Abstract
Recent development in high-throughput experiments has provided great amount of data that is being used in translational personalized medicine. Data available in public databases is increasing exponentially as a result of the progress in omics technologies including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Advancements in computing power and machine intelligence are affecting large-scale data analysis and integration. Two types of data integration are often considered: horizontal and vertical meta-analysis. The former integrates multiple studies of the same type, while the latter integrates data at different biological levels. This integrative approach provides a better understanding of systems complexity as a result of the global view that it offers from a biological point of view. This chapter describes the different types of omics analysis and discusses the methods of integrating multi-omics data using a case study.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
1000 Genomes Project Consortium, Auton A, Brooks LD et al (2015) A global reference for human genetic variation. Nature 526:68–74
Abaffy T, Möller MG, Riemer DD et al (2013) Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study. Metabolomics 9:998–1008
Abou-Abbass H, Abou-El-Hassan H, Bahmad H et al (2016) Glycosylation and other PTMs alterations in neurodegenerative diseases: current status and future role in neurotrauma. Electrophoresis 37:1549–1561
Adams MD, Kelley JM, Gocayne JD et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656
Alberts B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92:291–294
Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51:786–794
Anderson S (1981) Shotgun DNA sequencing using cloned DNase I-generated fragments. Nucleic Acids Res 9:3015–3027
Arnes L, Akerman I, Balderes DA et al (2016) betalinc1 encodes a long noncoding RNA that regulates islet beta-cell formation and function. Genes Dev 30:502–507
Assfalg M, Bortoletti E, D’Onofrio M et al (2012) An exploratory 1H-nuclear magnetic resonance metabolomics study reveals altered urine spectral profiles in infants with atopic dermatitis. Br J Dermatol 166:1123–1125
Atlas SA (2007) The renin-angiotensin aldosterone system: pathophysiological role and pharmacologic inhibition. J Manag Care Pharm JMCP 13:9–20
Balog J, Sasi-Szabo L, Kinross J et al (2013) Intraoperative tissue identification using rapid evaporative ionization mass spectrometry. Sci Transl Med 5:194ra93–194ra93
Barrett T, Wilhite SE, Ledoux P et al (2013) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41:D991–D995
Bird A, Taggart M, Frommer M et al (1985) A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40:91–99
Buermans HPJ, den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 1842:1932–1941
Byron SA, Van Keuren-Jensen KR, Engelthaler DM et al (2016) Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet 17:257–271
Cantor RM, Lange K, Sinsheimer JS (2010) Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Am J Hum Genet 86:6–22
Carichon M, Pallet N, Schmitt C et al (2014) Urinary metabolic fingerprint of acute intermittent porphyria analyzed by 1H NMR spectroscopy. Anal Chem 86:2166–2174
Carithers LJ, Moore HM (2015) The Genotype-Tissue Expression (GTEx) Project. Biopreserv Biobank 13:307–308
Caskey CT, Gonzalez-Garay ML, Pereira S, McGuire AL (2014) Adult genetic risk screening. Annu Rev Med 65:1–17
Chen R, Mias GI, Li-Pook-Than J et al (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148:1293–1307
Civelek M, Lusis AJ (2013) Systems genetics approaches to understand complex traits. Nat Rev Genet 15:34–48
Clark SJ, Lee HJ, Smallwood SA et al (2016) Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol 17:72
Consortium IH 3 (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467:52–58
Consortium IHGS (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Crutchfield CA, Thomas SN, Sokoll LJ, Chan DW (2016) Advances in mass spectrometry-based clinical biomarker discovery. Clin Proteomics 13:1
Das MK, Arya R, Debnath S et al (2016) Global urine metabolomics in patients treated with first-line tuberculosis drugs and identification of a novel metabolite of ethambutol. Antimicrob Agents Chemother 60:2257–2264
DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498
Dirks RAM, Stunnenberg HG, Marks H (2016) Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 8:122
Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138
