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<p><span style="font-size:36px"><nbsp;Index of Chpater 9></span></p>
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<p><span style="color:#0000CD"><strong>Introduction</strong></spanh2>You Will Learn</ph2>
<pul>Microarrays provide the link between the static <li>The principles of genetics, genes and traits</li> <li>The applications and implications of genome sequencing</li> <li>How personal genomics might impact healthcare</li> <li>Tools used to diagnose and treat diseases</li> <li>Methods for determining the dynamic proteome. We use microarrays heritability of traits and diseases</li></pul>
<p>(<strong>Genomics</strong> refers to the study of the <a href="https://en.wikipedia.org/wiki/Genome" title="Genome">genome</a><sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-gov2010a-1">[1) To analyse ]</a></sup> in contrast to <a href="https://en.wikipedia.org/wiki/Genetics" title="Genetics">genetics</a> which refers to the mRNAs study of genes and their roles in inheritance.<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-gov2010a-1">[1]</a></sup> Genomics can be considered a discipline in genetics. It applies <a href="https://en.wikipedia.org/wiki/Recombinant_DNA" title="Recombinant DNA">recombinant DNA</a>, <a href="https://en.wikipedia.org/wiki/DNA_sequencing" title="DNA sequencing">DNA sequencing</a> methods, and <a href="https://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> to sequence, assemble, and analyze the function and structure of genomes (the <em>complete</em> set of DNA within a single cellof an organism).<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-gov2010-2">[2]</a></sup><sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-Klug_2012-3">[3]</a></sup> Advances in genomics have triggered a revolution in discovery-based research to understand even the most complex biological systems such as the brain.<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-Kadakkuzha_2013-4">[4]</a></sup> The field includes efforts to determine the entire <a href="https://en.wikipedia.org/wiki/DNA_sequence" title="DNA sequence">DNA sequence</a> of organisms and fine-scale <a href="https://en.wikipedia.org/wiki/Genetic_mapping" title="Genetic mapping">genetic mapping</a>. The field also includes studies of intragenomic phenomena such as <a href="https://en.wikipedia.org/wiki/Heterosis" title="Heterosis">heterosis</a>, <a href="https://en.wikipedia.org/wiki/Epistasis" title="Epistasis">epistasis</a>, <a href="https://en.wikipedia.org/wiki/Pleiotropy" title="Pleiotropy">pleiotropy</a> and other interactions between <a href="https://en.wikipedia.org/wiki/Locus_(genetics)" title="Locus (genetics)">loci</a> and <a href="https://en.wikipedia.org/wiki/Allele" title="Allele">alleles</a> within the genome.<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-Pevsner_2009-5">[5]</a></sup> In contrast, the investigation of the roles and functions of single genes is a primary focus of <a href="https://en.wikipedia.org/wiki/Molecular_biology" title="Molecular biology">molecular biology</a> or <a href="https://en.wikipedia.org/wiki/Genetics" title="Genetics">genetics</a> and is a common topic of modern medical and biological research. Research carried out into single genes does not generally fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to reavel the expression patterns of proteinsentire genomes networks.<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-Culver_2002-6">[6]</a></sup><sup>[<em><a href="https://en.wikipedia.org/wiki/Wikipedia:Verifiability" title="Wikipedia:Verifiability">not specific enough to verify</a></em>]</sup></p> <p> </p>
<p>(2) To detect genomic DNA sequences to reveal absent or mutated genes. </p>
<ph3>The transcriptome of "omics" revolution[<a cell is the set of RNA molecules it containshref="https://en. wikipedia.org/w/index.php?title=Genomics&action=edit&section=6" title="Edit section: The proteome is its proteins ."omics" revolution">edit</a>]</ph3>
<p>Main articles: <a href="https://en.wikipedia.org/wiki/Omics" title="Omics">Omics</a> and <a href="https://en.wikipedia.org/wiki/Human_proteome_project" title="Human proteome project">Human proteome project</a></p>
