Good afternoon,

I recently found the following document (within the clusterProfiler folders)

"clusterProfiler_for_unsupported_organisms.pdf"

and I´m trying now to use the enrichGO() function, which does not work with my organism yet.

The databases pointed out in the example: "bacteria_mart_14", "fungi_mart_13", "fungi"

do not exist in listMarts() of the package biomaRt.

How can I proceed?

Thank you in advance for any help and suggestions. 

Best wishes,

                      Cristina

That document is pretty old. After bacteria_mart_14, the bacteria_mart_* was removed from biomaRt, and now the fungi_mart has version 26.

You can use listMarts() in biomaRt package to list all available marts:

> listMarts()
                                 biomart
1                                ensembl
2                                    snp
3                             regulation
4                                   vega
5                          fungi_mart_26
6                    fungi_variations_26
7                        metazoa_mart_26
8                  metazoa_variations_26
9                         plants_mart_26
10                  plants_variations_26
11                      protists_mart_26
12                protists_variations_26
13                                   msd
14                            cg_mart_02
15                                 WS220
16                         parasite_mart
17                               biomart
18                               example
19                      prod-intermart_1
20                               unimart
21                             biomartDB
22                              biblioDB
23                    Eurexpress Biomart
24                        phytozome_mart
25                         metazome_mart
26                          HapMap_rel27
27                            GermOnline
28   Sigenae_Oligo_Annotation_Ensembl_61
29 Sigenae Oligo Annotation (Ensembl 59)
30 Sigenae Oligo Annotation (Ensembl 56)
31                        Breast_mart_69
32                          K562_Gm12878
33                             Hsmm_Hmec
34                              allo2012
35                            Pancreas63
36                    Public_OBIOMARTPUB
37                          Public_VITIS
38                      Public_VITIS_12x
39                            Prod_WHEAT
40                        Public_TAIRV10
41                          Public_MAIZE
42                           Prod_TOMATO
43                           Prod_POPLAR
44                        Prod_POPLAR_V2
45                     Prod_BOTRYTISEDIT
46                            Prod_BOFUB
47                    Prod_LMACULANSEDIT
48                     vb_gene_mart_1504
49                      vb_snp_mart_1504
50                            expression
51                    ENSEMBL_MART_PLANT
52                ENSEMBL_MART_PLANT_SNP

Please bare in mind that this step is only for demonstration of preparing your own GO annotation and there are many alternative ways to do it. You can access other resource for instance uniprot or use blastGO to annotate yourself.

After you have done this, you can use buildGOmap to prepare the annotation files for enrichGO function.

You can also use enricher function for other kinds of annotation, see http://ygc.name/2015/05/11/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/

Hi,

I´m working with Streptococcus pyogenes.

Ok, thanks, I will use blastGO to annotate it my self and then try enrichGO.

Best,

         Cristina