Commit 5a7cc518 authored by mcariou's avatar mcariou
Browse files

update comp datasets

parent 37bda7a4
......@@ -240,16 +240,13 @@ options(tidy=TRUE, width=70)
<<>>=
# Reading the Krogan table
tab<-read.delim(paste0(workdir,
"data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"),
"covid_comp/covid_comp_complete.txt"),
fill=T, h=T, dec=",")
dim(tab)
#Formating the column Gene.name and changing one wierd name
tab$Gene.name<-as.character(tab$Gene.name)
tab$Gene.name[tab$PreyGene=="MTARC1"]<-"MTARC1"
#Adding ACE2 and TMPRSS2
krogan<-c(tab$Gene.name, "ACE2", "TMPRSS2")
krogan<-c(as.character(tab$merge.Gene), "ACE2", "TMPRSS2")
# The list
length(krogan)
......
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......@@ -794,20 +794,16 @@ Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
\begin{alltt}
\hlcom{# Reading the Krogan table}
\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"}\hlstd{),}
\hlstr{"covid_comp/covid_comp_complete.txt"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{","}\hlstd{)}
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\begin{verbatim}
## [1] 332 84
## [1] 332 141
\end{verbatim}
\begin{alltt}
\hlcom{#Formating the column Gene.name and changing one wierd name}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[tab}\hlopt{$}\hlstd{PreyGene}\hlopt{==}\hlstr{"MTARC1"}\hlstd{]}\hlkwb{<-}\hlstr{"MTARC1"}
\hlcom{#Adding ACE2 and TMPRSS2}
\hlstd{krogan}\hlkwb{<-}\hlkwd{c}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name,} \hlstr{"ACE2"}\hlstd{,} \hlstr{"TMPRSS2"}\hlstd{)}
\hlstd{krogan}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{merge.Gene),} \hlstr{"ACE2"}\hlstd{,} \hlstr{"TMPRSS2"}\hlstd{)}
\hlcom{# The list}
\hlkwd{length}\hlstd{(krogan)}
......@@ -819,73 +815,73 @@ Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
\hlstd{krogan}
\end{alltt}
\begin{verbatim}
## [1] "PCNT" "PVR" "POLA1" "FASTKD5" "PRIM2"
## [6] "ITGB1" "CNTRL" "SIRT5" "CEP250" "MRPS5"
## [11] "CENPF" "TRMT1" "SAAL1" "CEP68" "NINL"
## [16] "AKAP9" "NDUFAF2" "GOLGB1" "UGGT2" "SEPSECS"
## [21] "ABCC1" "CDK5RAP2" "PDE4DIP" "ACADM" "PRRC2B"
## [26] "SLC25A21" "PUSL1" "NDUFB9" "TOR1AIP1" "MDN1"
## [31] "GCC2" "ERLEC1" "FYCO1" "GHITM" "GORASP1"
## [36] "USP54" "ATE1" "MRPS27" "VPS39" "CEP350"
## [41] "ALG11" "MPHOSPH10" "SLC27A2" "ALG8" "BCS1L"
## [46] "STOM" "NUP210" "GOLGA2" "EDEM3" "DCTPP1"
## [51] "GIGYF2" "UBAP2" "DDX21" "RAB18" "MARK1"
## [56] "PRIM1" "C19orf52" "ZNF318" "ALG5" "EXOSC3"
## [61] "UBXN8" "PABPC1" "LMAN2" "RIPK1" "JAKMIP1"
## [66] "TARS2" "NDUFAF1" "PCSK6" "ANO6" "SNIP1"
## [71] "DNMT1" "PRKAR2B" "PLEKHA5" "FKBP15" "KDELC2"
## [76] "FBN1" "NUP88" "ATP13A3" "TRIM59" "NPC2"
## [81] "MEPCE" "PLAT" "EXOSC8" "CEP135" "GCC1"
## [86] "MIPOL1" "YIF1A" "AASS" "GLA" "FAM162A"
