Details of gene names in DE
1
0
Entering edit mode
r.clifford • 0
@rclifford-12781
Last seen 4.4 years ago

Hi All

I have performed gometh on a 450k methylation dataset and extracted the top 20 categories using topGO. My question is, is there a way to generate a list of the gene names in the returned "DE" column, for examples the 71 genes reported in the below example?

 Term                                                                                                      Ont    N  DE         
GO:0098742: cell-cell adhesion via plasma-membrane adhesion molecules  BP  214  71

P.DE              FDR

1.855565e-07 0.002030636

Best wishes

Rachel

missmethyl • 698 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 5 hours ago
United States

Using the example data from ?gometh as an example:

> example(gometh)

<snip>

> topGO(gst,number=1)
                                                                      Term Ont
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules  BP
             N DE         P.DE          FDR
GO:0007156 154 37 1.310866e-12 2.768287e-08

Now we have to map CpGs to Entrez Gene IDs

> z <- getMappedEntrezIDs(sigcpgs, allcpgs, "450K")

This gives us a list, where the first list item contains all the Entrez Gene IDs that correspond to significant CpGs. We can then map to GO terms and subset.

> gos <- select(org.Hs.eg.db, z[[1]], "GOALL")

> firstgos <- subset(gos, GOALL %in% "GO:0007156")

> firstgos$SYMBOL <- mapIds(org.Hs.eg.db, as.character(firstgos$ENTREZID), "SYMBOL","ENTREZID")
'select()' returned 1:1 mapping between keys and columns
> firstgos
       ENTREZID      GOALL EVIDENCEALL ONTOLOGYALL   SYMBOL
136        1002 GO:0007156         IEA          BP     CDH4
27086     22883 GO:0007156         IEA          BP   CLSTN1
27440     22997 GO:0007156         IEA          BP   IGSF9B
35396     26025 GO:0007156         IEA          BP PCDHGA12
80493     56099 GO:0007156         IEA          BP  PCDHGB7
80514     56100 GO:0007156         IEA          BP  PCDHGB6
80538     56101 GO:0007156         IEA          BP  PCDHGB5
80568     56102 GO:0007156         IEA          BP  PCDHGB3
80589     56103 GO:0007156         IEA          BP  PCDHGB2
80610     56104 GO:0007156         IEA          BP  PCDHGB1
80637     56105 GO:0007156         IEA          BP PCDHGA11
80658     56106 GO:0007156         IEA          BP PCDHGA10
80683     56107 GO:0007156         IEA          BP  PCDHGA9
80707     56108 GO:0007156         IEA          BP  PCDHGA7
80728     56109 GO:0007156         IEA          BP  PCDHGA6
80749     56110 GO:0007156         IEA          BP  PCDHGA5
80770     56111 GO:0007156         IEA          BP  PCDHGA4
80791     56112 GO:0007156         IEA          BP  PCDHGA3
80812     56113 GO:0007156         IEA          BP  PCDHGA2
80833     56114 GO:0007156         IEA          BP  PCDHGA1
80856     56135 GO:0007156         IEA          BP  PCDHAC1
80890     56136 GO:0007156         IEA          BP  PCDHA13
80911     56137 GO:0007156         IEA          BP  PCDHA12
80934     56138 GO:0007156         IEA          BP  PCDHA11
80972     56139 GO:0007156         IEA          BP  PCDHA10
81008     56140 GO:0007156         IEA          BP   PCDHA8
81044     56141 GO:0007156         IEA          BP   PCDHA7
81082     56142 GO:0007156         IEA          BP   PCDHA6
81118     56143 GO:0007156         IEA          BP   PCDHA5
81154     56144 GO:0007156         IEA          BP   PCDHA4
81190     56145 GO:0007156         IEA          BP   PCDHA3
81232     56146 GO:0007156         IEA          BP   PCDHA2
81285     56147 GO:0007156         IEA          BP   PCDHA1
83848     57463 GO:0007156         ISS          BP   AMIGO1
117026     8641 GO:0007156         IEA          BP  PCDHGB4
125152     9708 GO:0007156         IEA          BP  PCDHGA8
125456     9752 GO:0007156         IEA          BP   PCDHA9

 

 

ADD COMMENT
0
Entering edit mode

This was incredibly helpful for me, thank you. 

How would you perform the same type of extraction for genes in the topKEGG pathways?

Thank you in advance!

ADD REPLY
0
Entering edit mode

I figured it out, posting here for anyone that might find it useful:

> keggs <- select(org.Hs.eg.db, z[[1]], "PATH")

> firstkeggs <- subset(keggs, PATH %in% "04614")

> firstkeggs$SYMBOL <- mapIds(org.Hs.eg.db, as.character(firstkeggs$ENTREZID), "SYMBOL","ENTREZID")

ADD REPLY

Login before adding your answer.

Traffic: 255 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6