轉(zhuǎn)錄組常用圖形解讀瑞客

提前預(yù)仔細聽先運行再理緊跟步伐，跟不上的及時在課堂提出或?qū)ふ抑汤蠋熃庹n后復(fù)習(xí)，基礎(chǔ)知識學(xué)習(xí)靠背和反復(fù)書讀百變，其義自碼敲十遍，不會也2NGSFASTQ3位數(shù)、最大值；然后在圖上分別給予合適的標(biāo)記 Spitzer,Michaela,etal.BoxPlotR:awebtoolforgenerationofboxNaturemethods,11(2), 腫瘤樣本純度得分箱線

ABSOLUTE計算的腫瘤6腫瘤大小散點Tumourvolumeforindividualanimals(dots)onthedayofeuthanasiaintheconditionsindicated.Dataaremean±s.d. 單細 表達小提琴8Jitter-plot展示差 分Log2foldrelativeRNAprobedistributionshowingdifferentialgeneexpressionfrombonemarrow-derivedmacrophages(BMDMs)treatedinvitrowithmockorAza+ITF-2357.Angiogenicpathway-associatedgenesarehighlighted(microarray,BMDMdatarepresentativeofn=3mice). 差異OTU火山圖展 Molecularsignaturesofantibodyresponsesderivedfromasystemsbiologystudyoffivehuman 自對照樣品或樣品兩兩相比散點圖展Scatterplotoflog2FCofgenesfromReactomeG1pathwayineachLibrary1screen.Eachpairwisecomparisonisindicatedbycolor.Pearson’sproductmomentcorrelationcoefficientisindicated(r).展示某個通的在不同樣本表達的相對ProfoundTissueSpecificityinProliferationControlUnderliesCancerDriversandAneuploidy表達散點Dotplotvisualizationofeachcelltypeinlungsingle-celldata.Thesizeofthedotencodesthepercentageofcellswithinacelltype,andthecolor averageexpression theMouseCellAtlasbyMicrowell- GSEA–unsignedlog2FoldChange（差 GSEAysisofexpressedpredictedpost-transcriptionaldecoytargetsinMDA-MB-231;allexpressedgenesweresortedbysiOIP5-AS1toNTabsolutefoldchanges,GSEAusedweightedenrientstatisticsandratioofclasses,withp-valuescomputedusing1kgene-setpermutations.Cell GSEA–unsignedlog2FoldChange（差 HSCgene setsarenegativelyenrichedinZNF384r.

upregulatedinETP-ALL(astem

otherB-ALLcases.Nature GSEA的展示方式二Commoncell-essentialgenesareinvolvedinfundamentalbiologicalprocesses.GenesetenrientysiswasperformedongenesrankedbyaverageCS(crisprgenescore).EpigeneticmodificationlevelandGenesetenrientplotshowingthatgenesassociatedwithhighlevelsofH3K9acandH3K27acareenrichedfortwoindependentlydefinedpluripotencygenesets:MullerPluriNetandWongESCCorePvaluesarecalculatedbasedon1,000permutationsbytheGSEAalgorithmandwerenotadjustedformultiplecomparisons.Naturecell 相關(guān) 的GSEA富集分篩選與 表達顯著正相關(guān)和負相關(guān)的相關(guān)性系數(shù)作 值進行GSEA分析901個MFGO條目去冗余為396個MF條目，用做檢測基因集(條目 集重合小于75%)熱圖每一行為一個條目，每一列為一種 顏色表 normalizedenri entscoreGSEA標(biāo)準(zhǔn)化富集得分(NES)熱圖GSEAwasperformedusingPreRankedweightedmode.Log2FCvaluesforeachscreenwerecomputedintoZscores,andtheaverageZscoreofallORFscorrespondingtoagivengenewascalculated,andusedtogeneratetheGSEArankorderedlist.GSEAwasrunconsideringallthecanonicalpathwaysgenesets(c2.cp.V5.1.symbols)excepttheminimumgenesetsizewasreducedto10(fromdefault=15),tocompensateforthesmallersizeofthisdataset.Redundantgenesetswereexcluded(including,insomecases,genesetsthatwerenon-redundantinnamebutcontainedsimilargenes)andadditionalgenesetsaddedsothateachscreenhadatotaloftengenesetssetsGSEA通路FDR和NES 富集分析泡泡樣本突變數(shù)目分每 所有樣品過濾后的突變中每個樣本按過濾后的突變數(shù)（深藍點）排序，淺藍點表示未過1萬個shRNA敲除細胞系對Oct4表達的MediatorandcohesincomponentswerehighlyrepresentedinanshRNAscreenforregulatorsofEScellstate.增強子和超級增強子的ChIP結(jié)合圖Metagenerepresentationsofthemean

s.Metagenesarecenteredontheenhancerregion,andthelengthoftheenhancerreflectsthedifferencein

