Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
An annotation data object that maps KEGG pathway identifiers to Entrez Gene or Open Reading Frame identifiers.DescriptionKEGGPATHID2EXTID maps KEGG pathway identifiers to Entrez Gene (for human, mouse, and rat) or Open Reading Frame (for yeast) identifiers DetailsThis is an R object containing key and value pairs. Keys are KEGG pathway identifiers and values are Entrez Gene identifiers for human, mouse, and rat or Open Reading Frame (ORF) identifiers for yeast. Values are vectors of length 1 or greater depending on whether a pathway identifier can be maapped to one or more Entrez Gene or ORF identifiers. NAs are assigned to KEGG pathway identifiers that can not be mapped to any Entrez Gene or ORF identifiers. KEGG pathway identifiers are the identifiers used by KEGG for various pathways. Mappings between KEGG pathway identifiers and pathway names can be obtained through another annotation data object named KEGGPATHID2NAME. Mappings were based on data provided by: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15 Referencesftp://ftp.genome.ad.jp/pub/kegg/pathways See Also
Examples
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
xx <- as.list(KEGGPATHID2EXTID)
if(length(xx) > 0){
# Get the value of the first key
xx[[1]]
# Get the values for multiget for a few keys
if(length(xx) >= 3){
xx[1:3]
}
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(KEGG.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGG.db/KEGGPATHID2EXTID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGGPATHID2EXTID
> ### Title: An annotation data object that maps KEGG pathway identifiers to
> ### Entrez Gene or Open Reading Frame identifiers.
> ### Aliases: KEGGPATHID2EXTID
> ### Keywords: datasets
>
> ### ** Examples
>
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
>
> ## Bimap interface:
> xx <- as.list(KEGGPATHID2EXTID)
> if(length(xx) > 0){
+ # Get the value of the first key
+ xx[[1]]
+ # Get the values for multiget for a few keys
+ if(length(xx) >= 3){
+ xx[1:3]
+ }
+ }
$hsa00232
[1] "10" "1544" "1548" "1549" "1553" "7498" "9"
$hsa00983
[1] "10" "1066" "10720" "10941" "151531" "1548" "1549" "1551"
[9] "1553" "1576" "1577" "1806" "1807" "1890" "221223" "2990"
[17] "3251" "3614" "3615" "3704" "51733" "54490" "54575" "54576"
[25] "54577" "54578" "54579" "54600" "54657" "54658" "54659" "54963"
[33] "574537" "64816" "7083" "7084" "7172" "7363" "7364" "7365"
[41] "7366" "7367" "7371" "7372" "7378" "7498" "79799" "83549"
[49] "8824" "8833" "9" "978"
$hsa01100
[1] "10" "100" "10007" "100137049" "10020" "10026"
[7] "100510686" "10063" "10157" "10170" "10195" "10201"
[13] "10229" "10312" "10317" "10327" "10331" "1036"
[19] "10380" "10390" "1040" "10400" "10402" "10423"
[25] "10449" "10476" "10554" "10555" "10558" "1056"
[31] "10588" "10606" "10621" "10622" "10623" "10632"
[37] "10654" "1066" "10678" "10682" "10690" "10714"
[43] "10720" "10768" "10797" "10826" "10841" "10855"
[49] "10873" "10901" "10905" "10941" "10975" "10993"
