Commit e9dcd68b authored by mcariou's avatar mcariou
Browse files

update dataset

parent c3386bb1
x
ACAD9
ACADM
ACE2
ADAM9
AGPS
AKAP9
ATP6AP1
CDK5RAP2
CISD3
COL6A1
EDEM3
ERGIC1
GGH
......@@ -13,13 +20,20 @@ IMPDH2
INHBE
ITGB1
LMAN2
MARK2
MIPOL1
MOV10
NUP214
POLA1
PRIM1
PUSL1
RAB18
RAP1GDS1
SCCPDH
SLC27A2
SLC30A9
SLC44A2
SLC9A3R1
TBK1
TOR1AIP1
VPS39
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......@@ -29,7 +29,7 @@
Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
<<>>=
<<eval=FALSE>>=
workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
tab<-read.delim(paste0(workdir,
......@@ -38,6 +38,15 @@ dim(tab)
@
<<>>=
workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
tab<-read.delim(paste0(workdir,
"covid_comp/covid_comp_alldginn.txt"), h=T, sep="\t")
dim(tab)
@
\section{Comparison of dataset}
\subsection{Data}
......@@ -173,25 +182,25 @@ for (p in 0:5){
tmp<-tablo$`tmp$Gene.name`[tablo$nbats==0 & tablo$nprimates==1]
text(-0.4,-1.2, "p=1/n=0", cex=0.6)
text(seq(from=0.1, to=5.5, length.out = 18),-1.1, tmp[1:18], cex=0.4)
text(seq(from=0.1, to=3, length.out = length(tmp)-18),-1.3, tmp[19:length(tmp)], cex=0.4)
text(seq(from=0.1, to=5.5, length.out = length(tmp)-18),-1.3, tmp[19:length(tmp)], cex=0.4)
tmp<-tablo$`tmp$Gene.name`[tablo$nbats==1 & tablo$nprimates==1]
text(-0.4,-1.7, "p=1/n=1", cex=0.6)
text(seq(from=0.1, to=5.5, length.out = 18),-1.6, tmp[1:18], cex=0.4)
text(seq(from=0.1, to=2, length.out = length(tmp)-18),-1.8, tmp[19:length(tmp)], cex=0.4)
text(seq(from=0.1, to=4.5, length.out = length(tmp)-18),-1.8, tmp[19:length(tmp)], cex=0.4)
tmp<-tablo$`tmp$Gene.name`[tablo$nbats==0 & tablo$nprimates==0]
text(-0.4,-2.2, "p=0/n=0", cex=0.6)
text(-0.4,-2.3, "p=0/n=0", cex=0.6)
text(seq(from=0.1, to=5.5, length.out = 17),-2.1, tmp[1:17], cex=0.4)
text(seq(from=0.1, to=4.4, length.out = length(tmp)-17),-2.3, tmp[18:length(tmp)], cex=0.4)
tmp<-tablo$`tmp$Gene.name`[tablo$nbats==2 & tablo$nprimates==0]
text(-0.4,-2.7, "p=0/n=2", cex=0.6)
text(seq(from=0.1, to=5.5, length.out = 18),-2.6, tmp[1:18], cex=0.4)
text(seq(from=0.1, to=1, length.out = length(tmp)-18),-2.8, tmp[19:length(tmp)], cex=0.4)
text(seq(from=0.1, to=5.5, length.out = 17),-2.3, tmp[18:34], cex=0.4)
