Enrichment analysis using KEGG?

[Andrés Flórez]

Hi all,

I was wondering if there is any way to perform enrichment analysis of the networks in Cytoscape using KEGG pathways instead of GO categories,  Maybe using scripting?, or Is it possible with BINGO?.

I will appreciate any help

Best regards.

--
Andrés F. Flórez

Associate Researcher
Program for the Study and Control
of Tropical Diseases (PECET).
Universidad de Antioquia.
Medellín-Colombia.
Carrera 53 # 61 - 30, SIU, Lab 632
www.pecet-colombia.org
Phones: +57-4-219 6507 / 02
Fax: +57-4-219 6511
Cell phone: 3103462268
e-mail: andres...@pecet-colombia.org

[Keiichiro Ono]

Hi.
If you want to map genes on your network to KEGG pathways, you can use
NCBI Entrez Gene plugin to do that:

http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients

"Pathways" annotation includes KEGG and Reactome.

Thanks
Kei

2008/12/12 Andrés Flórez <andrew...@gmail.com>:

--
Keiichiro Ono ko...@ucsd.edu

Cytoscape Core Developer Team: http://www.cytoscape.org/
UCSD Bioengineering Ideker Lab: http://chianti.ucsd.edu/idekerlab/

[Andrés Flórez]

Thanks Dr. Kei. Once I import the annotation, how can I calculate
which pathways are overrepresented in one group of nodes using KEGG
anotation? I know that BinGO uses hypergeometric test but I want to
use KEGG categories instead of Gene ontology categories.

BEst wishes

[Keiichiro Ono]

Hi.
Sorry for the delay.
BinGO is implemented as an individual plugin (separated from core
features of Cytoscape) and there is no way to use KEGG annotation in
BinGO plugin.

I do not remember the exact function name, but I think you can use R +
Bioconductor to calculate over representation of KEGG pathways on a
network. Once you get the result as a simple table, you can import it
as attributes in Cytoscape. Then you can visualize the result based
on the output of Bioconductor.

Thanks.

[Andrés Flórez]

Dr. Kei,

Thanks for your help. I found a tutorial that allow to perform KEGG enrichment with bioconductor. I will take a look at it.

Andres

[Andrés Flórez]

Hi guys,

I just found an easier way of doing KEGG enrichment analysis with the
R package SubpathwayMiner:
http://cran.r-project.org/web/packages/SubpathwayMiner/index.html

1. Translate your Gene names list into NCBI gene IDs. you can do this
in KEGG database in this link.

ftp://ftp.genome.jp/pub/kegg/genes/organisms

2. Set the organism and type of identifier en SubpathwayMiner, like this

> updateOrgAndIdType("$org", "ncbi-geneid")

where $org is the KEGG three letter code for your organism.

3. once you have the list genes import those into R like this:

> geneList <- scan("file.txt", what = 'character')

then execute:

ann <- getAnn(geneList) # to anotate genes and calculates p-values

results <- printAnn(ann) # nice view of the results.

then you will have the enrichment result for your genes.

Best

On Mon, Jan 18, 2010 at 5:20 PM, zwangwustl <hugh...@hotmail.com> wrote:
> Hi Andres,
>
>  Which tutorial did you found? I am also looking for tools for KEGG
> pathway enrichment analysis instead of GO
>
> Best,
>
> On Jan 9 2009, 2:08 pm, "Andrés Flórez" <andrewflo...@gmail.com>

> wrote:
>> Dr. Kei,
>>
>> Thanks for your help. I found a tutorial that allow to perform KEGG
>> enrichment with bioconductor. I will take a look at it.
>>
>> Andres
>>