[55] "10998" "11019" "11041" "1109" "11112" "11128"
[61] "1119" "1120" "11226" "11227" "11232" "112483"
[67] "11253" "11282" "11285" "113026" "11320" "11343"
[73] "113451" "113612" "114805" "1152" "1158" "1159"
[79] "1160" "116285" "117248" "119548" "120227" "121278"
[85] "122481" "122622" "123099" "123745" "123876" "124"
[91] "124454" "124975" "125" "125061" "125965" "125981"
[97] "126" "126328" "126792" "127" "127124" "128"
[103] "128869" "129607" "129642" "130" "130013" "131"
[109] "1312" "131669" "132" "132158" "1327" "132789"
[115] "1329" "1337" "1339" "1340" "134147" "1345"
[121] "1349" "1350" "1351" "135152" "1352" "1353"
[127] "1355" "1371" "1373" "137964" "138050" "138429"
[133] "139596" "140838" "1431" "144193" "144245" "145226"
[139] "146664" "1491" "15" "1503" "150763" "151056"
[145] "151531" "1537" "154141" "1543" "1544" "1548"
[151] "1549" "155066" "1551" "1553" "1555" "1557"
[157] "1558" "1559" "1562" "1571" "1573" "157506"
[163] "1576" "1577" "1579" "158" "1581" "1582"
[169] "1583" "1584" "1585" "1586" "1588" "1589"
[175] "159" "1593" "1594" "1595" "160287" "1603"
[181] "1606" "1607" "1608" "160851" "1609" "1610"
[187] "1621" "162417" "162466" "1629" "1633" "1635"
[193] "1638" "1644" "1650" "166929" "168391" "169355"
[199] "170712" "171568" "1716" "1717" "1718" "1719"
[205] "1723" "1737" "1738" "1743" "1757" "178"
[211] "1786" "1787" "1788" "1789" "1798" "18"
[217] "1806" "1807" "1841" "1854" "189" "1890"
[223] "1892" "191" "192134" "1962" "197258" "199857"
[229] "201595" "2023" "2026" "2027" "203" "204"
[235] "205" "2053" "2058" "210" "211" "212"
[241] "2131" "2132" "2134" "2135" "2137" "216"
[247] "217" "218" "2180" "2181" "2182" "2184"
[253] "219" "2194" "220" "2203" "221" "221223"
[259] "221823" "222" "2222" "2224" "223" "2235"
[265] "224" "226" "2271" "22845" "22856" "229"
[271] "22928" "22929" "22934" "22978" "230" "23057"
[277] "231" "23193" "23236" "23305" "23382" "23396"
[283] "23417" "23475" "23483" "23498" "23530" "23545"
[289] "23553" "23556" "2356" "23600" "23649" "23761"
[295] "239" "240" "242" "245972" "245973" "246"
[301] "246721" "247" "248" "249" "250" "251"
[307] "2523" "2524" "2525" "2526" "2527" "2528"
[313] "2529" "2530" "2531" "253558" "2538" "2539"
[319] "254531" "2548" "256435" "2571" "2572" "25796"
[325] "2581" "2582" "2583" "25834" "2584" "2585"
[331] "2588" "25885" "2589" "2590" "25902" "2591"
[337] "2592" "259230" "2593" "259307" "2595" "2597"
[343] "26007" "26035" "2618" "262" "26227" "26229"
[349] "26275" "26279" "2628" "26289" "2629" "26290"
[355] "26301" "2632" "26330" "2639" "2643" "2645"
[361] "2650" "2651" "2673" "2678" "2683" "2686"
[367] "2687" "270" "27010" "27034" "27087" "27089"
[373] "27090" "271" "2710" "2712" "27124" "27165"
[379] "272" "2720" "27235" "2729" "2730" "27306"
[385] "2731" "27349" "27430" "2744" "2746" "2747"
[391] "275" "2752" "276" "2762" "277" "278"
[397] "279" "2799" "28" "280" "2805" "2806"
[403] "2821" "283208" "283871" "284098" "284541" "2875"
