Question: Is There A Free Alternative To Ingenuity Pathway Analysis?
39
gravatar for Gon
7.6 years ago by
Gon400
Bergen, Norway
Gon400 wrote:

I was wondering if it does exist a similar tool, but free... I' trying to reproduce some results I found on a recent paper, and I would rather prefer to try with a different tool. Otherwise, I think I'll go with the 2 free weeks that they offer...

network pathway • 87k views
ADD COMMENTlink modified 6 months ago by Francis Crick50 • written 7.6 years ago by Gon400
3

I know this is an old post, but it may be relevant to some people.  Our company, Advaita Bioinformatics www.advaitabio.com) has launched a free pathway analysis application called iPathwayGuide. (https://apps.advaitabio.com/ipg/home)  You can sign up for free and analyze gene-expression data for free.  The reports offer the following:

  • Gene Analysis
  • Gene OntologyAnalysis for, Biological Processes, Molecular Functions, and Cellular Components
  • Pathway Analysis
  • Drug Interactions
  • Over-represented Diseases
  • Associations to miRNAs
  • Associations with SNPs
  • and more.

You can sign up here.  http://www.advaitabio.com/ipathwayguide.html  

ADD REPLYlink modified 4.1 years ago • written 4.2 years ago by andrew440

Hello Andrew, thanks for sharing the link. can I find demo or any teturial will teach me how to use it.

Best

Shaima

ADD REPLYlink written 2.7 years ago by saj9880
1

Maybe this other Biostar question helps you http://biostar.stackexchange.com/questions/4709/any-tools-to-identify-significantly-altered-pathways

ADD REPLYlink written 7.6 years ago by Marina Manrique1.3k

Cognoscente (for visualizing biomolecular interaction knowledge) and StarNet (for visualizing gene expression correlation networks) may provide some of the functions that you are seeking.

-Vincent VanBuren

ADD REPLYlink written 4.4 years ago by vvanburen20
27
gravatar for Chris Evelo
7.6 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

The thing is that all those commercial pathway providers like Ingenuity and GeneGO offer a lot of content that they developed in house for specific fields. Ingenuity is quite good in the cardiovascular field and GeneGo's Metacore is good Toxicology for instance (and more metabolite directed research in general). So if you did something specifically in Ingenuity or want to reproduce that you might not easily find an alternative. Although all the content they offer is based on knowledge freely available in other pathway databases (Ingenuity started with a lot of KEGG pathways) and the literature.

That being said there are a lot of freely available pathway analysis tools and pathways. Check out Pathwaycommons for a kind of integrated approach (that includes Reactome a.o). You might also want to try our own WikiPathways and the accompanying pathway analysis tool PathVisio. At the PathVisio download page we also offer converted KEGG pathways for many species that you could also analyze using PathVisio.

ADD COMMENTlink modified 7.6 years ago • written 7.6 years ago by Chris Evelo9.9k
9
gravatar for Marina Manrique
7.6 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

Have you tried Reactome pathway analysis tool?

Maybe some kinds of analysis done with Ingenuity can be done with this tool. if you're working with human proteins maybe you find it useful

HTH,

Marina

ADD COMMENTlink written 7.6 years ago by Marina Manrique1.3k
5
gravatar for Francis Crick
6 months ago by
Francis Crick50 wrote:

QuaternaryProd is an open-source alternative to IPA. It is an R package which can be used to predict upstream regulators given gene expression data. The R package uses StringDB and the "Quaternary Statistic" for performing causal inference.

The R package can be downloaded from Bioconductor (link) and the latest version is on github (link)

The original paper can be found here.

ADD COMMENTlink modified 6 months ago • written 6 months ago by Francis Crick50

The first link is broken, contains wrong symbol at the beginning and missing column after https.

ADD REPLYlink written 6 months ago by aln160

@aln thanks I fixed it.

ADD REPLYlink written 6 months ago by Francis Crick50
4
gravatar for Qdjm
7.6 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

You could also try GeneMANIA: http://www.genemania.org

We include everything in Pathway Commons, plus genetic interactions, co-expression relationships, and predicted protein interactions.

ADD COMMENTlink written 7.6 years ago by Qdjm1.9k

What's the main advantage of GeneMANIA over STRING?

ADD REPLYlink written 4.4 years ago by Christian2.7k
3
gravatar for Ian
7.6 years ago by
Ian5.2k
University of Manchester, UK
Ian5.2k wrote:

Try STRING: http://string-db.org/

I haven't used it a great deal, but it certainly produces similar output to Metcore.