## [91] "FBXL12" "EXOSC5" "NGDN" "ATP6AP1" "LARP7"
## [96] "SIL1" "NUP62" "NDFIP2" "COLGALT1" "ECSIT"
## [101] "EMC1" "AP3B1" "POLA2" "CLIP4" "SLU7"
## [106] "CLCC1" "ERO1LB" "ATP5L" "ERMP1" "HS6ST2"
## [111] "NUPL1" "EIF4H" "ZYG11B" "EXOSC2" "ADCK4"
## [116] "WFS1" "TAPT1" "SPG20" "NGLY1" "FAR2"
## [121] "CHMP2A" "NLRX1" "NUP214" "PIGO" "PITRM1"
## [126] "ATP1B1" "PPT1" "HYOU1" "TUBGCP2" "KDELC1"
## [131] "WHSC1" "GDF15" "NARS2" "AKAP8" "TBK1"
## [136] "BRD4" "GRIPAP1" "PRKAR2A" "MOGS" "SCAP"
## [141] "AATF" "BRD2" "FBN2" "AKAP8L" "OS9"
## [146] "SIGMAR1" "MTCH1" "LARP4B" "FAM134C" "ARL6IP6"
## [151] "RBM28" "MRPS2" "CEP112" "LARP1" "INHBE"
## [156] "AGPS" "MRPS25" "MTARC1" "F2RL1" "MFGE8"
## [161] "SLC9A3R1" "CWC27" "CYB5B" "MAP7D1" "IDE"
## [166] "PMPCA" "GGH" "QSOX2" "GNG5" "PKP2"
## [171] "PMPCB" "RRP9" "NIN" "CUL2" "ADAM9"
## [176] "TMEM39B" "RAB8A" "CYB5R3" "GPAA1" "TM2D3"
## [181] "COMT" "SLC30A9" "PLD3" "CHPF" "SRP19"
## [186] "FKBP7" "DDX10" "ATP6V1A" "AAR2" "VIMP"
## [191] "NAT14" "MYCBP2" "ERC1" "DCAF7" "FBLN5"
## [196] "CSDE1" "TCEB1" "RAB14" "BZW2" "VPS11"
## [201] "CIT" "SLC30A6" "DPY19L1" "RTN4" "AP2M1"
## [206] "RNF41" "TOR1A" "PSMD8" "SLC44A2" "MOV10"
## [211] "RAB10" "NEU1" "MIB1" "TYSND1" "USP13"
## [216] "ZC3H7A" "IMPDH2" "DNAJC11" "NEK9" "PLEKHF2"
## [221] "IL17RA" "GNB1" "GRPEL1" "ARF6" "FKBP10"
## [226] "PABPC4" "HMOX1" "FOXRED2" "NOL10" "SRP72"
## [231] "ZDHHC5" "PTGES2" "TMED5" "HOOK1" "POFUT1"
## [236] "SUN2" "ERP44" "PRKACA" "GOLGA3" "ADAMTS1"
## [241] "CSNK2B" "THTPA" "PIGS" "RBM41" "C1orf50"
## [246] "TMEM97" "RAB2A" "STC2" "SMOC1" "FAM98A"
## [251] "INTS4" "RAB7A" "HECTD1" "STOML2" "POR"
## [256] "CSNK2A2" "HS2ST1" "DCAKD" "SRP54" "SDF2"
## [261] "ZNF503" "SBNO1" "RAE1" "TUBGCP3" "UPF1"
## [266] "ERGIC1" "TLE1" "TOMM70A" "KIAA1033" "DPH5"
## [271] "UBAP2L" "CHPF2" "GFER" "TIMM8B" "RAB5C"
## [276] "GOLGA7" "TIMM10" "HSBP1" "BCKDK" "ACSL3"
## [281] "PDZD11" "GGCX" "RALA" "LOX" "TBKBP1"
## [286] "CCDC86" "NUP98" "SCCPDH" "SCARB1" "CRTC3"
## [291] "ETFA" "FGFR1OP" "SLC30A7" "HEATR3" "COL6A1"
## [296] "RDX" "G3BP1" "TCF12" "ZC3H18" "G3BP2"
## [301] "AP2A2" "PLOD2" "MARK2" "TIMM9" "TIMM10B"
## [306] "RHOA" "REEP5" "REEP6" "FAM8A1" "PPIL3"
## [311] "TLE3" "AES" "RAP1GDS1" "HDAC2" "GTF2F2"
## [316] "NUP54" "MAT2B" "TCEB2" "MARK3" "PTBP2"
## [321] "RPL36" "TBCA" "NUTF2" "EIF4E2" "GPX1"
## [326] "RAB1A" "DNAJC19" "RBX1" "CISD3" "NPTX1"
## [331] "BAG5" "ACAD9" "ACE2" "TMPRSS2"
## [1] "AAR2" "AASS" "AATF" "ABCC1" "ACAD9"
## [6] "ACADM" "ACSL3" "ADAM9" "ADAMTS1" "AGPS"
## [11] "AKAP8" "AKAP8L" "AKAP9" "ALG11" "ALG5"
## [16] "ALG8" "ANO6" "AP2A2" "AP2M1" "AP3B1"
## [21] "ARF6" "ARL6IP6" "ATE1" "ATP13A3" "ATP1B1"
## [26] "ATP5MG" "ATP6AP1" "ATP6V1A" "BAG5" "BCKDK"
## [31] "BCS1L" "BRD2" "BRD4" "BZW2" "C1orf50"