<p>We infer protein expression patterns from measuements The English-language <a href="https://en.wikipedia.org/wiki/Neologism" title="Neologism">neologism</a> <strong>omics</strong> informally refers to a field of study in <a href="https://en.wikipedia.org/wiki/Biology" title="Biology">biology</a> ending in <em>-omics</em>, such as genomics, <a href="https://en.wikipedia.org/wiki/Proteomics" title="Proteomics">proteomics</a> or <a href="https://en.wikipedia.org/wiki/Metabolomics" title="Metabolomics">metabolomics</a>. The related suffix <strong>-ome</strong> is used to address the objects of study of such fields, such as the relative amounts <a href="https://en.wikipedia.org/wiki/Genome" title="Genome">genome</a>, <a href="https://en.wikipedia.org/wiki/Proteome" title="Proteome">proteome</a> or <a href="https://en.wikipedia.org/wiki/Metabolome" title="Metabolome">metabolome</a> respectively. The suffix <em>-ome</em> as used in molecular biology refers to a <em>totality</em> of some sort; similarly <strong>omics</strong> has come to refer generally to the corresponding mRNAsstudy of large, comprehensive biological data sets. Hybridization While the growth in an accurate and sensitive sequence is presentthe use of the term has led some scientists (<a href="https://en.wikipedia.org/wiki/Jonathan_Eisen" title="Jonathan Eisen">Jonathan Eisen</a>, among others<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-Eisen_2012-41">[41]</a></sup>) to claim that it has been oversold,<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-wsj_2012-42">[42]</a></sup> it reflects the change in orientation towards the quantitative analysis of complete or near-complete assortment of all the constituents of a system.<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-scudellari2011-43">[43]</a></sup> In the study of <a href="https://en.wikipedia.org/wiki/Symbiosis" title="Symbiosis">symbioses</a>, for example, researchers which were once limited to the study of a single gene product can now simultaneously compare the total complement of several types of biological molecules.<sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-Chaston_2012-44">[44]</a></sup><sup><a href="https://en.wikipedia.org/wiki/Genomics#cite_note-McCutcheon_2011-45">[45]</a></sup></p>
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<p>The English-language <a href="https://en.wikipedia.org/wiki/Neologism" title="Neologism">neologism</a> <strong>omics</strong> informally refers to a field of study in <a href="https://en.wikipedia.org/wiki/Biology" title="Biology">biology</a> ending in <em>-omics</em>, such as <a href="https://en.wikipedia.org/wiki/Genomics" title="Genomics">genomics</a>, <a href="https://en.wikipedia.org/wiki/Proteomics" title="Proteomics">proteomics</a> or<nbsp;<a href="https://en.wikipedia.org/wiki/Metabolomics" title="Metabolomics">metabolomics</a>. The basic innovation related suffix <strong>-ome</strong> is used to address the objects of microarrays is parallel processingstudy of such fields, such as the <a href="https://en.wikipedia.org/wiki/Genome" title="Genome">genome</a>, <a href="https://en.wikipedia.org/wiki/Proteome" title="Proteome">proteome</a> or <a href="https://en.wikipedia.org/wiki/Metabolome" title="Metabolome">metabolome</a>>nbsp;respectively. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.</p>
<p>1<a href="https://en. One-to-one wikipedia. To detect whether one oligonucleotide has org/wiki/Functional_genomics" title="Functional genomics">Functional genomics</a particular known sequence, test whether it can hybridize to > aims at identifying the oligonucleotide functions of as many genes as possible of a given organism. It combines different -omics techniques such as transcriptomics and proteomics with the complementar sequencesaturated mutant collections.<sup><a href="https://en.wikipedia. org/wiki/Omics#cite_note-1">[1]</a></sup></p>
<p>2. Many The suffix <em>-ome</em> as used in molecular biology refers to one. To detect the presence or absence of a query oligonucleotide in a mixture, spread the mixture out and test component <em>totality</em> of the mixture for binding to the oligonucleotide complementary to the query. This some sort; it is an example of a nothern or Southern blot."neo-suffix" formed by abstraction from various Greek terms in -ωμα, a sequence that does not form an identifiable suffix in Greek.</p>
<p>3. Many to many. To detect the presence or absence of many oligonucleotides in a mixture, synthesize a set of oligonucleotides, one complemantary to each sequence of the query list and test each component of the mixture for binding to each memeber of the set of complementary oligonucleotides. </p>
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<ph2>The immobilized material on the chip is the probeCurrent usage[<a href="https://en.wikipedia. THe sample tested is the targetorg/w/index.php?title=Omics&action=edit amp;section=12" title="Edit section: Current usage">edit</a>]</ph2>
