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## windows## library(org.Mm.eg.db)## We will derive genome level information for nicotinic acetylcholine receptor (nAChR) subunits. The genes for the subunits are called CHOLINERGIC RECEPTOR NICOTINIC ALPHA (CHRNA), BETA (CHRNB), GAMMA (CHRNG), DELTA (CHRND) and EPSILON (CHRNE).
There are 9 nAChR alpha subunit genes in humans: CHRNA1, CHRNA2, CHRNA3, CHRNA4, CHRNA5, CHRNA6, CHRNA7, CHRNA9 and CHRNA10.
There are 4 nAChR beta subunit gene in humans: CHRNB1, CHRNB2, CHRNB3 and CHRNB4.
There is 1 nAChR gamma subunit gene in humans: CHRNG.
There is 1 nAChR delta subunit gene in humans: CHRND.
There is 1 nAChR epsilon subunit gene in humans: CHRNE.
Below is the list of the human (Homo sapeins, Hs) nAChR subunit genes and their corresponding ENTRENZ identification numbers:
CHRNA1=“1134”, CHRNA2=“1135”, CHRNA3=“1136”, CHRNA4=“1137”, CHRNA5=“1138”, CHRNA6 =“8973”, CHRNA7=“1139”, CHRNA9=“55584”, CHRNA10=“57053”, CHRNB1=“1140”, CHRNB2=“1141”, CHRNB3=“1142”, CHRNB4=“1143”, CHRND=“1144”, CHRNE=“1145”, CHRNG=“1146”
CHRNinfo = select(org.Hs.eg.db,
keys=c("CHRNA1", "CHRNA2", "CHRNA3", "CHRNA4", "CHRNA5",
"CHRNA6", "CHRNA7", "CHRNA9", "CHRNA10", "CHRNB1",
"CHRNB2", "CHRNB3", "CHRNB4", "CHRNG", "CHRND", "CHRNE"),
columns=c("ENTREZID","ENSEMBLPROT"),
keytype="SYMBOL")## 'select()' returned 1:many mapping between keys and columnshead(CHRNinfo) # CHRNinfo is a dataframe of 38X3## SYMBOL ENTREZID ENSEMBLPROT
## 1 CHRNA1 1134 <NA>
## 2 CHRNA2 1135 <NA>
## 3 CHRNA3 1136 <NA>
## 4 CHRNA4 1137 <NA>
## 5 CHRNA5 1138 <NA>
## 6 CHRNA6 8973 ENSP00000276410CHRNinfoAll = select(org.Hs.eg.db,
keys=c("CHRNA1", "CHRNA2", "CHRNA3", "CHRNA4", "CHRNA5",
"CHRNA6", "CHRNA7", "CHRNA9", "CHRNA10", "CHRNB1",
"CHRNB2", "CHRNB3", "CHRNB4", "CHRNG", "CHRND", "CHRNE"),
columns=columns(org.Hs.eg.db)[c(6, 3, 4)],
keytype="SYMBOL")## 'select()' returned 1:many mapping between keys and columnshead(CHRNinfoAll) ## SYMBOL ENTREZID ENSEMBL ENSEMBLPROT
## 1 CHRNA1 1134 ENSG00000138435 <NA>
## 2 CHRNA2 1135 ENSG00000120903 <NA>
## 3 CHRNA3 1136 ENSG00000080644 <NA>
## 4 CHRNA4 1137 ENSG00000101204 <NA>
## 5 CHRNA5 1138 ENSG00000169684 <NA>
## 6 CHRNA6 8973 ENSG00000147434 ENSP00000276410# CHRNinfoAll[1:8,] will yield first eight rows, CHRNinfoAll will yiled a dataframe of 50 X 4table(is.na(CHRNinfoAll))##
## FALSE TRUE
## 193 7NoNaCHRN=na.omit(CHRNinfoAll)
unique(NoNaCHRN$ENSEMBLPROT)## [1] "ENSP00000276410" "ENSP00000433871" "ENSP00000434659"
## [4] "ENSP00000405989" "ENSP00000488147" "ENSP00000494974"
## [7] "ENSP00000312663" "ENSP00000250699" "ENSP00000437107"
## [10] "ENSP00000432757" "ENSP00000492221" "ENSP00000491344"
## [13] "ENSP00000491163" "ENSP00000491113" "ENSP00000491764"
## [16] "ENSP00000492078" "ENSP00000357461" "ENSP00000489703"
## [19] "ENSP00000490474" "ENSP00000490203" "ENSP00000433913"
## [22] "ENSP00000289957" "ENSP00000408819" "ENSP00000404950"