>> On Thu, Jan 8, 2009 at 2:11 PM, Keiichiro Ono <k...@ucsd.edu> wrote:
>>
>> > Hi.
>> > Sorry for the delay.
>> > BinGO is implemented as an individual plugin (separated from core
>> > features of Cytoscape) and there is no way to use KEGG annotation in
>> > BinGO plugin.
>>
>> > I do not remember the exact function name, but I think you can use R +
>> > Bioconductor to calculate over representation of KEGG pathways on a
>> > network.  Once you get the result as a simple table, you can import it
>> > as attributes in Cytoscape.  Then you can visualize the result based
>> > on the output of Bioconductor.
>>
>> > Thanks.
>> > Kei
>>

>> > 2008/12/12 Andrés Flórez <andrewflo...@gmail.com>:

>>
>> > > Thanks Dr. Kei.  Once I import the annotation, how can I calculate
>> > > which pathways are overrepresented in one group of nodes using KEGG
>> > > anotation? I know that BinGO uses hypergeometric test but I want to
>> > > use KEGG categories instead of Gene ontology categories.
>>
>> > > BEst wishes
>>

>> > > On Fri, Dec 12, 2008 at 1:30 PM, Keiichiro Ono <k...@ucsd.edu> wrote:
>>
>> > >> Hi.
>> > >> If you want to map genes on your network to KEGG pathways, you can use
>> > >> NCBI Entrez Gene plugin to do that:
>>
>> > >>http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients
>>
>> > >> "Pathways" annotation includes KEGG and Reactome.
>>
>> > >> Thanks
>> > >> Kei
>>

>> > >> 2008/12/12 Andrés Flórez <andrewflo...@gmail.com>:

>>
>> > >>> Hi all,
>>
>> > >>> I was wondering if there is any way to perform enrichment analysis of
>> > the
>> > >>> networks in Cytoscape using KEGG pathways instead of GO categories,
>> >  Maybe
>> > >>> using scripting?, or Is it possible with BINGO?.
>>
>> > >>> I will appreciate any help
>>
>> > >>> Best regards.
>>
>> > >>> --
>> > >>> Andrés F. Flórez
>>
>> > >>> Associate Researcher
>> > >>> Program for the Study and Control
>> > >>> of Tropical Diseases (PECET).
>> > >>> Universidad de Antioquia.
>> > >>> Medellín-Colombia.
>> > >>> Carrera 53 # 61 - 30, SIU, Lab 632
>> > >>>www.pecet-colombia.org
>> > >>> Phones: +57-4-219 6507 / 02
>> > >>> Fax: +57-4-219 6511
>> > >>> Cell phone: 3103462268

>> > >>> e-mail: andres.flo...@pecet-colombia.org
>>
>> > >> --
>> > >> Keiichiro Ono    k...@ucsd.edu

>>
>> > >> Cytoscape Core Developer Team:http://www.cytoscape.org/
>> > >> UCSD Bioengineering Ideker Lab:http://chianti.ucsd.edu/idekerlab/
>>
>> > > --
>> > > Andrés F. Flórez
>>
>> > > Associate Researcher
>> > > Program for the Study and Control
>> > > of Tropical Diseases (PECET).
>> > > Universidad de Antioquia.
>> > > Medellín-Colombia.
>> > > Carrera 53 # 61 - 30, SIU, Lab 632
>> > >www.pecet-colombia.org
>> > > Phones: +57-4-219 6507 / 02
>> > > Fax: +57-4-219 6511
>> > > Cell phone: 3103462268

>> > > e-mail: andres.flo...@pecet-colombia.org
>>
>> > --
>> > Keiichiro Ono    k...@ucsd.edu

>>
>> > Cytoscape Core Developer Team:http://www.cytoscape.org/
>> > UCSD Bioengineering Ideker Lab:http://chianti.ucsd.edu/idekerlab/
>

--
Andres Florez

Research Associate

Program for the Study and Control
of Tropical Diseases (PECET).

University of Antioquia.

Medellín-Colombia.
Carrera 53 # 61 - 30, SIU, Lab 632
www.pecet-colombia.org

Phones: +57-4-219 6502 / 219 6622