enhancers).Additional3kbeachenhancerregionisalso Meta-gene

的結(jié)合位點分布。Random把啟動 生存曲線折線Cell轉(zhuǎn)錄因子結(jié)合Tabledepictingtranscriptionfactorbindingmotifsenrichedatconstituentenhancerswithinsuper-enhancerregionsandassociatedpvalues.R繪制 繪制motif組瀏覽器展示多組學(xué)信BindingprofilesforEScelltranscriptionfactors(Oct4,NanogandSox2),mediator(Med1andMed12),cohesin(Smc1a,Smc3andNipbl),CTCFandcomponentsofthetranscriptionapparatus(Pol2andTBP)attheOct4andNanogloci.ChIP-Seqdataareshowninreadspermillionwiththeyaxisfloorsetto0.5readspermillion.Oct4/Sox2,CTCFandTBP(TATAbox)sequencemotifsareindicated.Sashimiplotsaroundanactivatedexonwithinthe3′UTRoftheHNRNPDLgene(inclusionofwhichcreatesanNMD-substratetranscript)ineithertheabsenceorpresenceofMAGOHBknockdownineitherChagoK1cellsorMAGOH-V5reconstitutedChagoK1cells.Numbersreflectjunctionspanningreadsaveragedoverthreereplicatesforeachcondition. TAD三維 OSNandMed1attheKlf4locus

(normalizedinctioncounts)andgenomiccoordinatescomprisingaportionofa (Dixonetal.,2012)areindicatedabovethebindingprofiles.Venn圖和ChIP-seq信號熱Venndiagramshowingtheoverlapofhigh-confidence(P<10?9)cohesin(Smc1a)occupiedsiteswiththoseboundbyCTCF,mediator(Med12)andNipbl.c,RegionmapshowingthatSmc1a,NipblandMed12co-occupiedsitesgenerallyoccurincloseproximitytoPol2andintheabsenceofCTCF.ForeachSmc1aoccupiedregion,theoccupancyofMed12,Nipbl,Pol2andCTCFisindicatedwithina10-kbwindowcentredontheSmc1aregion.與PCA聚類相似的是相關(guān)系數(shù)層級聚類，也可以展示樣品之間的同時可以增加樣品的屬性信息借以查看不同的屬性信息與分組的關(guān)系，從而確定有沒有哪些意料相關(guān)性熱圖加樣本屬性標(biāo)小鼠不同株野生型和KLA處理組 ClusteredSpearmancorrelationmatrixfordifferentRNA-seqreplicatesfornotreatmentandKLA1h. OTU與表型相關(guān)性熱 前期差異分類單元(每一列)與臨床指標(biāo)(每一行)之。。Aberrantintestinalmicrobiotainindividualswith 差異OTU豐度熱 Rootmicrobiotashiftinricecorrelateswithresidenttimeinthefieldanddevelopmentalstage lncRNAs調(diào)節(jié)的轉(zhuǎn)錄因子和RNA結(jié)合蛋白 lncRNAs,includingOIP5-AS1,NEAT1, modulateregulatorsofTFsandRBPs expressionofthetargetsoftheseTFsandRBPs.The40lncRNAswiththemostTFandRBPtargetsandthe40mostfrequenttargetTFsandRBPs predictedin ctionsacrossthe14tumortypesisgivenatright. 每組樣品共有和特有Gene 組的所有。的部分表示樣品組之間都表達的。每個圈特有的部分表示樣品特異表達的。中間的219表示3個樣品組中都表達的。注：表達的OTU是個偽概念，只能說聲高于某個表達水平的或篩選出的特異高表達的。 UpSetView

的數(shù)目。單個點表示單個樣品組特有。因。三個點相連表示三個樣品共有的。擬桿菌門、厚壁菌門OTUs在不同季節(jié)中物種動態(tài)變化；隨著時間變化，哪些OTUs保留 ，哪些新來的，以及在每個階段中的變化SeasonalcyclinginthegutmicrobiomeoftheHadzahunter-gatherersofTanzania.miRNA- 和通路的關(guān)系諾貝兒化學(xué)獎獲得者屬性分布?；S恩，UpSetView，?；鶊D的繪輸入數(shù)據(jù)都可以是如下格式，第一列是OTU的名字，第二列是OTU從屬于哪個樣品分組，如果一個OTU從屬于多個樣品分組，分不同的行分別錄入。直接拷貝到ImageGP每個對應(yīng)的圖的Datamatrix中即可繪制。樣本聚類PCA分主成分分析(PCA,principalcomponentysis)是一種數(shù)學(xué)降維方法,利用假 個 以 層樣果個 可以在一個平面對樣本分類；如果有個 如果有 的 ，比如說個，那么每個樣品就是n 上展示樣品的分類關(guān)系。利用分析，我們可以選取貢獻最大的個或的 。PCA實現(xiàn)原PCA分析不是簡單地選取2個或3個變化最大的，而是先把原始的PCA結(jié)果展不同預(yù)處理對PCA結(jié)果的影不同標(biāo)準(zhǔn)化的本質(zhì)在于研究者認為是數(shù)值的量度本身重要還是數(shù)值的變化數(shù)值的量度重要則選擇原始數(shù)據(jù)或log數(shù)值的變化重要則PCA繪制的輸入和輸tSNE聚類t-Distributedstochasticneighborembedding(t-SNE)ysisof60,000singlecell