Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells

BioData Mining

Volumn 7, Issue 1, 2014, Pages

  Laurila, Kirsti ^a   Autio, Reija ^b   Kong, Lingjia ^b,c   Närvä, Elisa ^c   Hussein, Samer ^d,e   Otonkoski, Timo ^e   Lahesmaa, Riitta ^c   Lähdesmäki, Harri ^a,c  

^a AALTO UNIVERSITY   (Finland)

^b TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^c UNIVERSITY OF TURKU   (Finland)

^d MOUNT SINAI HOSPITAL   (Canada)

^e UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Association analysis; CNV; Exon expression; Gene expression; hESC; hiPSC; SNP; Transcript expression

Indexed keywords

TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DOWN REGULATION; EMBRYO; EMBRYONIC STEM CELL; EXON; GENE EXPRESSION; GENE ONTOLOGY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOMICS; HETEROZYGOSITY; HUMAN; HUMAN CELL; INDUCED PLURIPOTENT STEM CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS;

EID: 84989894640     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/s13040-014-0032-2     Document Type: Article

References (53)

1. The International HapMap Consortium: The International HapMap Project. Nature 2003, 426: 789-796.
2. 1000 Genomes, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA: An integrated map of genetic variation from 1, 092 human genomes. Nature 2012, 491: 56-65.
3. Wang L, Luhm R, Lei M: SNP and mutation analysis. Adv Exp Med Biol 2007, 593: 105-116.
4. Hull J, Campino S, Rowlands K, Chan M-S, Copley RR, Taylor MS, Rockett K, Elvidge G, Keating B, Knight J, Kwiatkowski D: Identification of Common Genetic Variation That Modulates Alternative Splicing. PLoS Genet 2007, 3: e99.
5. Coulombe-Huntington J, Lam KCL, Dias C, Majewski J: Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals. PLoS Genet 2009, 5: e1000766.
6. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai S-L, Arepalli S, Dillman A, Rafferty IP, Troncoso J, Johnson R, Zielke HR, Ferrucci L, Longo DL, Cookson MR, Singleton AB: Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain. PLoS Genet 2010, 6: e1000952.
7. Zhang W, Edwards A, Zhu D, Flemington EK, Deininger P, Zhang K: miRNA-mediated relationships between Cis-SNP genotypes and transcript intensities in lymphocyte cell lines. PloS One 2012, 7: e31429.
8. Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brustle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O, Lahesmaa R: High-resolution DNA analysis of human embryonic stem cell lines reveals cultureinduced copy number changes and loss of heterozygosity. Nat Biotech 2010, 28: 371-377.
9. Järvinen A-K, Autio R, Haapa-Paananen S, Wolf M, Saarela M, Grénman R, Leivo I, Kallioniemi O, Mäkitie AA, Monni O: Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene 2006, 25: 6997-7008.
10. Skotheim RI, Autio R, Lind GE, Kraggerud SM, Andrews PW, Monni O, Kallioniemi O, Lothe RA: Novel genomic aberrations in testicular germ cell tumors by array-CGH, and associated gene expression changes. Cell Oncol Off J Int Soc Cell Oncol 2006, 28: 315-326.
11. Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET: Patterns of Cis Regulatory Variation in Diverse Human Populations. PLoS Genet 2012, 8: e1002639.
12. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG: Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 2007, 39: 226-231.
13. Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, Beaulieu P, Hudson TJ, Sladek R, Majewski J: Genome-wide analysis of transcript isoform variation in humans. Nat Genet 2008, 40: 225-231.
14. Zhang W, Duan S, Bleibel WK, Wisel SA, Huang RS, Wu X, He L, Clark TA, Chen TX, Schweitzer AC, Blume JE, Dolan ME, Cox NJ: Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet 2009, 125: 81-93.
15. Richards JB, Rivadeneira F, Inouye M, Pastinen TM, Soranzo N, Wilson SG, Andrew T, Falchi M, Gwilliam R, Ahmadi KR, Valdes AM, Arp P, Whittaker P, Verlaan DJ, Jhamai M, Kumanduri V, Moorhouse M, van Meurs JB, Hofman A, Pols HAP, Hart D, Zhai G, Kato BS, Mullin BH, Zhang F, Deloukas P, Uitterlinden AG, Spector TD: Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. Lancet 2008, 371: 1505-1512.
16. Lee Y, Gamazon ER, Rebman E, Lee Y, Lee S, Dolan ME, Cox NJ, Lussier YA: Variants affecting exon skipping contribute to complex traits. PLoS Genet 2012, 8: e1002998.
17. Degner JF, Pai AA, Pique-Regi R, Veyrieras J-B, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK: DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 2012, 482: 390-394.
18. Heap G, Trynka G, Jansen R, Bruinenberg M, Swertz M, Dinesen L, Hunt K, Wijmenga C, van Heel D, Franke L: Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Med Genomics 2009, 2: 1.
19. Gerrits A, Li Y, Tesson BM, Bystrykh LV, Weersing E, Ausema A, Dontje B, Wang X, Breitling R, Jansen RC, de Haan G: Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State. PLoS Genet 2009, 5: e1000692.
20. Lee J-H, Park I-H, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM: A robust approach to identifying tissuespecific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet 2009, 5: e1000718.
