Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Toleno, Donna M ^a   Renaud, Gabriel ^b   Wolfsberg, Tyra G ^b   Islam, Munirul ^c   Wildman, Derek E ^c   Siegmund, Kimberly D ^d   Hacia, Joseph G ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPRESSION ANALYSIS; EXPRESSION VARIATIONS; GENE EXPRESSION ANALYSIS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE MICROARRAY; OLIGONUCLEOTIDE PROBES; SENSITIVITY AND SPECIFICITY; TRANSCRIPTOME ANALYSIS;

GENE EXPRESSION; HISTOLOGY; MICROARRAYS; OLIGONUCLEOTIDES; TISSUE;

PROBES;

ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; CHIMPANZEE; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC VARIABILITY; GENOME ANALYSIS; HEART; HUMAN; HUMAN TISSUE; HYBRIDIZATION; KIDNEY PARENCHYMA; LIVER PARENCHYMA; NONHUMAN; OLIGONUCLEOTIDE PROBE; SENSITIVITY AND SPECIFICITY; SPECIES COMPARISON; TESTIS; TRANSCRIPTOMICS; ANIMAL; BIOLOGY; CHEMISTRY; DNA PROBE; EVALUATION; GENETIC DATABASE; GENETICS; GENOME; METHODOLOGY; PAN TROGLODYTES;

PAN;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA PROBES; GENE EXPRESSION PROFILING; GENOME; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PAN TROGLODYTES;

EID: 63349085347     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-77     Document Type: Article

References (60)

1. Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995, 270(5235):467-470 10.1126/science.270.5235.467 7569999
2. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H et al Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996, 14(13):1675-1680 10.1038/nbt1296-1675 9634850
3. Wodicka L Dong H Mittmann M Ho MH Lockhart DJ Genome-wide expression monitoring in Saccharomyces cerevisiae Nat Biotechnol 1997, 15(13):1359-1367 10.1038/nbt1297-1359 9415887
4. White KP Rifkin SA Hurban P Hogness DS Microarray analysis of Drosophila development during metamorphosis Science 1999, 286(5447):2179-2184 10.1126/science.286.5447.2179 10591654
5. Hill AA Hunter CP Tsung BT Tucker-Kellogg G Brown EL Genomic analysis of gene expression in C. elegans Science 2000, 290(5492):809-812 10.1126/ science.290.5492.809 11052945
6. Schena M Shalon D Heller R Chai A Brown PO Davis RW Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes Proc Natl Acad Sci USA 1996, 93(20):10614-10619 38202 8855227 10.1073/ pnas.93.20.10614
7. Bar-Or C Czosnek H Koltai H Cross-species microarray hybridizations: A developing tool for studying species diversity Trends Genet 2007, 23(4):200-207 10.1016/j.tig.2007.02.003 17313995
8. Karaman MW Houck ML Chemnick LG Nagpal S Chawannakul D Sudano D Pike BL Ho VV Ryder OA Hacia JG Comparative analysis of gene-expression patterns in human and african great ape cultured fibroblasts Genome Res 2003, 13(7):1619-1630 403735 12840040 10.1101/gr.1289803
9. Enard W Khaitovich P Klose J Zollner S Heissig F Giavalisco P Nieselt-Struwe K Muchmore E Varki A Ravid R et al Intra- and interspecific variation in primate gene expression patterns Science 2002, 296(5566):340-343 10.1126/science.1068996 11951044
10. Caceres M Lachuer J Zapala MA Redmond JC Kudo L Geschwind DH Lockhart DJ Preuss TM Barlow C Elevated gene expression levels distinguish human from non-human primate brains Proc Natl Acad Sci USA 2003, 100(22):13030-13035 240739 14557539 10.1073/pnas.2135499100
11. Uddin M Wildman DE Liu G Xu W Johnson RM Hof PR Kapatos G Grossman LI Goodman M Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles Proc Natl Acad Sci USA 2004, 101(9):2957-2962 365727 14976249 10.1073/ pnas.0308725100
12. Khaitovich P Muetzel B She X Lachmann M Hellmann I Dietzsch J Steigele S Do HH Weiss G Enard W et al Regional patterns of gene expression in human and chimpanzee brains Genome Res 2004, 14(8):1462-1473 509255 15289471 10.1101/gr.2538704
13. Khaitovich P Hellmann I Enard W Nowick K Leinweber M Franz H Weiss G Lachmann M Paabo S Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees Science 2005, 309(5742):1850-1854 10.1126/science.1108296 16141373
14. Calarco JA Xing Y Caceres M Calarco JP Xiao X Pan Q Lee C Preuss TM Blencowe BJ Global analysis of alternative splicing differences between humans and chimpanzees Genes Dev 2007, 21(22):2963-2975 2049197 17978102 10.1101/gad.1606907
15. Hacia JG Fan JB Ryder O Jin L Edgemon K Ghandour G Mayer RA Sun B Hsie L Robbins CM et al Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays Nat Genet 1999, 22(2):164-167 10.1038/9674 10369258
16. Hacia JG Makalowski W Edgemon K Erdos MR Robbins CM Fodor SP Brody LC Collins FS Evolutionary sequence comparisons using high-density oligonucleotide arrays Nat Genet 1998, 18(2):155-158 10.1038/ng0298-155 9462745
17. Blekhman R Oshlack A Chabot AE Smyth GK Gilad Y Gene regulation in primates evolves under tissue-specific selection pressures PLoS Genet 2008, 4(11):e1000271 2581600 19023414 10.1371/journal.pgen.1000271
18. Gilad Y Rifkin SA Bertone P Gerstein M White KP Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles Genome Res 2005, 15(5):674-680 1088295 15867429 10.1101/ gr.3335705
19. Oshlack A Chabot AE Smyth GK Gilad Y Using DNA microarrays to study gene expression in closely related species Bioinformatics 2007, 23(10):1235-1242 10.1093/bioinformatics/btm111 17384014
20. Kurtz S Phillippy A Delcher AL Smoot M Shumway M Antonescu C Salzberg SL Versatile and open software for comparing large genomes Genome Biol 2004, 5(2):R12 395750 14759262 10.1186/gb-2004-5-2-r12
21. Doring A Weese D Rausch T Reinert K SeqAn an efficient, generic C++ library for sequence analysis BMC Bioinformatics 2008, 9:11 2246154-18184432 10.1186/1471-2105-9-11
22. Liu H Zeeberg BR Qu G Koru AG Ferrucci A Kahn A Ryan MC Nuhanovic A Munson PJ Reinhold WC et al AffyProbeMiner: A web resource for computing or retrieving accurately redefined Affymetrix probe sets Bioinformatics 2007, 23(18):2385-2390 10.1093/bioinformatics/btm360 17660211
23. Carter SL Eklund AC Mecham BH Kohane IS Szallasi Z Redefinition of affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements Bmc Bioinformatics 2005:6 1127107 15850491
24. Dai M Wang P Boyd AD Kostov G Athey B Jones EG Bunney WE Myers RM Speed TP Akil H et al Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Nucleic Acids Res 2005, 33(20):e175 1283542 16284200 10.1093/nar/gni179
25. Gautier L Moller M Friis-Hansen L Knudsen S Alternative mapping of probes to genes for Affymetrix chips BMC Bioinformatics 2004, 5:111 514699 15310390 10.1186/1471-2105-5-111
26. Kong SW Hwang KB Kim RD Zhang BT Greenberg SA Kohane IS Park PJ CrossChip: A system supporting comparative analysis of different generations of Affymetrix arrays Bioinformatics 2005, 21(9):2116-2117 10.1093/bioinformatics/bti288 15684227
27. Sandberg R Larsson O Improved precision and accuracy for microarrays using updated probe set definitions BMC Bioinformatics 2007, 8:48 1805763 17288599 10.1186/1471-2105-8-48
28. Lu J Lee JC Salit ML Cam MC Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays BMC Bioinformatics 2007, 8:108 1853115 17394657 10.1186/ 1471-2105-8-108
29. Elo LL Lahti L Skottman H Kylaniemi M Lahesmaa R Aittokallio T Integrating probe-level expression changes across generations of Affymetrix arrays Nucleic Acids Res 2005, 33(22):e193 1316121 16356924 10.1093/nar/gni193