ENCODE Project Consortium {fname} (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74
Farley AR, Link AJ (2009) Identification and quantification of protein posttranslational modifications. Methods Enzymol 463:725–763
Farrah T, Deutsch EW, Omenn GS et al (2014) State of the human proteome in 2013 as viewed through peptideatlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven human proteome project. J Proteome Res 13:60–75
Fiehn O (2002) Metabolomics—the link between genotyopes and phenotypes. Plant Mol Biol 48:155–171
Friedrich N (2012) Metabolomics in diabetes research. J Endocrinol 215:29–42
García-Cañaveras JC, Jiménez N, Gómez-Lechón MJ et al (2015) LC-MS untargeted metabolomic analysis of drug-induced hepatotoxicity in HepG2 cells. Electrophoresis 36:2294–2302
GTEx Consortium TGte (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45:580–585
Guo L, Milburn MV, Ryals JA et al (2015) Plasma metabolomic profiles enhance precision medicine for volunteers of normal health. Proc Natl Acad Sci USA 112:E4901–E4910
Gupta RA, Shah N, Wang KC et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076
Heller MJ (2002) DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 4:129–153
Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226–232
Hotchkiss RD (1948) The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem 175:315–332
International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945
Ishii N, Ozaki K, Sato H et al (2006) Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 51:1087–1099
Jung J, Kim SH, Lee HS et al (2013) Serum metabolomics reveals pathways and biomarkers associated with asthma pathogenesis. Clin Exp Allergy 43:425–433
Khare SP, Habib F, Sharma R et al (2012) HIstome—a relational knowledgebase of human histone proteins and histone modifying enzymes. Nucleic Acids Res 40:D337–D342
Khurana E, Fu Y, Chakravarty D et al (2016) Role of non-coding sequence variants in cancer. Nat Rev Genet 17:93–108
Kim K, Aronov P, Zakharkin SO et al (2009) Urine metabolomics analysis for kidney cancer detection and biomarker discovery. Mol Cell Proteomics MCP 8:558–570
Kim Y, Jeon J, Mejia S et al (2016) Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer. Nat Commun 7:11906
Klein RJ, Zeiss C, Chew EY et al (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308:385–389
Koussounadis A, Langdon SP, Um IH et al (2015) Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system. Sci Rep 5:10775
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Kulis M, Esteller M (2010) DNA methylation and cancer. Adv Genet 70:27–56
Lehmann S, Brede C, Lescuyer P et al (2017) Clinical mass spectrometry proteomics (cMSP) for medical laboratory: what does the future hold? Clin Chim Acta 467:51–58
Li S, Todor A, Luo R (2016) Blood transcriptomics and metabolomics for personalized medicine. Comput Struct Biotechnol J 14:1–7
Licata L, Briganti L, Peluso D et al (2012) MINT, the molecular interaction database: 2012 Update. Nucleic Acids Res 40:D857–D861
Lindskog C (2015) The potential clinical impact of the tissue-based map of the human proteome. Expert Rev Proteomics 12:213–215
Lister R, Pelizzola M, Kida YS et al (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471:68–73
Maier T, Güell M, Serrano L (2009) Correlation of mRNA and protein in complex biological samples. FEBS Lett 583:3966–3973
Manolio TA, Collins FS (2009) The HapMap and genome-wide association studies in diagnosis and therapy. Annu Rev Med 60:443–456
Maraganore DM, de Andrade M, Lesnick TG et al (2005) High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet 77:685–693
Mun J-H, Lee H, Yoon D et al (2016) Discrimination of basal cell carcinoma from normal skin tissue using high-resolution magic angle spinning 1H NMR spectroscopy. PLoS One 11:e0150328
Nehme A, Zibara K (2017a) Cellular distribution and interaction between extended renin-angiotensin-aldosterone system pathways in atheroma. Atherosclerosis 263:334–342
Nehme A, Zibara K (2017b) Efficiency and specificity of RAAS inhibitors in cardiovascular diseases: how to achieve better end-organ protection? Hypertens Res 40:903–909
Nehme A, Cerutti C, Dhaouadi N et al (2015) Atlas of tissue renin-angiotensin-aldosterone system in human: a transcriptomic meta-analysis. Sci Rep 5:10035
Nehme A, Cerutti C, Zibara K (2016a) Transcriptomic analysis reveals novel transcription factors associated with renin–angiotensin–aldosterone system in human atheroma. Hypertension HYPERTENSIONAHA.116.08070
