Estimating the efficiency of fish cross-species cDNA microarray hybridization

Marine Biotechnology

Volumn 9, Issue 4, 2007, Pages 491-499

  Cohen, Raphael ^a   Chalifa Caspi, Vered ^a   Williams, Timothy D ^c   Auslander, Meirav ^b,e   George, Stephen G ^d   Chipman, James K ^c   Tom, Moshe ^b  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b ISRAEL OCEANOGRAPHIC AND LIMNOLOGICAL RESEARCH   (Israel)

^c UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^d UNIVERSITY OF STIRLING   (United Kingdom)

^e TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

Bony fish; cDNA hybridization; Cross species; Microarray; Transcriptome sequence comparisons

Indexed keywords

BONY FISH; CDNA HYBRIDIZATION; CROSS-SPECIES; TRANSCRIPTOME SEQUENCE COMPARISONS;

BIOINFORMATICS; DNA SEQUENCES; GENE EXPRESSION; MICROARRAYS; THERMODYNAMICS;

FISH;

ARRAY; DNA; ESTIMATION METHOD; GENE EXPRESSION; HYBRIDIZATION; TAXONOMY; TELEOST;

ANIMAL; ANIMAL DISEASE; ARTICLE; DNA MICROARRAY; FISH; GENE EXPRESSION PROFILING; GENETICS; MALE; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PRODUCTIVITY; SPECIES DIFFERENCE; STANDARD;

ANIMALS; CONSERVED SEQUENCE; EFFICIENCY; FISHES; GENE EXPRESSION PROFILING; MALE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECIES SPECIFICITY;

OSTEICHTHYES;

EID: 34848859844     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-007-9010-8     Document Type: Article

References (17)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402
2. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc Ser B 57, 289-300
3. Chapman RW (2001) Ecogenomics: a consilience for comparative immunology. Dev Comp Immunol 25, 549-551
4. Chen Y, Chou C-C, Lu X, Slate E, Peck K, Xu W, Voit E, Almeida J (2006) A multivariate prediction model for microarray cross-hybridization. BMC Bioinformat 7, 101
5. Enard W, Khaitovich P, Klose J, Zöllner S, Heissig F, Giavalisco P, Nieselt-Struwe K, Muchmore E, Varki A, Ravid R, Doxiadis GM, Bontrop RE, Pääbo S (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296, 340-343
6. Flikka K, Yadetie F, Laegreid A, Jonassen I (2004) XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformat 5, 117
7. Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S, eds (2005) Statistics for Biology and Health: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. (New York: Springer) pp 473
8. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC (2005) Whole-genome prokaryotic phylogeny. Bioinformatics 21, 2329-2335
9. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Gen Res 9, 868-877
10. Renn SCP, Aubin-Horth N, Hofmann HA (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genom 5, 42
11. Sambrook J, Russell DW (2001) Molecular Cloning, A Laboratory Manual. 3rd ed (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press)
12. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol http://www.bepress.com/sagmb/vol3/iss1/art3
13. Smyth GK (2005) "Limma: linear models for microarray data". In: Gentleman R, et al. (eds), Statistics for Biology and Health. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. (New York: Springer) pp 397-420
14. Snape JR, Maund SJ, Pickford DB, Hutchinson TH (2004) Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. Aquat Toxicol 67, 143-154
15. von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs AR, Nelson, CC, Davidson WS, Koop BF (2005) Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genom 6, 126
16. Williams TD, Diab AM, George SG, Godfrey RE, Sabine V, Conesa A, Minchin SD, Watts PC, Chipman JK. (2006) Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose. Environ Sci Technol 40, 6479-6488
17. Wren J, Kulkarni A, Joslin J, Butow R, Garner H. (2002) Cross-hybridization on PCR-spotted microarrays. IEEE Eng Med Biol Mag 21, 71-75