ADD COMMENTlink written 7.6 years ago by Ian5.2k
1

As far as I know STRING produces a network of known and predicted protein associations only, while Metacore includes metabolism and thus metabolism. But since the initial question was about Ingenuity STRING might just do the trick.

ADD REPLYlink written 7.6 years ago by Chris Evelo9.9k
3
gravatar for User 8516
7.6 years ago by
User 851630
User 851630 wrote:

Ingenuity's pathways and networks are available for free in Sigma's Your Favorite Gene powered by Ingenuity tool. There are also several other datasets consolidated in one location, as well as a tag cloud view of PubMed literature.

www.sigma.com/yfg

ADD COMMENTlink written 7.6 years ago by User 851630
3
gravatar for Peter Karp
7.5 years ago by
Peter Karp30
United States
Peter Karp30 wrote:

HumanCyc plus Pathway Tools provides another set of options. HumanCyc has well curated content on human metabolic pathways. The associated Pathway Tools software will let you paint gene expression, proteomics, or metabolomics data onto the HumanCyc pathway map, and Pathway Tools will also perform enrichment analysis. See BioCyc.org. The pathway painting is available through the web site, but to perform enrichment analysis you must download and install the software.

(My group develops these two tools.)

ADD COMMENTlink written 7.5 years ago by Peter Karp30
2
gravatar for Doo
7.6 years ago by
Doo230
Doo230 wrote:

Innate DB is also nice and handy. They have a lot of curators. http://www.innatedb.ca/

ADD COMMENTlink written 7.6 years ago by Doo230
2
gravatar for kissaj
3.7 years ago by
kissaj80
United States
kissaj80 wrote:

None of these programs are very good at all - they are all centered around disease, or "model" organisms.
 

ADD COMMENTlink written 3.7 years ago by kissaj80
2
gravatar for andrew
3.7 years ago by
andrew440
United States
andrew440 wrote:

Thanks to Kissaj for bringing this back to the top.  It made me realize it's time for an update about iPathwayGuide.

The application now accepts a wide variety of gene-expression data including:

  • CuffDiff
  • DESeq(2)
  • JMP Genomics
  • Affy CEL files
  • Limma/GEO2R
  • custom *.txt file (must have gene symbol, FC, p-value)

With these data we provide a free platform to look at your data in the context of Genes, GO Tems, Predicted miRNAs, Pathways, or Diseases.  There are a number of advantages to using iPathwayGuide beyond it being 100% free to use, but the key difference is that we use Impact Analysis to score the pathways.  This approach uses two forms of evidence to score pathways, enrichment and perturbation.

Some of the new features since my last post in this thread include: 

Predicted miRNA Analysis - We offer evidence of possible active miRNAs based on gene-expression signatures
Meta-Analysis - Quickly compare unique or common significant elements between experiments. 
Affy CEL file support - Upload your CEL files directly and find your DEGenes in a couple minutes

Here's a link to an overview video.  http://youtu.be/5maN9krw-nI

Below is a screenshot of the Meta-Analysis.

ADD COMMENTlink written 3.7 years ago by andrew440

But you must pay to download the results from ipathway guide, is that correct?

ADD REPLYlink written 3.1 years ago by yourA20
1
gravatar for User 1543
7.6 years ago by
User 154320
User 154320 wrote:

You can also try Ariadne Pathway Studio, they are for pay, but offer a free trial.

ADD COMMENTlink written 7.6 years ago by User 154320
1
gravatar for enunvillafer
5.4 years ago by
enunvillafer100
Cuba
enunvillafer100 wrote:

Course there are a lots of soft-wares you can use to perform a similar analysis: -network analysis and visualization Cytoscape, sure you have heard of it (lots of plugins) -pathway enrichment analysis with topological information, read the paper 10 years of pathway analysis. -ORA, MEA: DAVID -gene-disease association CTD database, DIsGeNET plugin from Cytoscape.

An important thing is that you design a workflow for the analysis of data that include all of the suggested tool (at least some of them).

Personally, I really enjoy interpreting comparative proteomics results with free tools. Never used IPA Cheers Teresa ;)

ADD COMMENTlink written 5.4 years ago by enunvillafer100
1
gravatar for Charles Warden
3.7 years ago by
Charles Warden5.2k
Duarte, CA
Charles Warden5.2k wrote:

There have been a lot of good suggestions.

