How to visualize unique and overlapping genes in upSet R plot
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Entering edit mode
8 weeks ago

Hello everyone

I am still a newbie in the field of bioinformatics. I have been attempting to visualize unique and common genes across six different tissues using the UpSetR plot package. This script was used to generate the plot; however, out of the six tissues, only six could be on the plot.

library(data.table)


library(UpSetR)


d <-  data.table::fread(text = "Brainstem   Cerebellum  Olfactory Bulb  Heart   Kidney  Liver
    Rac3    Coq9    Ndufs7  Slc25a10    Aacs    Acss3
    Ndufb5  Mtnd5   Cotl1   Adhfe1  Aass    Cyp4v2
    Clic6   Kpna4   Gabarapl2   Ddx5    Abcc4   Slc7a2
    Rbmx    Snrpg   Rbm3    Pgd Acot12  Ehhadh
    Ptcd3   Micos13 Atp5f1e Gss Acsf2   Selenbp2
    Ndufa13 Ndufa5  Ndufb3  Arl3    Acsm3   Ugt2b17
    Amt Ndufa10 Cstf3   Shmt2   Acy3    Gstp1
    Ndufs1  Bcr Mtco2   Tpt1    Adk Pdk1
    Acan    Mpc1    Bcap31  Me1 Ahcyl1  Bgn
    Wasl    Cfdp1   Ndufaf2 Abcg2   Aif1l   Col4a2
    Rbm3    Rps15   Gfap    H1-1    Akr1b1  Ttn
    Mtnd5   Snu13   Atp6v0c Pcbp2   Amacr   Cox6b1
    Ddc Lin7c   Tmed10  Ddx17   Atp2b1  Mup2
    Tmc7    Ndufb5  S100a5  Slc25a1 Ca5b    Cyp2d9
    Erc1    Ampd3   Ap3b1   H1-3    Cbr1    Cyp2b10
    Nup35   Ipo5    Gja1    Cstb    Cbr3    Ftl1
    Ndufb2  Ndufb10 Ndufb7  Tst Ces1f   Cyp8b1
    Ndufb1  Ebp Ciapin1 Vat1    Cnpy2   Rbm3
    Rexo2   Rabac1  Ndufb4  Glul    Col1a1  Ehd1
    Cbln3   Wdfy2   Adk Rpl29   Col1a2  Cyp4a10
    Arfgef3 Clcn6   Gfpt1   Pc  Col4a1  Ndufaf2
    Dagla   Vbp1    Rpl28   Acy3    Col4a2  Cops2
    Slc25a31    Nae1    Dgkz    Akr1a1  Cox7a1  Cyp2a4
    Tph2    Gucy1a1 Tpbg    Pecr    Cpne5   Rbp1
    Actbl2  Ap1s1   Gprc5b  Hnrnpd  Creg1   S100a13
    Ndufb9  Ndufs1  Acyp2   Serpina1c   Crot    Gsta4
    Timm10b Ndufa3  Kirrel2 Hsd17b11    Cryab   Ldhb
    Syt12   Ndufs4  Ndufb11 Rpn1    Cyp2d26 Dhtkd1
    Unc13c  Dnajb4  Ndufb10 Acly    Cyp2d9  Ndufb7
    Serpina1d   Chmp4b  Wdr6    Atp6v1b2    Cyp2j6  Acot13
    Yme1l1  Pdcd6   Mpst    Pxmp2   Cyp4a10 Fmo3
    Aprt    Ndufaf2 Smdt1   Arpc3   Cyp4a14 Clta
    Mtnd1   Igsf21  Sec61g  Kpna6   Cyp4b1  Eftud2
    Jpt2    Stxbp3  C1qb    Atp6v1g1    Cyp7b1  Tex15
    Ndufv3  Ndufb1  Ndufa2  Slc25a31    Ddc Ndufs1
    Chordc1 Tpd52l2 Hddc2   Aldh3a2 Dpyd    Sult1c2
    Cbln1   Sh3gl1  Agfg1   Gng12   Echdc3  Srl
    Rbbp4   Pnn Manf    Tmpo    Eea1    Aimp1
    Ndufaf2 Prodh   Kcnj10  Acox1   Ehhadh  Cyp2b9
    Egfr    Exoc7   Ptgds   Rhoa    Folh1   Cyp4a14
    Ca4 Ubxn1   Rpa3    Mapre1  Fth1    Csad
    Vps33b  Nfu1    Eif3e   Gk  Ftl1    Gck
    Ndufb11 Etnppl  Isg15   Rps2    Gsta2   Ss18l2
    Gatad2b Spock1  Tmsb10  Atp6v1e1    Gsta3   Hebp1
    Scn8a   Tagln2  Chmp1a  Sult1d1 Gsta4   Mup20
    Ensa    Cbln1   Mobp    Plin1   Hacl1   Nudt7
    Hkdc1   Sart3   Mtmr9   Idh1    Hmgb2   Tmem19
    Ndufa5  Ndufs6  Ptprf   Cpne1   Hmgcs2  Mup18
    Prpf6   Tagln   Hmox2   Prodh   Hmgn2   Selenbp1
    Glipr2  Ndufs8  Ptprd   Asl Hpd Mpp1
