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Question: Is There A Free Alternative To Ingenuity Pathway Analysis? (https://www.biostars.org/p/6203/)

Elchicopalo290 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…

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modified 6 weeks ago by andrew110 • written 4.0 years ago by Elchicopalo290

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

ADD REPLYlinkwritten 4.0 years ago by Marina Manrique1.2k

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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 REPLYlinkmodified 6 months ago • written 8 months ago by andrew110

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 REPLYlinkwritten 10 months ago by vvanburen20

Chris Evelo9.3k 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 COMMENTlinkmodified 4.0 years ago • written 4.0 years ago by Chris Evelo9.3k

Marina Manrique1.2k 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 COMMENTlinkwritten 4.0 years ago by Marina Manrique1.2k

Qdjm1.7k 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 COMMENTlinkwritten 4.0 years ago by Qdjm1.7k

What’s the main advantage of GeneMANIA over STRING?

ADD REPLYlinkwritten 10 months ago by Christian1.5k

Ian3.8k wrote:

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

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

ADD COMMENTlinkwritten 4.0 years ago by Ian3.8k

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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 REPLYlinkwritten 4.0 years ago by Chris Evelo9.3k

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 COMMENTlinkwritten 4.0 years ago by User 851630

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 COMMENTlinkwritten 4.0 years ago by Peter Karp30

Doo200 wrote:

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

ADD COMMENTlinkwritten 4.0 years ago by Doo200

User 154320 wrote:

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

ADD COMMENTlinkwritten 4.0 years ago by User 154320

enunvillafer60 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 COMMENTlinkwritten 22 months ago by enunvillafer60

Charles Warden3.4k 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):

http://sourceforge.net/projects/bdfunc/ (standalone version)

http://www.bioconductor.org/packages/release/bioc/html/sRAP.html (functions implemented in the sRAP package)

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

ADD COMMENTlinkwritten 6 weeks ago by Charles Warden3.4k

andrew110 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 COMMENTlinkwritten 6 weeks ago by andrew110

Amos20 wrote:

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

ADD COMMENTlinkwritten 17 months ago by Amos20

marko.k.laakso60 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 outputhttp://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 COMMENTlinkwritten 17 months ago by marko.k.laakso60

Is that logo supposed to be a sad face.

ADD REPLYlinkwritten 8 months ago by Hranjeev1.3k

kissaj30 wrote:

None of these programs are very good at all – they are all centered around disease, or “model” organisms.

ADD COMMENTlinkwritten 6 weeks ago by kissaj30

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