## [36] "CCDC86" "CDK5RAP2" "CENPF" "CEP112" "CEP135"
## [41] "CEP250" "CEP350" "CEP43" "CEP68" "CHMP2A"
## [46] "CHPF" "CHPF2" "CISD3" "CIT" "CLCC1"
## [51] "CLIP4" "CNTRL" "COL6A1" "COLGALT1" "COMT"
## [56] "COQ8B" "CRTC3" "CSDE1" "CSNK2A2" "CSNK2B"
## [61] "CUL2" "CWC27" "CYB5B" "CYB5R3" "DCAF7"
## [66] "DCAKD" "DCTPP1" "DDX10" "DDX21" "DNAJC11"
## [71] "DNAJC19" "DNMT1" "DPH5" "DPY19L1" "ECSIT"
## [76] "EDEM3" "EIF4E2" "EIF4H" "ELOB" "ELOC"
## [81] "EMC1" "ERC1" "ERGIC1" "ERLEC1" "ERMP1"
## [86] "ERO1B" "ERP44" "ETFA" "EXOSC2" "EXOSC3"
## [91] "EXOSC5" "EXOSC8" "F2RL1" "FAM162A" "FAM8A1"
## [96] "FAM98A" "FAR2" "FASTKD5" "FBLN5" "FBN1"
## [101] "FBN2" "FBXL12" "FKBP10" "FKBP15" "FKBP7"
## [106] "FOXRED2" "FYCO1" "G3BP1" "G3BP2" "GCC1"
## [111] "GCC2" "GDF15" "GFER" "GGCX" "GGH"
## [116] "GHITM" "GIGYF2" "GLA" "GNB1" "GNG5"
## [121] "GOLGA2" "GOLGA3" "GOLGA7" "GOLGB1" "GORASP1"
## [126] "GPAA1" "GPX1" "GRIPAP1" "GRPEL1" "GTF2F2"
## [131] "HDAC2" "HEATR3" "HECTD1" "HMOX1" "HOOK1"
## [136] "HS2ST1" "HS6ST2" "HSBP1" "HYOU1" "IDE"
## [141] "IL17RA" "IMPDH2" "INHBE" "INTS4" "ITGB1"
## [146] "JAKMIP1" "LARP1" "LARP4B" "LARP7" "LMAN2"
## [151] "LOX" "MAP7D1" "MARC1" "MARK1" "MARK2"
## [156] "MARK3" "MAT2B" "MDN1" "MEPCE" "MFGE8"
## [161] "MIB1" "MIPOL1" "MOGS" "MOV10" "MPHOSPH10"
## [166] "MRPS2" "MRPS25" "MRPS27" "MRPS5" "MTCH1"
## [171] "MYCBP2" "NARS2" "NAT14" "NDFIP2" "NDUFAF1"
## [176] "NDUFAF2" "NDUFB9" "NEK9" "NEU1" "NGDN"
## [181] "NGLY1" "NIN" "NINL" "NLRX1" "NOL10"
## [186] "NPC2" "NPTX1" "NSD2" "NUP210" "NUP214"
## [191] "NUP54" "NUP58" "NUP62" "NUP88" "NUP98"
## [196] "NUTF2" "OS9" "PABPC1" "PABPC4" "PCNT"
## [201] "PCSK6" "PDE4DIP" "PDZD11" "PIGO" "PIGS"
## [206] "PITRM1" "PKP2" "PLAT" "PLD3" "PLEKHA5"
## [211] "PLEKHF2" "PLOD2" "PMPCA" "PMPCB" "POFUT1"
## [216] "POGLUT2" "POGLUT3" "POLA1" "POLA2" "POR"
## [221] "PPIL3" "PPT1" "PRIM1" "PRIM2" "PRKACA"
## [226] "PRKAR2A" "PRKAR2B" "PRRC2B" "PSMD8" "PTBP2"
## [231] "PTGES2" "PUSL1" "PVR" "QSOX2" "RAB10"
## [236] "RAB14" "RAB18" "RAB1A" "RAB2A" "RAB5C"
## [241] "RAB7A" "RAB8A" "RAE1" "RALA" "RAP1GDS1"
## [246] "RBM28" "RBM41" "RBX1" "RDX" "REEP5"
## [251] "REEP6" "RETREG3" "RHOA" "RIPK1" "RNF41"
## [256] "RPL36" "RRP9" "RTN4" "SAAL1" "SBNO1"
## [261] "SCAP" "SCARB1" "SCCPDH" "SDF2" "SELENOS"
## [266] "SEPSECS" "SIGMAR1" "SIL1" "SIRT5" "SLC25A21"
## [271] "SLC27A2" "SLC30A6" "SLC30A7" "SLC30A9" "SLC44A2"
## [276] "SLC9A3R1" "SLU7" "SMOC1" "SNIP1" "SPART"
## [281] "SRP19" "SRP54" "SRP72" "STC2" "STOM"
## [286] "STOML2" "SUN2" "TAPT1" "TARS2" "TBCA"
## [291] "TBK1" "TBKBP1" "TCF12" "THTPA" "TIMM10"
## [296] "TIMM10B" "TIMM29" "TIMM8B" "TIMM9" "TLE1"
## [301] "TLE3" "TLE5" "TM2D3" "TMED5" "TMEM39B"
## [306] "TMEM97" "TOMM70" "TOR1A" "TOR1AIP1" "TRIM59"
## [311] "TRMT1" "TUBGCP2" "TUBGCP3" "TYSND1" "UBAP2"
## [316] "UBAP2L" "UBXN8" "UGGT2" "UPF1" "USP13"
## [321] "USP54" "VPS11" "VPS39" "WASHC4" "WFS1"
## [326] "YIF1A" "ZC3H18" "ZC3H7A" "ZDHHC5" "ZNF318"
## [331] "ZNF503" "ZYG11B" "ACE2" "TMPRSS2"
\end{verbatim}