[409] "290" "29071" "2937" "2954" "29796" "2987"
[415] "29880" "2990" "29906" "29920" "29922" "29925"
[421] "29926" "29929" "29947" "29958" "29968" "30"
[427] "3028" "3030" "3032" "3033" "3034" "3067"
[433] "3073" "3074" "3081" "30814" "30815" "30833"
[439] "30834" "3098" "3099" "31" "3101" "314"
[445] "3141" "3145" "3155" "3156" "3157" "3158"
[451] "316" "317749" "32" "3242" "3251" "326625"
[457] "3283" "3284" "3290" "3291" "3292" "3293"
[463] "3294" "3295" "33" "3340" "3373" "337876"
[469] "339221" "34" "340485" "341392" "3417" "3418"
[475] "3419" "341947" "3420" "3421" "3422" "3423"
[481] "3425" "348158" "349565" "35" "353" "36"
[487] "3612" "3613" "3614" "3615" "3620" "3628"
[493] "3631" "3632" "3633" "3636" "37" "3703"
[499] "3704" "3705" "3706" "3707" "3712" "374291"
[505] "374378" "3795" "38" "383" "384" "387787"
[511] "39" "3906" "391013" "3938" "3939" "3945"
[517] "3948" "3990" "4047" "4048" "4051" "4056"
[523] "411" "4121" "4122" "4124" "4128" "4129"
[529] "4143" "4144" "4190" "4191" "4199" "4245"
[535] "4247" "4248" "4249" "427" "4329" "435"
[541] "4351" "4357" "438" "440" "440138" "440567"
[547] "441024" "441531" "442117" "445" "4507" "4508"
[553] "4509" "4512" "4513" "4514" "4519" "4522"
[559] "4524" "4535" "4536" "4537" "4538" "4539"
[565] "4540" "4541" "4548" "4594" "4597" "4598"
[571] "4669" "4694" "4695" "4696" "4697" "4698"
[577] "47" "4700" "4701" "4702" "4704" "4705"
[583] "4706" "4707" "4708" "4709" "471" "4710"
[589] "4711" "4712" "4713" "4714" "4715" "4716"
[595] "4717" "4718" "4719" "4720" "4722" "4723"
[601] "4724" "4725" "4726" "4728" "4729" "4731"
[607] "48" "4830" "4831" "4832" "4833" "4837"
[613] "4842" "4843" "4846" "4860" "4907" "493911"
[619] "4942" "4952" "4953" "4967" "498" "50"
[625] "5009" "501" "5033" "5048" "50484" "50487"
[631] "5049" "5050" "5051" "5053" "506" "50614"
[637] "50617" "50700" "50814" "509" "5091" "5095"
[643] "5096" "51" "51004" "5105" "51056" "5106"
[649] "51074" "51082" "51084" "51102" "51109" "51144"
[655] "51166" "51179" "51181" "51196" "51227" "51251"
[661] "51268" "513" "5130" "51301" "51380" "51382"
[667] "514" "51477" "51478" "515" "51540" "516"
[673] "5160" "51601" "51604" "51606" "5161" "5162"
[679] "5167" "5169" "517" "51703" "51727" "51728"
[685] "51733" "51763" "518" "51805" "51809" "5198"
[691] "521" "5211" "5213" "5214" "522" "5223"
[697] "5224" "5226" "523" "5230" "5232" "5236"
[703] "525" "526" "527" "5277" "5279" "528"
[709] "5281" "5283" "5286" "5287" "5288" "5289"
[715] "529" "5297" "5298" "5313" "5315" "5319"
[721] "5320" "5321" "5322" "533" "5330" "5331"
[727] "5332" "5333" "5335" "53354" "5336" "5337"
[733] "5338" "534" "535" "53630" "537" "5372"
[739] "5373" "539" "53947" "5406" "5407" "5408"
[745] "5409" "54107" "54187" "5422" "5424" "5425"
[751] "5426" "5427" "5428" "5430" "5431" "5432"
[757] "5433" "5434" "54344" "5435" "5436" "54363"
[763] "5437" "5438" "5439" "5440" "5441" "5444"
[769] "5445" "5446" "54480" "54490" "54575" "54576"
[775] "54577" "54578" "54579" "54600" "54657" "54658"