    Serpina3k   Drc7    Pmm1    Stmn1   Hsd3b2  Gstt2
    Serpina1a   Hspg2   Pde6d   Abhd14b Iqgap2  Tmco1
    Camk2g  Aamdc   Ipo7    Cryz    Krt18   Slc30a5
    Nmnat1  Rpl26   Ndufc2  Amacr   Krt7    Hsd17b6
    Tbcd    Nmral1  Csde1   Hmgb2   Krt8    Dusp3
    Ckm Uck1    Itpa    Sfxn1   Ldhd    Aass
    Mtif2   Lysmd2  Ndufa5  Acad11  Lmnb2   Sh3bgrl3
    Hmgn5   Sars2   Actr3b  Alox12  Lsm6    Tex44
    Tmem245 Cep170b Meis2   H2ac20  Mapre1  Cyp7b1
    Cbx3    Bzw1    Bcas3   Csad    Mbp Tymp
    Gjc3    Apex2   Ensa    Ucp1    Mpv17l  Fth1
    Ugt8    Nucks1  Serpina1a   Gpd1    Mrpl22  Serpina3m
    Lsmem1  Ndufb6  Serpina3k   Xab2    Mrpl23  Ces3a
    Rbsn    Cp  Tnks1bp1    Adh1    Mrpl40  Trmt112
    Cpped1  Npm1    Prnp    Dcps    Mrps26  Rdh16
    Arpp19  Rhoa    Uap1l1  Dhx9    Myh6    Ndufs4
    Ndufa6  Ndufa8  Ndufs3  Ezr Ndufa10 Hspa1b
    Ndufs2  Ndufb2  Ndufv2  Sri Ndufa12 Ndufv1
    Mug1    Ndufv2  Ndufs4  Ptrh2   Ndufa2  Sult1d1
    Ndufs8  Nek9    Cltb    Mecr    Ndufa5  Acot3
    Ndufb7  Ndufa12 Ndufa12 Sqor    Ndufa6  Ndufa12
    Ndufv1  Ndufs5  Wdfy2   Echdc2  Ndufa7  Upb1
    Ndufs3  Ndufa2  Ndufa10 Fabp1   Ndufa9  Ttc39c
    Dnah8   Lin7b   Mtnd1   Atp2a3  Ndufaf2 Sult1a1
    Ndufc2  Nek7    Ctsa    Gsr Ndufb7  Sqor
    Ndufa10 Ndufs3  Ndufv3  Adrm1   Ndufs1  Aox3
    Ndufs7  Ndufv1  Ndufs6  Egfr    Ndufs2  Sult2a8
    Ndufs5  Ndufb4  Clybl   Gmpr    Ndufs3  Hyou1
    Gcfc2   Ndufa9  Stat1   Gdap2   Ndufs4  Egfr
    Ndufb3  Ndufa13 Rpl23   Ywhaq   Ndufs6  Ndufa7
    Ndufb4  Ndufv3  Ndufv1  Serpina1e   Ndufv1  Ndufa6
    Ndufa12 Ndufs7  Rif1    Lta4h   Ndufv2  Ndufa9
    Ndufb8  Ndufb3  Ndufb8  Kifbp   Ndufv3  Srd5a1
    Serpina1e   Pgam2   Capg    Psma4   Nqo1    Mpc1
    Ndufb10 Ndufc2  Amt Mtr Nucks1  Keg1
    Ndufs6  Ndufa6  Ndufs1  Cps1    Nudt19  Serpina3k
    Fam136a Cltb    Cep170b Ehhadh  Pals2   Gsta2
    Ndufv2  Ndufb11 Ndufa13 Flii    Pecr    Gstt3
    Ndufa11 Pcdhga4 Vwa1    Aldob   Ppid    Metap1d
    Ndufa1  Mif Tinagl1 H1-4    Ptprk   Igf2bp3
    Ndufb6  Ndufb9  Ndufa11 Kyat3   Pyroxd2 Ndufs5
    S100b   H1-0    Actl6b  Coasy   Rbm3    Nudt19
    Acta1   Rpl29   Ndufa8  Snrpe   Reep6   Atp6v1g1
    Ndufa2  Ndufs2  Lsmem1  Vta1    Retsat  Maoa
    Nfia    Acad8   Ilk Osbpl8  Sephs2  Mgst3
    Ndufa7  Ndufa11 Ndufa7  Agpat2  Serpina3m   Comt
    Ndufa8  Ech1    Ndufs5  Clic1   Sh3bgrl3    Mat1a
    Ndufs4  Chmp2a  Msn Macroh2a1   Slc12a3 Acot4
    Alas1   Micos10 Nup85   Sars1   Slc22a27    Fuom
    Phyhd1  S100b   Nucks1  Pabpc1  Slc22a6 Mrpl14
    Mtnd4   Synpr   Tceal3  H2ac21  Slc6a19 Serpinb1a
    Ndufa9  Ndufa7  Ndufa9  Nudt8   Stat1   Ces3b
    Cdh10   Gnpda2  Cep152  Krt18   Tor1aip1    Prelp
    Ring1   Rbfox2  Etnppl  Fuom    Ugt1a2  Mup3
    Tmsb10  S1pr1   Acta1   Cyb5b       Cyp2c37
    Mrpl43  mt-Nd2  Myh11   Slc25a35        Col12a1
    Icmt    Rnps1   Ddx46   Rbm3        Endov
    Ncln    Ap3s1   Slc44a2 Gpd1l       S100a9
    Gh1 Rbx1    Ndufa6  Lrrc59      Slc25a4
    Bola3   Cat Ifit1   Hmgn2       Lum
    Ahsg    Atp5if1 Vps52   Tkt     Myl1