<p>Microarrays are also need Main article: <a href="https://en.wikipedia.org/wiki/List_of_omics_topics_in_biology" title="List of omics topics in biology">List of omics topics in biology</a></p> <p>Many “omes” beyond the original “<a href="https://en.wikipedia.org/wiki/Genome" title="Genome">genome</a>” have become useful and have been widely adopted by research scientists. “<a href="https://en.wikipedia.org/wiki/Proteomics" title="Proteomics">Proteomics</a>” has become well-established as a term for studying <a href="https://en.wikipedia.org/wiki/Proteins" title="Proteins">proteins</a> at a large scale. "Omes" can provide an easy shorthand to screen encapsulate a field; for mutations and polymorphismsexample, an <a href="https://en.wikipedia. Microarrays containing many sequence variants org/wiki/Interactomics" title="Interactomics">interactomics</a> study is clearly recognisable as relating to large-scale analyses of a single gene can detect differences from -gene, protein-protein, or protein-ligand interactions. Researchers are rapidly taking up omes and omics, as shown by the explosion of the use of these terms in <a standard reference sequencehref="https://en.wikipedia.org/wiki/PubMed" title="PubMed">PubMed</a> since the mid '90s.<sup><a href="https://en.wikipedia.org/wiki/Omics#cite_note-10">[10]</a></sup></p>
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<p>Different types of chip support different investigation <img alt="" src="/ckfinder/userfiles/images/genomics%20omics.PNG" style="height:217px;width:1132px" /></p>
<p>Expression chip / mismatched oligonucleotide / probe pair/ genomic hybridization / Mutation or polymorphism microarray analysis / protein microarrays / tissue microarrays. </p>
<p> Genomics is the new science that deals with the discovery and noting of all the sequences in the entire genome of a particular organism. The genome can be defined as the complete set of genes inside a cell. Genomics, is, therefore, the study of the genetic make-up of organisms.</p>
<p>Determining the genomic sequence, however, is only the beginning of genomics. Once this is done, the genomic sequence is used to study the function of the numerous genes (functional genomics), to compare the genes in one organism with those of another (comparative genomics), or to generate the 3-Applications D structure of DNA microarraysone or more proteins from each protein family, thus offering clues to their function (structural genomics).</p>
<p>>Investigating cellular states In crop agriculture, the main purpose of the application of genomics is to gain a better understanding of the whole genome of plants. Agronomically important genes may be identified and processestargeted to produce more nutritious and safe food while at the same time preserving the environment.</p>
<p>Genomics is an entry point for looking at the other >lsquo; COmparision omics’ sciences. The information in the genes of an organism, its genotype, is largely responsible for the final physical makeup of related speciesthe organism, referred to as the “phenotype”. However, the environment also has some influence on the phenotype.</p>
<p>DNA in the genome is only one aspect of the complex mechanism that keeps an organism running >ndash; Diagnosis of genetic diseaseso decoding the DNA is one step towards understanding the process. However, by itself, it does not specify everything that happens within the organism.</p>
<p>The basic flow of genetic information in a cell is as follows. The DNA is transcribed or copied into a form known as >ldquo; Genetic warning signsRNA”. The complete set of RNA (also known as its transcriptome) is subject to some editing (cutting and pasting) to become messenger-RNA, which carries information to the ribosome, the protein factory of the cell, which then translates the message into protein.</p>
<table border="0" cellpadding="0" cellspacing="0" style="width:405px"> <tbody> <tr> <td> <p>Figure 1. Genes, proteins, and molecular machines</p> </td> </tr> <tr> <td> <p><img src="http://www.isaaa.org/siteimages/pocketkimages/clip_image002_0014.jpg" style="height:416px; width:405px" /></p> </td> </tr> <tr> <td> <p>Source: U.S. Department of Energy Genomes to Life Program,>nbsp; Preciese diagnosis of disease<a href="http://doegenomestolife.org/" target="_blank">http://doegenomestolife.org</a></p> </td> </tr> </tbody></table>
<ph3>> Drug selectionThe International Rice Genome Sequencing Project</ph3>
<table align="left" border="0" cellpadding="5" cellspacing="0"> <tbody> <tr> <td> <p>><img src="http://www.isaaa.org/siteimages/pocketkimages/clip_image003_0012.jpg" style="height:82px; Determination of gene functionwidth:125px" /></p> </td> </tr> </tbody></table>