## [25] "ENSP00000258385" "ENSP00000398143" "ENSP00000410801"
## [28] "ENSP00000438380" "ENSP00000293780" "ENSP00000497829"
## [31] "ENSP00000496907"NoNaCHRN$ENTREZID## [1] "8973" "8973" "8973" "1139" "1139" "1139" "1139" "1139"
## [9] "1139" "1139" "1139" "1139" "55584" "57053" "57053" "57053"
## [17] "1140" "1140" "1140" "1140" "1140" "1140" "1140" "1140"
## [25] "1140" "1140" "1140" "1140" "1141" "1141" "1141" "1141"
## [33] "1142" "1142" "1144" "1144" "1144" "1144" "1144" "1144"
## [41] "1145" "1145" "1145"# These IDs are same as those introduced earlier.columns(org.Mm.eg.db)## [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT"
## [5] "ENSEMBLTRANS" "ENTREZID" "ENZYME" "EVIDENCE"
## [9] "EVIDENCEALL" "GENENAME" "GO" "GOALL"
## [13] "IPI" "MGI" "ONTOLOGY" "ONTOLOGYALL"
## [17] "PATH" "PFAM" "PMID" "PROSITE"
## [21] "REFSEQ" "SYMBOL" "UNIGENE" "UNIPROT"keytypes(org.Mm.eg.db)## [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT"
## [5] "ENSEMBLTRANS" "ENTREZID" "ENZYME" "EVIDENCE"
## [9] "EVIDENCEALL" "GENENAME" "GO" "GOALL"
## [13] "IPI" "MGI" "ONTOLOGY" "ONTOLOGYALL"
## [17] "PATH" "PFAM" "PMID" "PROSITE"
## [21] "REFSEQ" "SYMBOL" "UNIGENE" "UNIPROT"MmCHRNinfoAll = select(org.Mm.eg.db,
keys=c("Chrna1", "Chrna2", "Chrna3", "Chrna4",
"Chrna5", "Chrna6", "Chrna7", "Chrna9",
"Chrna10", "Chrnb1", "Chrnb2", "Chrnb3",
"Chrnb4", "Chrng", "Chrnd", "Chrne"),
columns=columns(org.Mm.eg.db)[c(6, 3, 4)],
keytype="SYMBOL")## 'select()' returned 1:many mapping between keys and columnsMmCHRNinfoAll## SYMBOL ENTREZID ENSEMBL ENSEMBLPROT
## 1 Chrna1 11435 ENSMUSG00000027107 ENSMUSP00000028515
## 2 Chrna2 110902 ENSMUSG00000022041 <NA>
## 3 Chrna3 110834 ENSMUSG00000032303 ENSMUSP00000034851
## 4 Chrna3 110834 ENSMUSG00000032303 ENSMUSP00000150636
## 5 Chrna4 11438 ENSMUSG00000027577 <NA>
## 6 Chrna5 110835 ENSMUSG00000035594 <NA>
## 7 Chrna6 11440 ENSMUSG00000031491 <NA>
## 8 Chrna7 11441 ENSMUSG00000030525 ENSMUSP00000032738
## 9 Chrna9 231252 ENSMUSG00000029205 <NA>
## 10 Chrna10 504186 ENSMUSG00000066279 ENSMUSP00000081891
## 11 Chrna10 504186 ENSMUSG00000066279 ENSMUSP00000147577
## 12 Chrnb1 11443 ENSMUSG00000041189 ENSMUSP00000047270
## 13 Chrnb2 11444 ENSMUSG00000027950 ENSMUSP00000143441
## 14 Chrnb2 11444 ENSMUSG00000027950 ENSMUSP00000029562
## 15 Chrnb3 108043 ENSMUSG00000031492 <NA>
## 16 Chrnb4 108015 ENSMUSG00000035200 ENSMUSP00000034854
## 17 Chrng 11449 ENSMUSG00000026253 <NA>
## 18 Chrnd 11447 ENSMUSG00000026251 <NA>
## 19 Chrne 11448 ENSMUSG00000014609 <NA>NoNaMmCHRN=na.omit(MmCHRNinfoAll)
unique(NoNaMmCHRN$ENSEMBLPROT)## [1] "ENSMUSP00000028515" "ENSMUSP00000034851" "ENSMUSP00000150636"
## [4] "ENSMUSP00000032738" "ENSMUSP00000081891" "ENSMUSP00000147577"
## [7] "ENSMUSP00000047270" "ENSMUSP00000143441" "ENSMUSP00000029562"
## [10] "ENSMUSP00000034854"NoNaMmCHRN$ENTREZID## [1] "11435" "110834" "110834" "11441" "504186" "504186" "11443"
## [8] "11444" "11444" "108015"