Gene Expression Study of Arachis Hypogaea L.

Figure 6. Pairwise similarities of three RNA-Seq samples.

3. Gene density plot

groupingsȱ ofȱ conditionsȱ andȱ Figureȱ 6ȱ providesȱ

Figureȱ3ȱshowsȱgeneȱdensityȱplotȱofȱthreeȱRNA-Seqȱ

theȱ csDistHeat()ȱ methodȱ toȱ visualizeȱ theȱ pairȱ wiseȱ

samples,ȱ whichȱ showsȱ theȱ distributionsȱ ofȱ FPKMȱ

similaritiesȱbetweenȱthreeȱconditions.

scoresȱacrossȱthreeȱsamplesȱwithȱdifferentȱscores.

Conclusion

4. Dendrogram

Next-generationȱ sequencingȱ (NGS)ȱ hasȱ becomeȱ aȱ

Figureȱ4ȱshowsȱtheȱdendrogramȱofȱthreeȱRNA-Seqȱ

feasibleȱmethodȱforȱincreasingȱsequencingȱdepthȱandȱ

samplesȱforȱthreeȱdifferentȱconditions.ȱSampleȱthreeȱ

coverageȱwhileȱreducingȱtimeȱandȱcostȱcomparedȱtoȱ

isȱdistantlyȱrelatedȱwithȱrespectȱtoȱsamplesȱoneȱandȱ

theȱtraditionalȱSangerȱmethodȱ(LȱJȱCollinsȱ et al. 2008).ȱ

two.ȱWhileȱsampleȱoneȱandȱtwoȱshareȱcommonȱnodeȱ

Thereȱareȱseveralȱsoftwareȱpackagesȱexistsȱforȱshortȱ

formȱaȱclade.ȱ

readȱalignment,ȱandȱrecentlyȱspecializedȱalgorithmsȱ

forȱ transcriptomeȱ alignmentȱ haveȱ beenȱ developed,ȱ

5. Volcano plots

e.g.ȱTopHat2ȱforȱaligningȱreadsȱtoȱaȱreferenceȱgenomeȱ

toȱ discoverȱ spliceȱ sites,ȱ Cufflinksȱ toȱ assembleȱ theȱ

Figureȱ5ȱshowsȱtheȱvolcanoȱplotsȱofȱthreeȱRNA-Seqȱ

transcriptsȱ andȱ compare/mergeȱ themȱ withȱ othersȱ

dataȱinȱwhich,ȱredȱdotsȱshowsȱsignificantȱgenesȱwhileȱ

andȱCummeRbundȱisȱdesignedȱtoȱhelpȱsimplifyȱtheȱ

blackȱdotsȱshowsȱnon-significantȱgenes.

analysisȱ andȱ explorationȱ portionȱ ofȱ RNA-Seqȱ dataȱ

derivedȱfromȱtheȱoutputȱofȱaȱdifferentialȱexpressionȱ

6. Similarities between conditions

analysisȱ usingȱ Cuffdiffȱ withȱ theȱ goalȱ ofȱ providingȱ

Similaritiesȱ betweenȱ conditionsȱ canȱ provideȱ usefulȱ fastȱandȱintuitiveȱaccessȱofȱresults.ȱ(LȱJȱCollinsȱ et al.

insightȱ intoȱ theȱ relationshipȱ betweenȱ variousȱ 2008).ȱ

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