Analysis of microarray data - VSN International

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2Analysis of Microarray Data in GenStatMicroarray example filesThe microarray data files must be installed either from the GenStat CD or downloaded separately if youhave downloaded the GenStat installation from the web. For example, when installed with the EleventhEdition of GenStat these will be in the folder C:\Program Files\Gen11ed\Data\Microarrays. If you haveinstalled GenStat on a network drive or non-standard folder, they will be found in the folderData\Microarrays under the main GenStat folder. The Microarrays folder should contain the followingfiles:FileAPoAIGeneNames.tabAPoAIGenes.gshApoAIKnockOut.gshApoAIKnockOutContrast.gshApoAIKnockOutEffects.gshApoAIKnockOutSlides.gshApoAIKnockOutStacked.gshAPoAISlides.csv13-6-data.gpr – 3-9-data.gprContrasts13-6-9.gshData13-6-9.gwbSlides13-6-9.gshEstimates13-6-9.gshATH1-121501B.CDFHyb1191.CEL – Hyb1400.CELHyb-AllData.gwbHyb-PM_MM.gwbHyb-ANOVA.gwbHybContrasts.gshHyb-Expressions.gshHybFiles.gshSwirl1.csv – Swirl4.csvSwirl_layout.csvSwirl_layout.gwbSwirlSample.csvSwirlSample.gshSwirl.gshDescriptionGene names for APO knock-out mouse expt as downloaded from webGene names for APO Knock-out mouse expt in GenStat formatData for spots on all slides in APO knockout expt in unstacked formatMatrix holding contrast between knock-out & standard treatmentsEstimated effects for APO knock-out exptDescription of 16 slides used in APO knock-out exptAll data in APO knock-out exptData for spots on all slides in APO knock-out expt as downloaded4 GenePix analysis results filesMatrix holding contrast between GenePix treatmentsCombined data set containing 4 GenePix slidesTreatments on each of the 4 GenePix slidesEstimated effects for GenePix exptChip information (layout and probes) for Affymetrix Arabidopis exptAffymetrix files containing image analysis results for Arabidopis chipsAll data for Arabidopis expt emerged into a single fileArabidopis data reorganised into PM/MM columnsResults of ANOVA from Arabidopis exptMatrix holding contrasts between treatments for Arabidopis exptEstimated expression values for Arabidopis exptDescription of 9 chips used in Arabidopis exptData on 4 slides for Zebra Fish Swirl expt as downloadedLayout of slides for Zebra Fish Swirl expt as downloadedLayout of slides for Zebra Fish Swirl expt in GenStat formatSamples on slides for Zebra Fish Swirl expt as downloadedSamples on slides for Zebra Fish Swirl expt in GenStat formatCombined data for Zebra Fish Swirl expt in GenStat format
Analysis of Microarray Data in GenStat 3IntroductionDNA is used to carry the instructions for cell processes. DNA is made up of fournucleotide bases: adenine, cytosine, guanine and thymine (abbreviated as A, C, Gand T respectively). These bases join into two complementary pairs, with A onlybinding to T and C with G. The bases are arranged in a double stranded helix (thebackbone of the strands being made up of phosphate, the 5-carbon sugardeoxyribose) with complementary pairs of bases on each strand. Two single strandsof DNA with sequences of bases have complementary bases at all matchingpositions (such as ACTGTGA and TGACACT) are known as a complementarysequence. In a solution of the right temperature, these two single stands will bindtogether, to form a single double stranded section of DNA. If the temperature of thesolution is raised the doubled stranded DNA will split back intotwo single stranded sections of DNA.To reproduce, a cell must copy and transmit its genetic information(DNA) to all of its progeny. To do so, DNA replicates, followingthe process of semi-conservative replication. The two strandsseparate and each strand of the original molecule acts as a templatefor the synthesis of a new complementary DNA molecule.DNA is permanent/long term copy of the cells information kept inthe cell’s nucleus. To express the information in the DNA, a singlestranded copy of the bases is made. This single strand is known asRNA, and it uses the base uridine (U), in place of the base T. DNAserves as the template to make RNA. This process is known astranscription where information in the form of a sequence ofbases is transferred from a double stranded DNA molecule to asingle stranded RNA molecule, as shown to the right. Eachgroup of three bases in RNA (a codon) code for a protein (seethe diagram below right). The amino acids and the codons thatcode for each are given in Table 1.The RNA code is converted to a sequence of proteins in theribosome in a process called translation. The section of theDNA that is transcribed as a unit is known as a gene, and startswith a start sequence (start codon, e.g. AUG or GUG) andfinishes with a end sequence (stop codon, e.g. UAG etc).
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