\begin{alltt}
\hlcom{#In the table, I select line that match the krogan gene name liste}
......@@ -901,15 +897,14 @@ Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
\hlkwd{dim}\hlstd{(tabloK)}
\end{alltt}
\begin{verbatim}
## [1] 311 3
## [1] 320 3
\end{verbatim}
\begin{alltt}
\hlcom{# Les gènes perdus (dans le tableau mais pas dans la liste de Krogan)}
\hlkwd{sort}\hlstd{(tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{`tmp$Gene.name`} \hlopt{%in%} \hlstd{krogan}\hlopt{==}\hlstd{F])}
\end{alltt}
\begin{verbatim}
## [1] COQ8B ELOC ERO1B MARC1 NSD2 NUP58 PCSK5 RETREG3
## [9] SPART TIMM29 TOMM70 WASHC4
## [1] KDELC1 KDELC2 PCSK5
## 442 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... ZYG11B
\end{verbatim}
\begin{alltt}
......@@ -917,10 +912,9 @@ Restreindre ce tableau aux gènes présent dans l'analyse de Krogan.
\hlkwd{sort}\hlstd{(krogan[krogan} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`}\hlopt{==}\hlstd{F])}
\end{alltt}
\begin{verbatim}
## [1] "ADCK4" "AES" "ARL6IP6" "ATP5L" "BCS1L" "C19orf52"
## [7] "C1orf50" "CYB5R3" "ERO1LB" "FAM134C" "FGFR1OP" "KIAA1033"
## [13] "MFGE8" "MTARC1" "NUPL1" "SIGMAR1" "SPG20" "TCEB1"
## [19] "TCEB2" "TOMM70A" "USP13" "VIMP" "WHSC1"
## [1] "ARL6IP6" "ATP5MG" "BCS1L" "C1orf50" "CEP43" "CYB5R3"
## [7] "ELOB" "MFGE8" "POGLUT2" "POGLUT3" "SELENOS" "SIGMAR1"
## [13] "TLE5" "USP13"
\end{verbatim}
\begin{alltt}
\hlkwd{write.csv}\hlstd{(tabloK,} \hlstr{"primatesVbats_onlykrogan.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)}
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......@@ -50,6 +50,7 @@ CNTRL,1,3
COL6A1,3,2
COLGALT1,2,1
COMT,2,0
COQ8B,1,0
CRTC3,1,2
CSDE1,0,1
CSNK2A2,0,0
......@@ -71,11 +72,13 @@ 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
......@@ -136,14 +139,13 @@ 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
......@@ -177,9 +179,11 @@ 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
......@@ -237,6 +241,7 @@ RBX1,0,3
RDX,2,0
REEP5,0,0
REEP6,0,5
RETREG3,0,1
RHOA,0,0
RIPK1,2,4
RNF41,0,0
......@@ -262,6 +267,7 @@ SLC9A3R1,3,0
SLU7,1,2
SMOC1,0,2
SNIP1,0,0
SPART,1,0
SRP19,0,1
SRP54,0,0
SRP72,1,1
......@@ -278,6 +284,7 @@ TCF12,0,1
THTPA,0,0
TIMM10,1,0
TIMM10B,0,0
TIMM29,1,1
TIMM8B,0,3
TIMM9,0,0
TLE1,2,1
......@@ -287,6 +294,7 @@ TMED5,2,0
TMEM39B,2,4
TMEM97,0,1
TMPRSS2,0,4
TOMM70,0,1
TOR1A,1,1
TOR1AIP1,5,5
TRIM59,0,3
......@@ -302,6 +310,7 @@ UPF1,0,0
USP54,1,3
VPS11,1,1
VPS39,5,5
WASHC4,2,2
WFS1,2,2
YIF1A,0,0
ZC3H18,1,1
......
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