I would also recommend GATHER for a quick-function enrichment tool (for KEGG pathways) along with several other categories:

http://gather.genome.duke.edu/

I also developed a tool called BD-Func, which includes some categories that people would probably consider "pathways" (such as transcriptional regulators and some signatures for signaling pathways), although it tends to be most useful for custom signatures:

http://sourceforge.net/projects/bdfunc/

Of course, there are also tools like GSEA, FuncAssociate, DAVID, etc. (if you are more broad in what you define as a "pathway")

ADD COMMENTlink modified 16 months ago • written 3.7 years ago by Charles Warden5.2k
0
gravatar for Amos
5.0 years ago by
Amos30
European Union
Amos30 wrote:

Try Hanaylzer. There is a nice vid here showing it's use. http://hanalyzer.sourceforge.net/

ADD COMMENTlink written 5.0 years ago by Amos30
0
gravatar for marko.k.laakso
5.0 years ago by
European Union
marko.k.laakso80 wrote:

Moksiskaan (http://csbi.ltdk.helsinki.fi/moksiskaan/) is an integrative pathway analysis tookit, which supports data sources such as Ensembl, KEGG, PINA, PathwayCommons, DrugBank, GO, SNPs3D, COSMIC, WikiPathways, Tumourscape, and TSGene. Using the provided tools (http://csbi.ltdk.helsinki.fi/moksiskaan/anduril/index.html?q=Moksiskaan%20project), you can prepare all sorts of graph models representing genes, proteins, drugs, pathways, diseases, biological functions, etc. related to your data. Moksiskaan is an Anduril anduril.org) based open source project, which means that it can be used easily with other Anduril components to carry out complete analyses. Here's one example output http://csbi.ltdk.helsinki.fi/moksiskaan/archive/ProcessStudy.pdf, but you can find more from the web site and from the supplements of the articles.

ADD COMMENTlink written 5.0 years ago by marko.k.laakso80
0
gravatar for cocrajib
2.3 years ago by
cocrajib0
cocrajib0 wrote:

FunRich is a free good alternative.

available at http://funrich.org/

Example result

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by cocrajib0
0
gravatar for thiagovidotto
2.0 years ago by
thiagovidotto0 wrote:

IPA looks the best tool to view enriched pathways using P value and FC value. Do you guys know any other platform that could provide enriched pathways from differentially expressed genes? All the platforms that requires gene lists are not so informative because they lack FC values.

ADD COMMENTlink written 2.0 years ago by thiagovidotto0
0
gravatar for andrew
16 months ago by
andrew440
United States
andrew440 wrote:

As far as I know the only tool that actually uses the FC in the calculation to assess significance of a pathway is iPathwayGuide. IPA uses FC to select for DEGs and to perform its upstream regulator analysis, but still relies on an enrichment model to score pathways.

ADD COMMENTlink written 16 months ago by andrew440
0
gravatar for EagleEye
16 months ago by
EagleEye5.7k
Sweden
EagleEye5.7k wrote:

I cannot say it is an complete alternative to IPA. But you can use GeneSCF for some of its functionality,

Gene Set Clustering based on Functional annotation (GeneSCF)

Advantages

  • Real-time analysis, do not have to depend on enrichment tools to get updated.
  • Easy for computational biologists to integrate this simple tool with their NGS pipeline.

  • GeneSCF supports more organisms.

  • Enrichment analysis for Multiple gene list in single run.

  • Enrichment analysis for Multiple gene list using Multiple source database (GO,KEGG, REACTOME and NCG) in single run.

  • Download complete GO terms/Pathways/Functions with associated genes as simple table format in a plain text file (Check "Two step process" below in "GeneSCF USAGE" section).

ADD COMMENTlink modified 16 months ago • written 16 months ago by EagleEye5.7k
0
gravatar for bigmawen
16 months ago by
bigmawen270
United States
bigmawen270 wrote:

Pathview Web server provides a user friendly comprehensive solution for pathway analysis, data integration and visualization.
It was recently published in Nucleic Acids Research (NAR) Web Server issue:
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx372

Pathview Web server extends the core functions of Pathview with:
-a simple intuitive graphical user interface
-fast and programmatic access through RESTful API
-complete pathway analysis workflow supporting multiple omics data and integrated analysis
-interactive and hyperlinked results graphs for better data interpretation
-up-to-date pathway data via regular database synchronization
-open access to all analyses and resources
-analysis history and data sharing via free registered user accounts
-complete online help and documentation
-multiple quick-start example analyses

Particularly, the full pathway analysis workflow is shown in Example 4 online.
And you can find more ready-to-run examples on the Pathview Web server: https://pathview.uncc.edu/

ADD COMMENTlink modified 16 months ago • written 16 months ago by bigmawen270
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