21. Hussein SM, Batada NN, Vuoristo S, Ching RW, Autio R, Närvä E, Ng S, SourourM, Hamalainen R, Olsson C, Lundin K, MikkolaM, Trokovic R, PeitzM, Brustle O, Bazett-Jones DP, Alitalo K, Lahesmaa R, Nagy A, Otonkoski T: Copy number variation and selection during reprogramming to pluripotency. Nature 2011, 471: 58-62.
22. Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, Lynch C, Harness JV, Lee S, Barrero MJ, Ku S, Martynova M, Semechkin R, Galat V, Gottesfeld J, Belmonte JCI, Murry C, Keirstead HS, Park H-S, Schmidt U, Laslett AL, Muller F-J, Nievergelt CM, Shamir R, Loring JF: Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture. Cell Stem Cell 2011, 8: 106-118.
23. Lund RJ, Närvä E, Lahesmaa R: Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet 2012, 13: 732-744.
24. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavaré S, Deloukas P, Hurles ME, Dermitzakis ET: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315: 848-853.
25. Bengtson H, Simpson K, Bullard J, Hansen K: Aroma.affymetrix: A Generic Framework in R for Analyzing Small to Very Large Affymetrix Data Sets in Bounded Memory. Technical Report 745, University of California, Department of Statistics. University of California: Department of Statistics; 2008 [Technical Report 745].
26. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5: R80.
27. Ihaka R, Gentleman R: R: A Language for Data Analysis and Graphics. J Comput Graph Stat 1996, 5: 299-314.
28. 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. Biostat Oxf Engl 2003, 4: 249-264.
29. Hautaniemi S, Ringnér M, Kauraniemi P, Autio R, Edgren H, Yli-Harja O, Astola J, Kallioniemi A, Kallioniemi O-P: A strategy for identifying putative causes of gene expression variation in human cancers. Genomics Signal Process Stat 2004, 341: 77-88.
30. Järvinen A-K, Autio R, Kilpinen S, Saarela M, Leivo I, Grénman R, Mäkitie AA, Monni O: High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx. Genes Chromosomes Cancer 2008, 47: 500-509.
31. Myllykangas S, Junnila S, Kokkola A, Autio R, Scheinin I, Kiviluoto T, Karjalainen-Lindsberg M-L, Hollmén J, Knuutila S, Puolakkainen P, Monni O: Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes. Int J Cancer J Int Cancer 2008, 123: 817-825.
32. Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F: Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33: e175.
33. Kapur K, Jiang H, Xing Y, Wong WH: Cross-hybridization modeling on Affymetrix exon arrays. Bioinforma Oxf Engl 2008, 24: 2887-2893.
34. Cooper TA, Wan L, Dreyfuss G: RNA and Disease. Cell 2009, 136: 777-793.
35. Gamazon ER, Zhang W, Dolan ME, Cox NJ: Comprehensive Survey of SNPs in the Affymetrix Exon Array Using the 1000 Genomes Dataset. PLoS ONE 2010, 5: e9366.
36. Sela N, Mersch B, Hotz-Wagenblatt A, Ast G: Characteristics of transposable element exonization within human and mouse. PloS One 2010, 5: e10907.
37. Ciobanu DC, Lu L, Mozhui K, Wang X, Jagalur M, Morris JA, Taylor WL, Dietz K, Simon P, Williams RW: Detection, validation, and downstream analysis of allelic variation in gene expression. Genetics 2010, 184: 119-128.
38. Benovoy D, Kwan T, Majewski J: Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments. Nucleic Acids Res 2008, 36: 4417-4423.
39. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29: 308-311.
40. Bolstad BM, Irizarry R, Astrand M, Speed T: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19: 185-193.
41. Gautier L, Cope L, Bolstad BM, Irizarry RA: affy-analysis of Affymetrix GeneChip data at the probe level. Bioinforma Oxf Engl 2004, 20: 307-315.
42. Carvalho B, Bengtsson H, Speed TP, Irizarry RA: Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostat Oxf Engl 2007, 8: 485-499.
43. Guo L, Du Y, Chang S, Zhang K, Wang J: rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res 2014, 42: D1033-D1039.
44. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA: Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122: 947-956.
45. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34(Database issue): D108-110.
46. Stormo GD: DNA binding sites: representation and discovery. Bioinforma Oxf Engl 2000, 16: 16-23.
47. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4: P3.
48. Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4: 44-57.
49. Lin J, Kreisberg R, Kallio A, Dudley A, Nykter M, Shmulevich I, May P, Autio R: POMO - Plotting Omics analysis results for Multiple Organisms. BMC Genomics 2013, 14: 918.
50. McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH: PIR: a new resource for bioinformatics. Bioinforma Oxf Engl 2000, 16: 290-291.
51. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M: Variation in Transcription Factor Binding Among Humans. Science 2010, 328: 232-235.
52. Chen K, van Nimwegen E, Rajewsky N, Siegal ML: Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biol Evol 2010, 2: 697-707.
53. Hellman A, Chess A: Extensive sequence-influenced DNA methylation polymorphism in the human genome. Epigenetics Chromatin 2010, 3: 11.