[BioC] Genes annotated to GO:0031281 using org.Hs.eg.db
James W. MacDonald
jmacdon at uw.edu
Wed Mar 19 15:17:32 CET 2014
Hi Tim,
There may not be any IDs mapped to that term directly. You can use
GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs.
> get("GO:0031281", org.Hs.egGO2ALLEGS)
IDA IDA TAS TAS IDA TAS IEA TAS TAS
TAS
"49" "116" "116" "117" "135" "135" "136" "136" "140"
"153"
IDA IDA TAS IDA IEA IDA IDA TAS IDA
IEA
"154" "155" "554" "796" "796" "799" "1394" "1394" "1812"
"1812"
IDA IEA NAS TAS TAS IEA TAS TAS IEA
TAS
"1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774"
"2778"
IDA ISS ISS IBA IBA IMP ISS TAS TAS
TAS
"2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915"
"5032"
ISS NAS IEA IDA IEA TAS TAS
"5578" "5894" "7077" "7432" "7434" "10486" "10487"
Or the more powerful select() method:
> select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL")
GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL
1 GO:0031281 IDA BP 49 ACR
2 GO:0031281 IDA BP 116 ADCYAP1
3 GO:0031281 TAS BP 116 ADCYAP1
4 GO:0031281 TAS BP 117 ADCYAP1R1
5 GO:0031281 IDA BP 135 ADORA2A
6 GO:0031281 TAS BP 135 ADORA2A
7 GO:0031281 IEA BP 136 ADORA2B
8 GO:0031281 TAS BP 136 ADORA2B
9 GO:0031281 TAS BP 140 ADORA3
10 GO:0031281 TAS BP 153 ADRB1
11 GO:0031281 IDA BP 154 ADRB2
12 GO:0031281 IDA BP 155 ADRB3
13 GO:0031281 TAS BP 554 AVPR2
14 GO:0031281 IDA BP 796 CALCA
15 GO:0031281 IEA BP 796 CALCA
16 GO:0031281 IDA BP 799 CALCR
17 GO:0031281 IDA BP 1394 CRHR1
18 GO:0031281 TAS BP 1394 CRHR1
19 GO:0031281 IDA BP 1812 DRD1
20 GO:0031281 IEA BP 1812 DRD1
21 GO:0031281 IDA BP 1816 DRD5
22 GO:0031281 IEA BP 1816 DRD5
23 GO:0031281 NAS BP 1816 DRD5
24 GO:0031281 TAS BP 1816 DRD5
25 GO:0031281 TAS BP 1909 EDNRA
26 GO:0031281 IEA BP 2692 GHRHR
27 GO:0031281 TAS BP 2696 GIPR
28 GO:0031281 TAS BP 2740 GLP1R
29 GO:0031281 IEA BP 2774 GNAL
30 GO:0031281 TAS BP 2778 GNAS
31 GO:0031281 IDA BP 2852 GPER1
32 GO:0031281 ISS BP 3973 LHCGR
33 GO:0031281 ISS BP 4763 NF1
34 GO:0031281 IBA BP 4842 NOS1
35 GO:0031281 IBA BP 4843 NOS2
36 GO:0031281 IMP BP 4846 NOS3
37 GO:0031281 ISS BP 4846 NOS3
38 GO:0031281 TAS BP 4914 NTRK1
39 GO:0031281 TAS BP 4915 NTRK2
40 GO:0031281 TAS BP 5032 P2RY11
41 GO:0031281 ISS BP 5578 PRKCA
42 GO:0031281 NAS BP 5894 RAF1
43 GO:0031281 IEA BP 7077 TIMP2
44 GO:0031281 IDA BP 7432 VIP
45 GO:0031281 IEA BP 7434 VIPR2
46 GO:0031281 TAS BP 10486 CAP2
47 GO:0031281 TAS BP 10487 CAP1
Warning message:
In .generateExtraRows(tab, keys, jointype) :
'select' resulted in 1:many mapping between keys and return rows
Best,
Jim
On 3/19/2014 4:28 AM, Tim Smith wrote:
> Hi,
>
> I was trying to get the genes annotated to the GO term "GO:0031281". My code:
>
> library(org.Hs.eg.db)
>
> genes <- get("GO:0031281", org.Hs.egGO2EG)
>
> When I run the code, I get:
>
>> genes <- get("GO:0031281", org.Hs.egGO2EG)
> Error in .checkKeys(value, Rkeys(x), x at ifnotfound) :
> value for "GO:0031281" not found
>
> If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results?
>
> thanks!
> [[alternative HTML version deleted]]
>
>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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