    Pdlim1  Rpl18a  Rac2    Hmgb1       Col1a1
    Ca3 Cyp51a1 Tmco5b  H1-2        Tpm2
    Crim1   Pkn1    Bclaf1  H4c1        Myh7
    Supt4h1a    Ppp3r1  Ube2v2  Stat1       Dcn
    S100a9  Sltm    Atp5if1 Aldh9a1     Cyfip1
    Shisa6  Chmp7   Mcm6    Elavl1      Phf11
    Adcy5   Bcl7c   Vac14   H2bc7       Cse1l
    Slc4a2  Lama5   Aqp1    H1-5        Col1a2
    Rgs8    Prnp    Hnrnpul1    Fah     Fabp3
    Asph    Nup85   Dnajc5  Aldh1l2     Acta1
    Hsd17b2 Iah1    Fam136a H3-5        Myh8
    Prx Mbnl2   Ublcp1  H2ac4       Ogn
    Bzw2    Rbm3    Cmtm5   Ldhd        Soat2
    Mboat4  Hdgfl3  Nipa1   Cryl1       Sf3b5
    Cep76   Hacd2   Bzw1    Ncl     Btk
    Cacna1e Asph    Tgm2    Gpd2        Cela1
    Ldhd    Lpcat4  Akr1e2  Ndrg1       Uap1
        Iqsec3  Nek7    Acacb       Actn2
        Kyat3   Gabbr1  Rcc2        Tnnt3
        Hnrnpul1    Pld2    Fgb     Upp2
        Atp5f1e C1qa    Ces1f       Tgtp2
        Mrps21  Irgm1   Gclc        Tpm1
        Itpa    Try5    Pvalb       Myh1
        Sec61g  Alg2    Bdh1        Tex264
        Acads   Pik3c3  Sord        Amy2a5
        Poldip2 Dynll2  Ssb     Cela2a
        Rpl36a  Ckm Fabp4       Ckmt2
        Slc6a5  Gstm5   Apoc4       Fmod
        Fn1 Urod    Bpnt1       Des
        Usp19   Rbbp7   Fasn        Ckm
        Prtn3   Ociad1  Hcfc1       Myl3
        Sh3bgrl Rpl29   Cyp4b1      Try5
        Gclm    Ngef    Ganab       Nrde2
        Egfr    Cryab   Tkfc        Ctrb1
        Mobp    Rnps1   Acaca       Ldb3
        Abhd3   Ugdh    Cbr2        
        Cirbp   Iglon5  Lipe        
        Mast1   C1qc    Hnrnpa3     
        Slc44a2 Eif2b4  Septin9     
        Magi2   Ythdf3  Hnrnpf      
        Spag7   Rps15   Hnrnpab     
        C1qbp   Atg4b   Sfxn3       
        Pllp    Pvalb   Ctsz        
        Smad3   Lig1    Coro1c      
        Exoc6b  Ehd1    S100a11     
        Chtop   Fn3krp  Ssrp1       
        Hmgn2   Cxadr   Ptbp1       
        Abhd6   Tmem186 Rac2        
        Cers1   Lsm4    Nup85       
        Dsg2    Rpl10   Nherf1      
        Arl8b   Ca1 Coro1a      
        Rbck1   Mindy2  Atp6v1a     
        Abhd4   Rcc1    Arpc1b      
        Frrs1l  Sart1   Krt8        
        Rnf214  H3-5    Ruvbl1      
        Cdc42ep1    H1-0    Pck1        
        Sf3a3   Clca3a1 Hnrnpc      
        Metap2  Lpcat4  Rida        
        Eif2b4  H2-K1   Ces1d       
        Inpp5f  S100a13 Smarcc2     
        Urod    Trappc4 Ewsr1       
        Nmt2    Ca4 Akr1c21     
        Alg11   S100a4  Serpina3m       
        Rad23b  Hbb-b2  Chmp1a      
        Drap1   Celf1   Actbl2      
        Hddc2   Rap2a   Ndufa1      
        App Ca8 Ndufs4      
        Cpsf6   Fgg Rala        
        Ppp2r5c Ube2fb  C8a     
        Kiss1   Eif3k   Mug1        
        Rgs6    Ctnnbl1 Rrp12       
        Txndc9  Timm10  mt-Nd2      
        Ehd4    Uvrag   Apoa2       
        Slc25a31    Arid1a  Ndufaf2     
        Cpped1  Krt8    Mtx1        
        Rbm27   Bpifb9a N6amt1      
        Cmtm5   Col1a2  Mrpl49      