text(seq(from=0.1, to=5.5, length.out = length(tmp)-34),-2.5, tmp[35:length(tmp)], cex=0.4)
tmp<-tablo$`tmp$Gene.name`[tablo$nbats==2 & tablo$nprimates==0]
text(-0.4,-2.9, "p=0/n=2", cex=0.6)
text(seq(from=0.1, to=5.5, length.out = 18),-2.8, tmp[1:18], cex=0.4)
text(seq(from=0.1, to=1, length.out = length(tmp)-18),-3.0, tmp[19:length(tmp)], cex=0.4)
@
......@@ -206,3 +215,6 @@ write.csv(tablo, "primatesVbats.csv", row.names=FALSE, quote=FALSE)
\end{document}
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......@@ -2,21 +2,35 @@ tmp$Gene.name,nbats,nprimates
AAR2,0,0
AASS,2,0
AATF,0,1
ABCC1,1,2
ACAD9,3,1
ACADM,4,5
ACE2,5,5
ACSL3,0,1
ADAM9,3,3
ADAMTS1,0,0
AGPS,3,1
AKAP8,0,0
AKAP8L,0,1
AKAP9,4,2
ALG11,1,0
ALG5,0,2
ALG8,1,1
ANO6,2,2
AP2A2,1,3
AP2M1,0,1
AP3B1,1,1
ARF6,0,0
ATE1,0,3
ATP13A3,0,2
ATP1B1,2,0
ATP6AP1,4,1
ATP6V1A,1,1
BAG5,0,0
BCKDK,0,1
BRD2,1,0
BRD4,2,4
BZW2,0,3
CCDC86,0,0
CDK5RAP2,3,5
CENPF,1,2
......@@ -28,63 +42,94 @@ CEP68,1,5
CHMP2A,2,1
CHPF,0,2
CHPF2,1,1
CISD3,4,1
CIT,1,2
CLCC1,0,1
CLIP4,2,4
CNTRL,1,3
COL6A1,3,2
COLGALT1,2,1
COMT,2,0
COQ8B,1,0
CRTC3,1,2
CSDE1,0,1
CSNK2A2,0,0
CSNK2B,0,1
CUL2,2,0
CWC27,1,2
CYB5B,2,0
CYB5B,1,0
DCAF7,0,1
DCAKD,0,0
DCTPP1,0,0
DDX10,2,0
DDX21,1,1
DNAJC11,1,0
DNAJC19,0,0
DNMT1,1,5
DPH5,0,4
DPY19L1,0,0
ECSIT,0,0
EDEM3,5,3
EIF4E2,1,3
EIF4H,0,0
ELOC,2,0
EMC1,2,5
ERC1,1,1
ERGIC1,4,0
ERLEC1,0,2
ERMP1,2,0
ERO1B,0,4
ERP44,1,0
ETFA,0,0
EXOSC2,0,3
EXOSC3,1,0
EXOSC5,0,0
EXOSC8,0,0
F2RL1,1,0
FAM162A,0,0
FAM8A1,1,1
FAM98A,0,0
FAR2,2,2
FASTKD5,0,0
FBLN5,1,1
FBN1,2,2
FBN2,2,2
FBXL12,0,2
FKBP10,1,0
FKBP15,0,0
FKBP7,0,2
FOXRED2,2,0
FYCO1,2,5
G3BP1,1,1
G3BP2,1,0
GCC1,1,0
GCC2,0,4
GDF15,2,1
GFER,0,1
GGCX,1,0
GGH,5,5
GHITM,0,4
GIGYF2,1,4
GLA,1,4
GNB1,0,1
GNG5,0,1
GOLGA2,2,2
GOLGA3,0,1
GOLGA7,5,5
GOLGB1,2,3
GORASP1,0,3
GPAA1,2,0
GPX1,0,1
GRIPAP1,3,1
GRPEL1,3,0
GTF2F2,0,0
HDAC2,0,3
HEATR3,1,0
HECTD1,2,5
HMOX1,1,1
HOOK1,0,0
HS2ST1,2,0
HS6ST2,0,3
HSBP1,0,1
HYOU1,2,1
IDE,4,4
......@@ -93,80 +138,140 @@ IMPDH2,4,1
INHBE,5,0
INTS4,1,0
ITGB1,4,5
JAKMIP1,2,0
KDELC1,1,1
KDELC2,0,0
LARP1,1,4
LARP4B,0,4
LARP7,0,3
LMAN2,4,4
LOX,1,1
MAP7D1,0,1
MARC1,0,0
MARK1,1,4
MARK2,3,0
MARK3,2,1
MAT2B,0,0
MDN1,2,3
MEPCE,2,0
MIB1,2,0
MIPOL1,3,4
MOGS,0,0
MOV10,3,3
MPHOSPH10,1,4