Nehme A, Marcelo P, Nasser R et al (2016b) The kinetics of angiotensin-I metabolism in human carotid atheroma: an emerging role for angiotensin (1-7). Vascul Pharmacol 85:50–56
Ng SB, Turner EH, Robertson PD et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272–276
Orchard S, Ammari M, Aranda B et al (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42:D358–D363
Palmer ND, Stevens RD, Antinozzi PA et al (2015) Metabolomic profile associated with insulin resistance and conversion to diabetes in the Insulin Resistance Atherosclerosis Study. J Clin Endocrinol Metab 100:E463–E468
Parkinson H, Kapushesky M, Shojatalab M et al (2007) ArrayExpress—a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35:D747–D750
Polak P, Karlić R, Koren A et al (2015) Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518:360–364
Qin W, Kozlowski P, Taillon BE et al (2010) Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex. Hum Genet 127:573–582
Rhodes DR, Yu J, Shanker K et al (2004) ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6, 6(1)
Rhodes DR, Kalyana-Sundaram S, Mahavisno V et al (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9:166–180
Ritchie MD, Holzinger ER, Li R et al (2015) Methods of integrating data to uncover genotype–phenotype interactions. Nat Rev Genet 16:85–97
Roy B, Haupt LM, Griffiths LR (2013) Review: alternative splicing (AS) of genes as an approach for generating protein complexity. Curr Genomics 14:182–194
Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441–448
Schaefer C, Meier A, Rost B, Bromberg Y (2012) Snpdbe: constructing an nsSnp functional impacts database. Bioinformatics 28:601–602
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470
Schmitz SU, Grote P, Herrmann BG (2016) Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci 73:2491–2509
Schoen C, Kischkies L, Elias J, Ampattu BJ (2014) Metabolism and virulence in Neisseria meningitidis. Front Cell Infect Microbiol 4:114
Shabman RS, Jabado OJ, Mire CE et al (2014) Deep sequencing identifies noncanonical editing of Ebola and Marburg virus RNAs in infected cells. mBio 5:e02011
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145
Smith LM, Kelleher NL, Linial M et al (2013) Proteoform: a single term describing protein complexity. Nat Methods 10:186–187
Stadler ZK, Thom P, Robson ME et al (2010) Genome-wide association studies of cancer. J Clin Oncol Off J Am Soc Clin Oncol 28:4255–4267
Tessarz P, Kouzarides T (2014) Histone core modifications regulating nucleosome structure and dynamics. Nat Rev Mol Cell Biol 15:703–708
Tomescu OA, Mattanovich D, Thallinger GG (2014) Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data. BMC Syst Biol 8:S4
Trushina E, Mielke MM (2014) Recent advances in the application of metabolomics to Alzheimer’s disease. Biochim Biophys Acta Mol Basis Dis 1842:1232–1239
Uhlén M, Fagerberg L, Hallström BM et al (2015) Proteomics. Tissue-based map of the human proteome. Science 347:1260419
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487
Verdin E, Ott M (2014) 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Nat Rev Mol Cell Biol 16:258–264
Vizcaíno JA, Deutsch EW, Wang R et al (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32:223–226
Waddington CH (1942) The epigenotype. Endeavour 1:18–20. https://doi.org/10.1093/ije/dyr184
Weis JH, Tan SS, Martin BK, Wittwer CT (1992) Detection of rare mRNAs via quantitative RT-PCR. Trends Genet 8:263–264. https://doi.org/10.1016/0168-9525(92)90242-V
Welter D, MacArthur J, Morales J et al (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res 42:D1001–D1006
Worrall JA, Kolczak U, Canters GW, Ubbink M (2001) Interaction of yeast iso-1-cytochrome c with cytochrome c peroxidase investigated by [15N, 1H] heteronuclear NMR spectroscopy. Biochemistry (Mosc) 40:7069–7076
Wu JR, Zeng R (2012) Molecular basis for population variation: from SNPs to SAPs. FEBS Letters.:2841–2845
Xenarios I (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30:303–305
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Nehme, A., Awada, Z., Kobeissy, F., Mazurier, F., Zibara, K. (2018). Coupling Large-Scale Omics Data for Deciphering Systems Complexity. In: Rajewsky, N., Jurga, S., Barciszewski, J. (eds) Systems Biology. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-92967-5_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-92967-5_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-92966-8
Online ISBN: 978-3-319-92967-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)