Question: Any Tools To Identify Significantly Altered Pathways?
12
gravatar for Dejian
8.2 years ago by
Dejian1.2k
United States
Dejian1.2k wrote:

Recently I am analyzing microarray data and I want to know which pathways are significantly altered. I am using KOBAS now,which is based on KEGG. Are there some other tools that can identify altered pathways based on statistics?

pathway kegg microarray • 20k views
ADD COMMENTlink modified 2.2 years ago by bioinfo8120 • written 8.2 years ago by Dejian1.2k
17
gravatar for Chris Evelo
8.1 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

The relevance of complex statistical algorithms for pathway statistics is often overestimated. There are many biological and technological reasons why pathway statistics can never be perfect. As a result it should always be used to get an impression of the relevant pathways which should then be visually inspected or analyzed using different tools.

Just some of those reasons...

  • The input data (often gene expression data) themselves are often not trustworthy.
  • The importance of a single gene product in a pathway can differ. It can be an important hub or something in a subbranch.
  • Along the same line for two consecutive reactions the first could be catalyzed by one enzyme and the second by four. The single enzyme probably is important, but you just don't know about each of the four individually.
  • Pathways can contain parts that are not really relevant to the question studied (you could say that part is not relevant to your question), now adding an irrelevant part where no changes occur will lower the statistical significance, while it does not affect the biological meaning at all.
  • On the other hand significant changes in pathways can occur in parts that are not really meaningful for the question studied. So you would list the pathway as being changed but the core process itself is not really affected.

That being said PathVisio has plugins that allow Z-score based pathway statistics and another plugin that does gene set enichment analysis is currently being tested. See: http://www.pathvisio.org/wiki/PluginDocumentation . The core advantage is that you can use whichever pathway set you prefer (WikiPathways, KEGG or your own set of tables transformed into pathways) and can immediately look at a data representation in the pathways that occur at the top of the list.

ADD COMMENTlink written 8.1 years ago by Chris Evelo9.9k
1

Thank you for this comment! As my adviso like o say: "There is no Systems Biology without Biology."

ADD REPLYlink written 4.3 years ago by mauroccm10
10
gravatar for Sophia
8.2 years ago by
Sophia300
Barcelona
Sophia300 wrote:

Try Gitools. It is free and allows you to download KEGG pathways and other modules and do enrichment analysis. Enrichment results are visualized nicely in heat maps.

ADD COMMENTlink written 8.2 years ago by Sophia300
5
gravatar for David Quigley
8.2 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

Many people have used Gene Set Enrichment Analysis, developed at the Broad, for this problem. The algorithm is wrapped in a very slick java application. In essence, quoting the overview, it's "a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes)." There are large libraries of pathway-associated genes to choose from. GSEA operates off of your normalized microarray data, as opposed to lists of genes. It's most convenient if you are using one of the mainstream commercial microarray platforms.

ADD COMMENTlink written 8.2 years ago by David Quigley11k
4
gravatar for Stew
8.2 years ago by
Stew1.4k
Cambridge
Stew1.4k wrote:

I use the bioconductor package SPIA, which also uses KEGG pathways. I find it works very well.

ADD COMMENTlink written 8.2 years ago by Stew1.4k
3
gravatar for Daniel Swan
8.2 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

I have some papers on Cite-U-Like for GSEA and it's alternatives, and some reviews on Gene Set analysis here

ADD COMMENTlink written 8.2 years ago by Daniel Swan13k
2
gravatar for Gww
8.2 years ago by
Gww2.6k
Canada
Gww2.6k wrote:

There's the Reactome FI Cytoscape plugin. It's quite nice.

ADD COMMENTlink written 8.2 years ago by Gww2.6k
2
gravatar for Khader Shameer
8.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

In addition to SPIA, I have used SubPathwayMiner for pathway enrichment analysis.

ADD COMMENTlink written 8.2 years ago by Khader Shameer18k
1
gravatar for Larry_Parnell
8.2 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Nothing different to add - just that all of the above are good tools and get my votes.

Actually, we've used Ingenuity, but it costs... You typically can get free access for a short time.

ADD COMMENTlink written 8.2 years ago by Larry_Parnell16k

Yep, we use Ingenuity too. I still like it a lot I have to say.

ADD REPLYlink written 8.2 years ago by Daniel Swan13k
1
gravatar for Guangchuang Yu
4.6 years ago by
Guangchuang Yu2.1k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.1k wrote:

clusterProfiler supports hypergeometric model and gene set enrichment analysis with several methods for graphing.

 

ADD COMMENTlink written 4.6 years ago by Guangchuang Yu2.1k
0
gravatar for cocrajib
2.8 years ago by
cocrajib0
cocrajib0 wrote:

Try FunRich which is free and you easy to use

download page http://funrich.org/download (for windows pc)

website : http://funrich.org

Example result

ADD COMMENTlink written 2.8 years ago by cocrajib0

Did anyone has used Ensembl dataset in the FunRich?

ADD REPLYlink written 2.2 years ago by bioinfo8120
0
gravatar for bioinfo8
2.2 years ago by
bioinfo8120
bioinfo8120 wrote:

Did anyone has used Ensembl dataset in the FunRich?

ADD COMMENTlink written 2.2 years ago by bioinfo8120
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