<p>This ongoing genomic research in rice is a collaborative effort of several public and private laboratories worldwide. This project aims to completely sequence the entire rice genome (12 rice chromosomes) and subsequently apply the knowledge to improve rice production.<br />In 2002, the draft genome sequences of two agriculturally important subspecies of rice, indica and japonica, were published. Once completed, the rice genome sequence will serve as a model system for other cereal grasses and will assist in identifying important genes in maize, wheat, oats, sorghum, and millet.<br />For more, visit>nbsp; Target selection for drug design<a href="http://rgp.dna.affrc.go.jp/IRGSP" target="_blank">http://rgp.dna.affrc.go.jp/IRGSP</a></p>
<ph2> Proteomics</ph2>
<p> Proteins are responsible for an endless number of tasks within the cell. The complete set of proteins in a cell can be referred to as its proteome and the study of protein structure and function and what every protein in the cell is doing is known as proteomics. The proteome is highly dynamic and it changes from time to time in response to different environmental stimuli. The goal of proteomics is to understand how the structure and function of proteins allow them to do what they do, what they interact with, and how they contribute to life processes.</p>
<p><span style="color:#0000CD"><strong>Analysis An application of microarrary data</strong></span>proteomics is known as protein “expression profiling” where proteins are identified at a certain time in an organism as a result of the expression to a stimulus. Proteomics can also be used to develop a protein-network map where interaction among proteins can be determined for a particular living system.</p>
<p>Two general approaches Proteomics can also be applied to map protein modification to determine the analysis of difference between a gene expression matrix involve wild type and a genetically modified organism. It is also used to study protein-protein interactions involved in plant defense reactions.</p>
<table align="right" border="0" cellpadding="5" cellspacing="0"> <tbody> <tr> <td> <p>1<img src="http://www. Comparisons focused on the genesisaaa. i.e. Comparing distrivbutions of expression patterns of different genes by comparing rows in the expression matrixorg/siteimages/pocketkimages/clip_image004_0011. jpg" style="height:82px;width:125px" /></p> </td> </tr> </tbody></table>
<p>2. Comparisons focused on samples. Comparing expression profiles of different samples by comparing columns of the expression matrix. For example, proteomics research at Iowa State University, USA includes:</p>
<pul>  <li>an examination of changes of protein in the corn proteome during low temperatures which is a major problem for young corn seedlings;</li> <li>analysis of the differences that occur in the genome expression in developing soybean stressed by high temperatures;and</li> <li>identifying the proteins expressed in response to diseases like soybean cyst nematode.</li></pul>
<ph2>Gene vectors/ sample vectors Metabolomics</ph2>
<p>Metabolomics is one of the newest  lsquo;omics’ sciences. The metabolome refers to the complete set of low molecular weight compounds in a sample. These compounds are the substrates and by-products of enzymatic reactions and have a direct effect on the phenotype of the cell. Thus, metabolomics aims at determining a sample’s profile of these compounds at a specified time under specific environmental conditions.</p>
<p>Depending on Genomics and proteomics have provided extensive information regarding the origin of genotype but convey limited information about phenotype. Low molecular weight compounds are the samples, what is already known about them and what we want closest link to learn data anaylsis can proceed in different directions phenotype.</p>
<p>1Metabolomics can be used to determine differences between the levels of thousands of molecules between a healthy and diseased plant. Known characteristicsThe technology can also be used to determine the nutritional difference between traditional and genetically modified crops, and in identifying plant defense metabolites.</p>
<table border="0" cellpadding="0" cellspacing="0" style="width:405px"> <tbody> <tr> <td> <p>Figure 2. Pre-assignExample of a metabolic network model for <em>E. coli</em></p> </td> </tr> <tr> <td> <p><img src="http://www.isaaa.org/siteimages/pocketkimages/clip_image005_0003.jpg" style="height:604px; width:400px" /></p> </td> </tr> <tr> <td> <p>Source: U.S. Department of Energy Genomes to Life Program, <a href="http://doegenomestolife.org/" target="_blank">http://doegenomestolife.org</a></p> </td> </tr> </tbody></table>
