Bioinformatics and Experimental Databases as Significant Research Paraphernalia in Oral Cancer - A Narrative Review
DOI:
https://doi.org/10.18311/jpfa/2023/32255Keywords:
Bioinformatics, Data Mining, Genome, Insilco, Microarrays, Next Generation Sequencing, Oral CancerAbstract
Among head and neck squamous cell carcinomas the incidence of Oral Squamous Cell Carcinoma (OSCC) is highest (80%). Bioinformatics provides a wide-ranging outlook to understand the significant genes, proteins, pathways, and molecular mechanisms fundamental to oral carcinogenesis. It is a promising branch in the field of biomedical research with emerging popularity in the field of dental research too, targeting immune-mediated, developmental, genetic, and malignant diseases. High-throughput experimental technologies have created large and complex genomic data, which has revolutionized genomic research. Advanced technologies including microarray, next-generation sequencing, and bioinformatics together play a decisive role in unraveling the molecular mechanism in the process of Head and Neck cancer. This article is an attempt to give an overview of the significant role of bioinformatics in the field of genomic research.
Downloads
Published
How to Cite
Issue
Section
License
All the articles published in JPFA are distributed under a creative commons license. The journal allows the author(s) to hold the copyright of their work (all usages allowed except for commercial purpose).
References
Saintigny P, Zhang L, Fan YH, El-Naggar AK, Papadimitrakopoulou V, Feng L et al. Gene expression profiling predicts the development of oral cancer. Cancer Prev Res (Phila). 2011; 4(2):218–29. https://doi. org/10.1158/1940-6207.CAPR-10-0155 PMid:21292635 PMCid:PMC3074595
Kuo WP. Overview of bioinformatics and its application to oral genomics. Adv Dent Res. 2003; 17:89-94. https://doi. org/10.1177/154407370301700121 PMid:15126216
Bennett NC, Farah CS. Next-generation sequencing in clinical oncology: Next steps towards clinical validation. Cancers (Basel). 2014; 6:2296-312. https://doi.org/10.3390/ cancers6042296 PMid:25412366 PMCid:PMC4276967
Mendez E, Cheng C, Farwell G, Ricks S, Agoff N, Futran ND, Weymulle EA. Transcriptional expression profiles of oral squamous cell carcinomas. Cancer. 2002; 95:1482–94. https://doi.org/10.1002/cncr.10875 PMid:12237917
Kim KY, Cha IH. Possibility of the use of public microarray database for identifying significant genes associated with oral squamous cell carcinoma. Genomics Inf. 2012; 10(1):23-32. https://doi.org/10.5808/GI.2012.10.1.23 PMid:23105925 PMCid:PMC3475481
Murray D, Doran P, MacMathuna P, Moss AC. In silico gene expression analysis – an overview. Molecular Cancer. 2007; 6:50-60. https://doi.org/10.1186/1476-4598-6-50 PMid:17683638 PMCid:PMC1964762
Singh S, Lall R, Jain P. In-silico analysis of micro array data for prostate cancer. Int J Pharm Sci Rev Res. 2010; 3(1):46- 8. ISSN 0976 – 044X
Singaraju S, Prasad H, Singaraju M. Evolution of dental informatics as a major research tool in oral pathology. J Oral Maxillofac Path. 2012; 16(1):83-7. https://doi. org/10.4103/0973-029X.92979 PMid:22434944 PMCid: PMC3303529
Rao VS, Das SK, Rao VJ, Srinubabu G. Recent developments in life sciences research: Role of bioinformatics. Afr J Biotechnol. 2008; 7:495-503. eISSN: 1684-5315
Verma C, Suhail S, Gupta OP, Gupta S. Recent developments in dent informatics: Role of bioinformatics. World J Pharm Res. 2015; 4(3):1299-1309
Zhang Y. Dental informatics and applications have an impact on dentistry. Eur J Biomed Inform. 2022; 18(4):32- 3. https://doi.org/10.1353/fair.2022.0007
Giacomelli L, Covani U. Bioinformatics and data mining studies in oral genomics and proteomics: New trends and challenges. Open Dent J. 2010; 4:67-71. https://doi. org/10.2174/1874210601004020067 PMid:20871759 PMCid:PMC2945006
Wright JT, Hart TC. The genome projects: Implications for dental practice and education. J Dent Educ. 2002; 66:659-71. https://doi.org/10.1002/j.0022-0337.2002.66.5.tb03545.x PMid:12056771
Strausberg RL, Simpson AJG, Wooster R. Sequence-based cancer genomics: Progress, lessons and opportunities. Nat Rev Genet. 2003; 4:409-18. https://doi.org/10.1038/ nrg1085 PMid:12776211
Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biology. 2011; 9:34-43. https://doi.org/10.1186/1741-7007-9-34 PMid:21627854 PMCid:PMC3104486
Koschmieder K, Zimmermann K, Tri S, Stoltmannand T, Leser U. Tools for managing and analyzing microarray data. Brief Bioinform. 2011; 13(1):46-60. https://doi.org/10.1093/ bib/bbr010 PMid:21422065
Nazmul-Hossain, ANM, Patel KJ, Rhodus NL, Moser KL. Microarrays: Applications in dental research. Oral Dis. 2008; 14(1):25-29. https://doi.org/10.1111/j.1601- 0825.2006.01342.x PMid:18173445
Parolin C, Giordani B, Palomino RAN, Biagi E, Severgnini M, Consolandi C, et al. Design and validation of a DNA microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants. Sci reports. 2017; 7:6280. https://doi.org/10.1038/s41598-017- 06743-6 PMid:28740183 PMCid:PMC5524749
Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJ. Microarrays and clinical dentistry. J Am Dent Assoc. 2003; 134(4):456-62. https:// doi.org/10.14219/jada.archive.2003.0195 PMid:12733779
Macgregor PF, Squire JA. Application of microarrays to the analysis of gene expression in cancer. Clin Chem. 2002; 48(8):1170–7. https://doi.org/10.1093/clinchem/48.8.1170 PMid:12142369
Monger C, Kelly PS, Gallagher C, Clynes M, Barron N, Clarke C. Towards next generation CHO cell biology: Bioinformatics methods for RNA-seq-based expression profiling. Biotechnol J. 2015; 10(7):950-66. https://doi. org/10.1002/biot.201500107 PMid:26058739
Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014; 30:418–26. https://doi.org/10.1016/j.tig.2014.07.001 PMid:25108476
Han Y, Gao S, Muegge K, Zhang W, Zhou B. Advanced applications of RNA sequencing and challenges. Bioinform Biol Insights. 2015; 9(1):29–46. https://doi.org/10.4137/ BBI.S28991 PMid:26609224 PMCid:PMC4648566
Upadhyay P, Dwivedi R, Dutt A. Applications of nextgeneration sequencing in cancer. Current Science. 2014; 107(5):795-802. https://www.jstor.org/stable/24105584
Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ. A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics. 2010; 11:282-94. https://doi.org/10.1186/1471-2164-11-282 PMid:20444259 PMCid:PMC2877694
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science. 1999; 286:531–7. https://doi.org/10.1126/science.286.5439.531 PMid:10521349
Gadewal N, Zingde SM. Database and interaction network of genes involved in oral cancer: Version II. Bioinformation. 2011; 6(4):169-170. https://doi.org/10.6026/97320630006169 PMid:21572887 PMCid:PMC3092954
Villalba GC, Ursula Matte U. Fantastic databases and where to find them: Web applications for researchers in a rush., Genet Mol Biol. 2021; 44(2):e20200203. https://doi.org/10.1590/1678-4685-gmb-2020-0203 PMid:33821874 PMCid:PMC8022358
Hide W. Genome Databases. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. 2000; 25(1):25–9 https://doi.org/10.1038/75556 PMid:10802651 PMCid:PMC3037419
Apweiler R, Bairoch A, Wu CH. Protein sequence databases. Current Opinion in Chemical Biology. 2004, 8:76–80 https://doi.org/10.1016/j.cbpa.2003.12.004 PMid:15036160
Levine AE, Steffen DL. OrCGDB: A database of genes involved in oral cancer. Nucleic Acids Res. 2001; 29(1):300-302. https://doi.org/10.1093/nar/29.1.300 PMid:11125119 PMCid:PMC29839
Kuo WP, Overview of bioinformatics and its application to oral genomics, Adv Dent Res. 2003; 17:89-94. https://doi. org/10.1177/154407370301700121 PMid:15126216
Kuo WP, Whipple ME, Epstein JB, Jenssen TK, Santos GS, Machado OL. Deciphering gene expression profiles generated from DNA microarrays and their applications in oral medicine. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2004; 97:584-91. https://doi.org/10.1016/j. tripleo.2003.11.016 PMid:15153870
Mehta JP, Rani S. Software and tools for microarray data analysis. Methods Mol Biol. 2011; 784:41-53. https://doi. org/10.1007/978-1-61779-289-2_4 PMid:21898212
Jaluria P, Konstantopoulos K, Betenbaugh M, Shiloach J. A perspective on microarrays: Current applications, pitfalls, and potential uses. Microb. Cell Factories. 2007, 6:4-18. https://doi.org/10.1186/1475-2859-6-4 PMid:17254338 PMCid:PMC1796898
Russo G, Zegar C,Giordano A. Advantages and limitations of microarray technology in human cancer. Oncogene 2003; 22:6497–650. https://doi.org/10.1038/sj.onc.1206865 PMid:14528274
Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011; 8(1):61-65. https://doi.org/10.1038/ nmeth.1527 PMid:21102452 PMCid:PMC3115693
Behjati S, Tarpey PS. What is next generation sequencing? Arch Dis Child Educ Pract Ed. 2013; 98(6):236-38. https://doi.org/10.1136/archdischild-2013-304340 PMid:23986538 PMCid:PMC3841808
Fan J, Ren Y. Statistical analysis of DNA microarray data in cancer research. Clin Cancer Res 2006; 12(15):4469-73. https://doi.org/10.1158/1078-0432.CCR- 06-1033 PMid:16899590
Aris VM, Cody MJ, Cheng J, Dermody JJ, Soteropoulos P, Michael R, Tolias PP. Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer. BMC Bioinformatics 2004, 5:185 https://doi.org/10.1186/1471- 2105-5-185 PMid:15569388 PMCid:PMC538261
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008; 26:1135-45. https://doi.org/10.1038/ nbt1486 PMid:18846087
Wolf B, Kuonen P, Dandekar T, Atlan D. DNAseq workflow in a diagnostic context and an example of a user friendly implementation. BioMed Res Int. 2015; 2015:1- 10. https://doi.org/10.1155/2015/403497 PMid:26137478 PMCid:PMC4475531
Jiang Q, Yu YC, Ding XN, Luo Y, Ruan H. Bioinformatics analysis reveals significant genes and pathways to target for oral squamous cell carcinoma. Asian Pac J Cancer Prev. 15(5):2273-78. https://doi.org/10.7314/APJCP.2014.15.5.2 273 PMid:24716969