Entering edit mode
Dear all, would you please let me know,
given a list of genes, what is the simplest way to retrieve all the GO categories (no GO ids) for specific genes ?
thank you !
-- bogdan
1
Entering edit mode
> z <- select(org.Hs.eg.db, "1", "GOALL")
'select()' returned 1:many mapping between keys and columns
> dim(z)
[1] 74 4
> library(GO.db)
> z$Term <- mapIds(GO.db, z$GOALL, "TERM", "GOID")
'select()' returned 1:1 mapping between keys and columns
> z
ENTREZID GOALL EVIDENCEALL ONTOLOGYALL
1 1 GO:0001775 TAS BP
2 1 GO:0002252 TAS BP
3 1 GO:0002263 TAS BP
4 1 GO:0002274 TAS BP
5 1 GO:0002275 TAS BP
6 1 GO:0002283 TAS BP
7 1 GO:0002366 TAS BP
8 1 GO:0002376 TAS BP
9 1 GO:0002443 TAS BP
10 1 GO:0002444 TAS BP
11 1 GO:0002446 TAS BP
12 1 GO:0002576 TAS BP
13 1 GO:0003674 ND MF
14 1 GO:0005575 HDA CC
15 1 GO:0005575 IDA CC
16 1 GO:0005575 TAS CC
17 1 GO:0005576 HDA CC
18 1 GO:0005576 IDA CC
19 1 GO:0005576 TAS CC
20 1 GO:0005615 HDA CC
21 1 GO:0005622 TAS CC
22 1 GO:0005737 TAS CC
23 1 GO:0006810 TAS BP
24 1 GO:0006887 TAS BP
25 1 GO:0006955 TAS BP
26 1 GO:0008150 ND BP
27 1 GO:0008150 TAS BP
28 1 GO:0009987 TAS BP
29 1 GO:0012505 TAS CC
30 1 GO:0016192 TAS BP
31 1 GO:0030141 TAS CC
32 1 GO:0030312 HDA CC
33 1 GO:0031012 HDA CC
34 1 GO:0031091 TAS CC
35 1 GO:0031093 TAS CC
36 1 GO:0031410 TAS CC
37 1 GO:0031974 TAS CC
38 1 GO:0031982 HDA CC
39 1 GO:0031982 TAS CC
40 1 GO:0031983 TAS CC
41 1 GO:0032940 TAS BP
42 1 GO:0034774 TAS CC
43 1 GO:0036230 TAS BP
44 1 GO:0042119 TAS BP
45 1 GO:0043226 HDA CC
46 1 GO:0043226 TAS CC
47 1 GO:0043227 HDA CC
48 1 GO:0043227 TAS CC
49 1 GO:0043230 HDA CC
50 1 GO:0043233 TAS CC
51 1 GO:0043299 TAS BP
52 1 GO:0043312 TAS BP
53 1 GO:0045055 TAS BP
54 1 GO:0045321 TAS BP
55 1 GO:0046903 TAS BP
56 1 GO:0050896 TAS BP
57 1 GO:0051179 TAS BP
58 1 GO:0051234 TAS BP
59 1 GO:0051641 TAS BP
60 1 GO:0051649 TAS BP
61 1 GO:0060205 TAS CC
62 1 GO:0062023 HDA CC
63 1 GO:0070062 HDA CC
64 1 GO:0071944 HDA CC
65 1 GO:0072562 HDA CC
66 1 GO:0097708 TAS CC
67 1 GO:0099503 TAS CC
68 1 GO:0101002 TAS CC
69 1 GO:0110165 HDA CC
70 1 GO:0110165 IDA CC
71 1 GO:0110165 TAS CC
72 1 GO:0140352 TAS BP
73 1 GO:1903561 HDA CC
74 1 GO:1904813 TAS CC
Term
1 cell activation
2 immune effector process
3 cell activation involved in immune response
4 myeloid leukocyte activation
5 myeloid cell activation involved in immune response
6 neutrophil activation involved in immune response
7 leukocyte activation involved in immune response
8 immune system process
9 leukocyte mediated immunity
10 myeloid leukocyte mediated immunity
11 neutrophil mediated immunity
12 platelet degranulation
13 molecular_function
14 cellular_component
15 cellular_component
16 cellular_component
17 extracellular region
18 extracellular region
19 extracellular region
20 extracellular space
21 intracellular anatomical structure
22 cytoplasm
23 transport
24 exocytosis
25 immune response
26 biological_process
27 biological_process
28 cellular process
29 endomembrane system
30 vesicle-mediated transport
31 secretory granule
32 external encapsulating structure
33 extracellular matrix
34 platelet alpha granule
35 platelet alpha granule lumen
36 cytoplasmic vesicle
37 membrane-enclosed lumen
38 vesicle
39 vesicle
40 vesicle lumen
41 secretion by cell
42 secretory granule lumen
43 granulocyte activation
44 neutrophil activation
45 organelle
46 organelle
47 membrane-bounded organelle
48 membrane-bounded organelle
49 extracellular organelle
50 organelle lumen
51 leukocyte degranulation
52 neutrophil degranulation
53 regulated exocytosis
54 leukocyte activation
55 secretion
56 response to stimulus
57 localization
58 establishment of localization
59 cellular localization
60 establishment of localization in cell
61 cytoplasmic vesicle lumen
62 collagen-containing extracellular matrix
63 extracellular exosome
64 cell periphery
65 blood microparticle
66 intracellular vesicle
67 secretory vesicle
68 ficolin-1-rich granule
69 cellular anatomical entity
70 cellular anatomical entity
71 cellular anatomical entity
72 export from cell
73 extracellular vesicle
74 ficolin-1-rich granule lumen
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Hi James, thank you very much for your reply ! I would like to add please :
we do have a list of genes for example Orai1, Tet1, KLF9, SOCS3, etc (it is a long list) ; what is the easiest way to extract the precise BP gene ontologies for all of these genes in the list ?
thank you very much !