PANTHER and DAVID can't recognized some Ensembl gene ID?

Question

[hellocita]

Hi all, I am trying to do GO terms annotation using a set of interesting human genes(with Ensembl gene id) and background, they are from RNA-seq data. However, whether I using PANTHER or DAVID, there's always more than 20% gene ids can't be mapped and I want to save these unmapped ids. I have try using Ensembl to convert ID to other id types like entrez or hgnc id, however the recognized gene number is even less... I wonder if there's anything I can do to mapped all of them? Thanks a lot! Some unmapped genes for example:

ENSG00000004660 ENSG00000005249 ENSG00000005448 ENSG00000005486 ENSG00000005812 ENSG00000214548 ENSG00000217325 ENSG00000218416 ENSG00000223839

Answer 1

[Guangchuang Yu]

> x= 'ENSG00000004660 ENSG00000005249 ENSG00000005448 ENSG00000005486 ENSG00000005812 ENSG00000214548 ENSG00000217325 ENSG00000218416 ENSG00000223839'
> id
[1] "ENSG00000004660" "ENSG00000005249" "ENSG00000005448" "ENSG00000005486"
[5] "ENSG00000005812" "ENSG00000214548" "ENSG00000217325" "ENSG00000218416"
[9] "ENSG00000223839"
> require(clusterProfiler)
> bitr(id, OrgDb='org.Hs.eg.db', fromType="ENSEMBL", toType='ENTREZID')
'select()' returned 1:1 mapping between keys and columns
          ENSEMBL  ENTREZID
1 ENSG00000004660     84254
2 ENSG00000005249      5577
3 ENSG00000005448     84058
4 ENSG00000005486     57414
5 ENSG00000005812     26224
6 ENSG00000214548     55384
8 ENSG00000218416 100130449
9 ENSG00000223839 100133036
Warning message:
In bitr(id, OrgDb = "org.Hs.eg.db", fromType = "ENSEMBL", toType = "ENTREZID") :
  11.11% of input gene IDs are fail to map...

You can try my package, clusterProfiler for ID conversion and enrichment analysis.

[hellocita]

Thank you Guangchuang! This package is very useful! The only problem is I need to updated my R version:)