MRPS2,0,1
MRPS25,1,0
MRPS27,1,2
MRPS5,2,3
MTCH1,1,0
MYCBP2,2,5
NARS2,1,1
NAT14,0,3
NDFIP2,0,1
NDUFAF1,0,2
NDUFAF2,0,5
NDUFB9,0,4
NEK9,2,0
NEU1,2,0
NGDN,0,0
NGLY1,1,3
NIN,1,0
NINL,0,2
NLRX1,1,2
NOL10,1,1
NPC2,0,3
NPTX1,1,0
NSD2,2,1
NUP210,2,2
NUP214,3,2
NUP54,0,0
NUP58,1,5
NUP62,1,1
NUP88,0,0
NUP98,0,1
NUTF2,0,1
OS9,0,0
PABPC1,0,0
PABPC4,1,2
PCNT,2,4
PCSK5,1,0
PCSK6,2,0
PDE4DIP,0,1
PDZD11,0,1
PIGO,0,1
PIGS,0,0
PITRM1,1,3
PKP2,0,1
PLAT,1,3
PLD3,0,1
PLEKHA5,0,0
PLEKHF2,2,0
PLOD2,1,3
PMPCA,0,2
PMPCB,2,3
POFUT1,2,1
POLA1,4,4
POLA2,1,0
POR,2,3
PPIL3,0,1
PPT1,1,0
PRIM1,3,2
PRIM2,0,5
PRKACA,1,0
PRKAR2A,1,4
PRKAR2B,1,2
PRRC2B,1,0
PSMD8,2,1
PTBP2,0,3
PTGES2,2,1
PUSL1,3,1
PVR,2,5
QSOX2,1,1
RAB10,0,0
RAB14,0,3
RAB18,5,1
RAB1A,0,3
RAB2A,0,3
RAB5C,0,2
RAB7A,0,1
RAB8A,1,0
RAE1,1,1
RALA,0,0
RAP1GDS1,5,3
RBM28,2,0
RBM41,0,2
RBX1,0,3
RDX,2,0
REEP5,0,0
REEP6,0,5
RETREG3,0,1
RHOA,0,0
RIPK1,2,4
RNF41,0,0
RPL36,1,3
RRP9,2,1
RTN4,1,2
SAAL1,1,4
SBNO1,2,2
SCAP,1,2
SCARB1,2,2
SCCPDH,3,3
SDF2,0,0
SEPSECS,2,5
SIL1,1,0
SIRT5,1,4
SLC25A21,0,4
SLC27A2,5,4
SLC30A6,0,0
SLC30A7,1,1
SLC30A9,3,0
SLC44A2,5,0
SLC9A3R1,3,0
SLU7,1,2
SMOC1,0,2
SNIP1,0,0
SPART,1,0
SRP19,0,1
SRP54,0,0
SRP72,1,1
STC2,0,0
......@@ -175,16 +280,24 @@ STOML2,0,0
SUN2,2,0
TAPT1,1,2
TARS2,0,1
TBCA,2,1
TBK1,5,2
TBKBP1,0,2
TCF12,0,1
THTPA,0,0
TIMM10,1,0
TIMM10B,0,0
TIMM29,1,1
TIMM8B,0,3
TIMM9,0,0
TLE1,2,1
TLE3,0,1
TM2D3,1,1
TMED5,2,0
TMEM39B,2,4
TMEM97,0,1
TMPRSS2,0,4
TOMM70,0,1
TOR1A,1,1
TOR1AIP1,5,5
TRIM59,0,3
......@@ -200,6 +313,10 @@ UPF1,0,0
USP54,1,3
VPS11,1,1
VPS39,5,5
WASHC4,2,2
WFS1,2,2
YIF1A,0,0
ZC3H18,1,1
ZC3H7A,1,1
ZDHHC5,1,2
ZNF318,0,5
......
x
ACADM
ACE2
ADAM9
AP2A2
ATE1
BRD4
BZW2
CDK5RAP2
CEP135
CEP68
CLIP4
CNTRL
DNMT1
DPH5
EDEM3
EIF4E2
EMC1
ERO1B
EXOSC2
FYCO1
GCC2
GGH
GHITM
GIGYF2
GLA
GOLGA7
GOLGB1
GORASP1
HDAC2
HECTD1
HS6ST2
IDE
ITGB1
LARP1
LARP4B
LARP7
LMAN2
MARK1
MDN1
MIPOL1
MOV10
MPHOSPH10
MRPS5
MYCBP2
NAT14
NDUFAF2
NDUFB9
NGLY1
NPC2
NUP58
PCNT
PITRM1
PLAT
PLOD2
PMPCB
POLA1
POR
PRIM2
PRKAR2A
PTBP2
PVR
RAB14
RAB1A
RAB2A
RAP1GDS1
RBX1
REEP6
RIPK1
RPL36
SAAL1
SCCPDH
SEPSECS
SIRT5
SLC25A21
......@@ -45,6 +77,7 @@ SLC27A2
STOM
TIMM8B
TMEM39B
TMPRSS2
TOR1AIP1
TRIM59
TRMT1
......
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