[781] "54659" "54675" "5471" "54802" "548596" "548644"
[787] "549" "54947" "54963" "54965" "5498" "54988"
[793] "54995" "55163" "55191" "55224" "55229" "55256"
[799] "55276" "55300" "55301" "55304" "55312" "55361"
[805] "5538" "55454" "55500" "55512" "55568" "5557"
[811] "5558" "55627" "55650" "55703" "55750" "55753"
[817] "55790" "55808" "55821" "55902" "55907" "56052"
[823] "5625" "56267" "5631" "5634" "56474" "56623"
[829] "56624" "56655" "56848" "56894" "56895" "56898"
[835] "56901" "56913" "56922" "56953" "56994" "570"
[841] "57016" "57026" "57134" "5723" "5730" "5740"
[847] "5742" "5743" "57452" "574537" "57678" "57804"
[853] "57818" "57834" "5805" "5831" "5832" "5833"
[859] "58510" "5859" "586" "5860" "587" "593"
[865] "594" "5980" "60490" "60495" "6120" "6184"
[871] "6185" "622" "6240" "6241" "6296" "6303"
[877] "6307" "6309" "6342" "635" "6389" "6390"
[883] "6391" "63917" "6392" "64087" "64131" "64132"
[889] "64409" "64425" "6448" "64579" "64600" "646625"
[895] "6470" "6472" "6476" "64768" "6480" "64802"
[901] "64816" "6482" "6483" "6484" "6487" "6489"
[907] "64902" "65220" "65263" "654364" "6609" "661"
[913] "6610" "6611" "6652" "6675" "6677" "669"
[919] "6697" "6713" "6718" "6723" "683" "686"
[925] "6888" "6898" "6916" "6999" "7054" "7083"
[931] "7084" "7086" "7108" "7166" "7167" "7173"
[937] "7263" "7264" "729020" "7298" "7299" "7306"
[943] "7357" "7358" "7360" "7363" "7364" "7365"
[949] "7366" "7367" "7368" "7371" "7372" "7378"
[955] "7381" "7384" "7385" "7386" "7388" "7389"
[961] "7390" "7498" "7841" "790" "79053" "79087"
[967] "7915" "79178" "7923" "79369" "7941" "79586"
[973] "79611" "79623" "79646" "79695" "79717" "79796"
[979] "79799" "79814" "79868" "79888" "7991" "80025"
[985] "80055" "80142" "80146" "80201" "80270" "80308"
[991] "80339" "80347" "8050" "81490" "81579" "81616"
[997] "81849" "81888" "8277" "8309" "8310" "83440"
[1003] "83549" "8372" "8382" "8394" "8395" "8398"
[1009] "8399" "84002" "84076" "84172" "84245" "84265"
[1015] "84274" "84284" "84532" "84618" "84620" "84647"
[1021] "84649" "84693" "847" "84701" "84706" "84720"
[1027] "84735" "84803" "84812" "84890" "84920" "84992"
[1033] "8509" "8513" "8525" "8526" "8527" "8529"
[1039] "85365" "8540" "85465" "8560" "8564" "8566"
[1045] "8608" "8611" "8612" "8613" "8630" "8639"
[1051] "8659" "8681" "8692" "8693" "8694" "8702"
[1057] "8703" "8704" "8705" "8706" "8707" "8708"
[1063] "873" "8733" "874" "875" "8760" "8789"
[1069] "8790" "8801" "8802" "8803" "8813" "8818"
[1075] "8821" "883" "8833" "8854" "8867" "8869"
[1081] "8871" "8877" "8879" "8942" "8972" "8974"
[1087] "89869" "8992" "9" "90423" "9060" "9061"
[1093] "9091" "9114" "91373" "9162" "91734" "9197"
[1099] "9245" "92483" "9249" "9296" "93034" "93183"
[1105] "9331" "9348" "9374" "9377" "9380" "9388"
[1111] "94005" "9453" "9468" "9487" "9488" "9489"
[1117] "95" "9514" "9517" "952" "9533" "9536"
[1123] "9550" "9551" "9563" "9588" "9615" "978"
[1129] "9791" "9942" "9945"
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and