        Gh1 Actbl2  Ndufs6      
        Elp3    Evl Cisd1       
        Atp6v0c Rpl39   Ndufa12     
        Ints3   Col6a1  Serpina3k       
        Tmem68  Map4k1          
        Tiam1   Atp6v1e2            
        Cox7a2l Col1a1          
        Arfgef3 Rpl35           
        Higd1a  Cpsf6           
        Ptgds   Lum         
        Eny2                
        Tmsb10              
        Per2                
        Tatdn1              
        Rpl30               
        Irag2               
        Otud6b              
        Myl1                
        Akap10              
        Cav1                
        Fbxl20              
        Adh1                
        Ehhadh              
        Atp4a               
        Naga                
        Tceal3              
        Col1a1              
        Celf1               
        Cops6               
        Vps11               
        Dync1i2             
        Hm13                
        Eif2s2              
        Fgg             
        Ralgapa1                
        Ipo7                
        Tmod3               
        Fgb             
        Phpt1               
        Eif3j2              
        Lars2               
        Snrpb2              
        Mug1                
        Slc4a1              
        Arg1                
        Celf2               
        Actbl2              
        Krt6a               
        Fga             
        Ufd1                
        Fam136a             
        Ntmt1               
        Opalin              
        Omp             
        Acsf3               
        Lig3                
        Xpo5                
        Tmem240             
        Aldob               
        Adprs               
        Stx1a               
        H2bc14              
        Serpina1d               
        Cldn11              
        Cyp2j5              
        Slc6a11             
        Cpm             
        Acp2                
        Ca1             
        Cd44                
        Cplx2")             




fld <- fromList(as.list(d))


upset(fld)

As it can be seen in the figure below, only five tissues could be seen, with the exception of the kidney, even in the presence of overlapping genes between the kidney and other tissues. Can you kindly assist in this regard, I do not know if there is something wrong with my input data or the script itself.enter image description here

R Proteomics UpsetR • 272 views
ADD COMMENT
1
Entering edit mode

The format of your data is not optimal because you have gene lists of different length. It would be more convenient to create a list of named vectors as recommended in the package documentation.

Except that, you could play with the arguments to customize your plot. In your case, you should increase the nsets argument to 6 : upset(fld,nsets=6)

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0
Entering edit mode

Let me try it, thank you.

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