30. Mecham BH Wetmore DZ Szallasi Z Sadovsky Y Kohane I Mariani TJ Increased measurement accuracy for sequence-verified microarray probes Physiol Genomics 2004, 18(3):308-315 10.1152/physiolgenomics.00066.2004 15161964
31. Oldham MC Horvath S Geschwind DH Conservation and evolution of gene coexpression networks in human and chimpanzee brains Proc Natl Acad Sci USA 2006, 103(47):17973-17978 1693857 17101986 10.1073/pnas.0605938103
32. Nagpal S Karaman MW Timmerman MM Ho VV Pike BL Hacia JG Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks Nucleic Acids Res 2004, 32(5):e51 390348 15031318 10.1093/nar/gnh048
33. Robinson MD Speed TP A comparison of Affymetrix gene expression arrays BMC Bioinformatics 2007, 8:449 2216046 18005448 10.1186/1471-2105-8-449
34. Okoniewski MJ Hey Y Pepper SD Miller CJ High correspondence between Affymetrix exon and standard expression arrays Biotechniques 2007, 42(2):181-185 10.2144/000112315 17373482
35. Irizarry RA Bolstad BM Collin F Cope LM Hobbs B Speed TP Summaries of Affymetrix GeneChip probe level data Nucleic Acids Res 2003, 31(4):e15 150247 12582260 10.1093/nar/gng015
36. Gibbs RA Rogers J Katze MG Bumgarner R Weinstock GM Mardis ER Remington KA Strausberg RL Venter JC Wilson RK et al Evolutionary and biomedical insights from the rhesus macaque genome Science 2007, 316(5822):222-234 10.1126/science.1139247 17431167
37. Wang HY Chien HC Osada N Hashimoto K Sugano S Gojobori T Chou CK Tsai SF Wu CI Shen CK Rate of evolution in brain-expressed genes in humans and other primates PLoS Biol 2007, 5(2):e13 1717015 17194215 10.1371/ journal.pbio.0050013
38. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 2003, 4(2):249-264 10.1093/biostatistics/4.2.249 12925520
39. Choe SE Boutros M Michelson AM Church GM Halfon MS Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset Genome Biol 2005, 6(2):R16 551536 15693945 10.1186/ gb-2005-6-2-r16
40. Xia X McClelland M Wang Y WebArray: An online platform for microarray data analysis BMC Bioinformatics 2005, 6:306 1327694 16371165 10.1186/ 1471-2105-6-306
41. Smyth G Limma: Linear models for microarray data Bioinformatics and Computational Biology Solutions using R and Bioconductor New York: Springer Gentleman RVC, Dudoit S, Irizarry R, Huber W 2005
42. Benovoy D Kwan T Majewski J Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments Nucleic Acids Res 2008, 36(13):4417-4423 2490733 18596082 10.1093/nar/gkn409
43. Kumari S Verma LK Weller JW AffyMAPSDetector: A software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs BMC Bioinformatics 2007, 8:276 1959249 17663786 10.1186/1471-2105-8-276
44. Ferrari F Bortoluzzi S Coppe A Sirota A Safran M Shmoish M Ferrari S Lancet D Danieli GA Bicciato S Novel definition files for human GeneChips based on GeneAnnot BMC Bioinformatics 2007, 8:446 2216044 18005434 10.1186/1471-2105-8-446
45. Lee JC Stiles D Lu J Cam MC A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences BMC Genomics 2007, 8:284 2000902 17708771 10.1186/1471-2164-8-284
46. Chalifa-Caspi V Yanai I Ophir R Rosen N Shmoish M Benjamin-Rodrig H Shklar M Stein TI Shmueli O Safran M et al GeneAnnot: Comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes Bioinformatics 2004, 20(9):1457-1458 10.1093/bioinformatics/bth081 14962929
47. Hwang KB Kong SW Greenberg SA Park PJ Combining gene expression data from different generations of oligonucleotide arrays BMC Bioinformatics 2004, 5:159 528726 15504239 10.1186/1471-2105-5-159
48. Alberts R Terpstra P Hardonk M Bystrykh LV de Haan G Breitling R Nap JP Jansen RC A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat BMC Bioinformatics 2007, 8:132 1865557 17448222 10.1186/ 1471-2105-8-132
49. Cooper GM Nickerson DA Eichler EE Mutational and selective effects on copy-number variants in the human genome Nat Genet 2007, 39(7 Suppl):S22-29 10.1038/ng2054 17597777
50. Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J et al Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004, 5(10):R80 545600 15461798 10.1186/gb-2004-5-10-r80
51. Bolstad BM Irizarry RA Astrand M Speed TP A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 2003, 19(2):185-193 10.1093/bioinformatics/ 19.2.185 12538238
52. Liu G Loraine AE Shigeta R Cline M Cheng J Valmeekam V Sun S Kulp D Siani-Rose MA NetAffx: Affymetrix probesets and annotations Nucleic Acids Res 2003, 31(1):82-86 165568 12519953 10.1093/nar/gkg121
53. Dai M Wang P Jakupovic E Watson SJ Meng F Web-based GeneChip analysis system for large-scale collaborative projects Bioinformatics 2007, 23(16):2185-2187 10.1093/bioinformatics/btm297 17586830
54. Gautier L Cope L Bolstad BM Irizarry RA affy - analysis of Affymetrix GeneChip data at the probe level Bioinformatics 2004, 20(3):307-315 10.1093/bioinformatics/btg405 14960456
55. Consortium TCSaA Initial sequence of the chimpanzee genome and comparison with the human genome Nature 2005, 437(7055):69-87 10.1038/ nature04072 16136131
56. Benjamini Y Hochberg Y Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing Journal of the Royal Statistical Society Series B-Methodological 1995, 57(1):289-300
57. Smyth GK Linear models and empirical bayes methods for assessing differential expression in microarray experiments Stat Appl Genet Mol Biol 2004:3 Article3 16646809
58. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997, 13(5):555-556 9367129
59. Liu G Uddin M Islam M Goodman M Grossman LI Romero R Wildman DE OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences Source Code Biol Med 2007, 2:5 2093931 17877817 10.1186/1751-0473-2-5
60. Uddin M Goodman M Erez O Romero R Liu G Islam M Opazo JC Sherwood CC Grossman LI Wildman DE Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution Proc Natl Acad Sci USA 2008, 105(9):3215-3220 2265188 18305157 10.1073/pnas.0712400105