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<table border="0" cellpadding="0" cellspacing="0" style="width:405px"> <tbody> <tr> <td> <p>Reduction Figure 2. Example of dimensionalitya metabolic network model for <em>E.coli</em></p> </td> </tr> <tr> <td> <p><img src="http://www.isaaa.org/siteimages/pocketkimages/clip_image006_0000.jpg" style="height:240px; width:400px" /></p> </td> </tr> <tr> <td> <p>Source: <a href="http://biotech.nature.com/" target="_blank">http://biotech.nature.com</a></p> </td> </tr> </tbody></table>
<p>>nbsp; Processing </p> <p>Genomics provides an overview of the complete set of genetic instructions provided by the data from a microarray experiment produces a DNA, while transcriptomics looks into gene expression table, or matrixpatterns. The rows index the genes Proteomics studies dynamic protein products and the columns index the samples. We can either focus on the genestheir interactions, and ask. How do patterns of epxpression of different genes very among the different samples? Or we can focus on the samples, and ask. How do the samples differ while metabolomics is also an intermediate step in teir gene expression pattterns?understanding organism rsquo;s entire metabolism.</p>
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<ph2> Glossary</ph2>
<p><span style="color:#0000CD"><strong>Expression patterns in different physiological statesChromosome</strong></span>: a grouping of coiled strands of DNA, containing many genes.</p>
<p>-The diauxic shift <strong>DNA (deoxyribonucleic acid)</strong>: a molecule found in Saccharomyces cerevisiaecells of organisms that encodes genetic information.</p>
<p>-Sleep in rats and fruit flies<strong>Gene</strong>: a biological unit that codes for distinct traits or characteristics.</p>
<p> <strong>Genome</strong>: the complete set of genes in a cell.</p>
<p><span style="color:#0000CD"><strong>Expression pattern changes in developmentGenotype</strong></span>: the genetic constitution of an organism.</p>
<p>-Variation <strong>Metabolome</strong>: complete set of expression patterns during the life cycle of Drosophila melanogasterlow molecular weight compounds in a cell at a given time.</p>
<p>-Flower formation in roses<strong>Phenotype</strong>: the physical appearance/observable characteristics of an organism.</p>
<p> <strong>Proteome</strong>: complete set of proteins in a cell at a given time.</p>
<p><span style="color:#0000CD"strong>RNA (ribonucleic acid)</strong>Expression patterns in learning and memory : Longa molecule, derived from DNA by transcription, that either carries information (messenger RNA), provides sub-term potentiation</strong></span>cellular structure (ribosomal RNA), transports amino acids (transfer RNA), or facilitates the biochemical modification of itself or other RNA molecules.</p>
<ph2>-Conserved clusters of co-expressing genesReferences</ph2>
<pol> <li>Genomics and Its impact on Medicine and Society. A 2001 primer. <a href="http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/1.html" target="_blank">http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/1.html</a></li> <li>Primer on Molecular Genetics. <a href="http://www.ornl.gov/TechResources/Human_Genome/publicat/primer/primer.pdf" target="_blank">http://www.ornl.gov/TechResources/Human_Genome/publicat/primer/primer.pdf</a></li> <li>Plant Sciences Institute Update. Iowa State University. October 2001. Volume 2 No.1.</li> <li>Genome Projects. <a href="http://www.tigr.org/tdb" target="_blank">http://www.tigr.org/tdb</a></li> <li>Meet the ‘omics’ 2003 Agbiotech Infosource. Saskatchewan Agricultural Biotechnology Information Centre, A service of Ag-West Biotech Inc.</li></pol>
<p><span style="color:#0000CD"><strong>Evolutionary changes in expression patterns </strong></span>Reference</p>
<p>1. https://en.wikipedia.org/wiki/Genomics</p>
<p><span style="color2. https:#0000CD"><strong>Applications of microarrays in medicine</strong></span>en.wikipedia.org/wiki/Omics</p>
<p>-Development of antibiotic resistance in bacteria3. http://www.isaaa.org/resources/publications/pocketk/15/default.asp</p>
<p>4. http://geneticscertificate.stanford.edu/courses/genomics-Childhood leukaemiasand-the-other-omics</p>
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<p><span style="color:#0000CD"><strong>Whole trranscriptome shotgun sequencing : RNA-seq</strong></span> </p>
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