescu V., Sultana R., Karamycheva S., Lee Y., White J., Cheung F., Parvizi B., Tsai J., Quackenbush J., TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets Bioinformatics 2003 19 5 651 652
15. Zhang Z., Schwartz S., Wagner L., Miller W., A greedy algorithm for aligning DNA sequences Journal of Computational Biology 2000 7 1-2 203 214
16. Huang X., Madan A., CAP3: a DNA sequence assembly program Genome Research 1999 9 9 868 877
17. Venktatraman A., Validation of a novel EST clustering method and development of a phylogenetic annotation pipeline for livestock gene families, Ph.D. dissertation 2008 College Station, Tex, USA Texas AM University
18. Slater G. S. C., Birney E., Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 2005 6 1, article 31
19. Katoh K., Misawa K., Kuma K. I., Miyata T., MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Research 2002 30 14 3059 3066
20. Felsenstein J., PHYLIP (Phylogeny Inference Package) Version 3.6. Distributed by the Author 2005 Seattle, Wash, USA Department of Genome Sciences, University of Washington
21. Fitch W. M., Margoliash E., Construction of phylogenetic trees Science 1967 155 760 279 284
22. Zmasek C. M., Eddy S. R., RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs BMC Bioinformatics 2002 3 1, article 14
23. Kapustin Y., Souvorov A., Tatusova T., Lipman D., Splign: algorithms for computing spliced alignments with identification of paralogs Biology Direct 2008 3, article 20
24. Finn R. D., Mistry J., Tate J., Coggill P., Heger A., Pollington J. E., Gavin O. L., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer E. L. L., Eddy S. R., Bateman A., The Pfam protein families database Nucleic Acids Research 2010 38 1 D211 D222
25. Ashburner M., Ball C. A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P., Dolinski K., Dwight S. S., Eppig J. T., Harris M. A., Hill D. P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J. C., Richardson J. E., Ringwald M., Rubin G. M., Sherlock G., Gene ontology: tool for the unification of biology Nature Genetics 2000 25 1 25 29
26. Zimin A. V., Delcher A. L., Florea L., Kelley D. R., Schatz M. C., Puiu D., Hanrahan F., Pertea G., Van Tassell C. P., Sonstegard T. S., Marais G., Roberts M., Subramanian P., Yorke J. A., Salzberg S. L., A whole-genome assembly of the domestic cow, Bos taurus Genome Biology 2009 10 4, article R42
27. Wu T. D., Watanabe C. K., GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21 9 1859 1875
28. Galbraith D. W., Elumalai R., Gong F. C., Integrative flow cytometric and microarray approaches for use in transcriptional profiling Flow Cytometry Protocols 2004 263 Totowa, NJ, USA Humana Press 259 279
29. Smyth G. K., Yang Y. H., Speed T., Statistical issues in cDNA microarray data analysis Methods in Molecular Biology 2003 224 4 111 136
30. r. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2005, http://www.r-project.org/
31. Kasprzk A., Keefe D., Smedley D., London D., Spooner W., Melsopp C., Hammond M., Rocca-Serra P., Cox T., Birney E., EnsMart: a generic system for fast and flexible access to biological data Genome Research 2004 14 1 160 169
32. Lee M., Xiang C. C., Trent J. M., Bittner M. L., Performance characteristics of 65-mer oligonucleotide microarrays Analytical Biochemistry 2007 368 1 70 78
33. Nielsen H. B., Wernersson R., Knudsen S., Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays Nucleic Acids Research 2003 31 13 3491 3496
34. Jongeneel C. V., Delorenzi M., Iseli C., Zhou D., Haudenschild C. D., Khrebtukova I., Kuznetsov D., Stevenson B. J., Strausberg R. L., Simpson A. J. G., Vasicek T. J., An atlas of human gene expression from massively parallel signature sequencing (MPSS) Genome Research 2005 15 7 1007 1014
35. Hsiao L. L., Dangond F., Yoshida T., Hong R., Jensen R. V., Misra J., Dillon W., Lee K. F., Clark K. E., Haverty P., Weng Z., Mutter G. L., Frosch M. P., Macdonald M. E., Milford E. L., Crum C. P., Bueno R., Pratt R. E., Mahadevappa M., Warrington J. A., Stephanopoulos G., Stephanopoulos G., Gullans S. R., A compendium of gene expression in normal human tissues Physiol Genomics 2001 7 2 97 104