Question: Network analysis software
3
gravatar for mahnazkiani
4.1 years ago by
mahnazkiani40
United States
mahnazkiani40 wrote:

I have RNA-seq data for a plant species (Sorghum) that its genome is already mapped, any suggestion for doing network analysis? I prefer to do it without using R packages.

 

Thanks

rna-seq • 2.7k views
ADD COMMENTlink modified 14 months ago by Kevin Blighe41k • written 4.1 years ago by mahnazkiani40
5
gravatar for Gary
4.1 years ago by
Gary450
Taiwan/Taichung/China Medical University Hospital
Gary450 wrote:

Cytoscape is a wonderful tool. There are other great tools I also used for your reference.

  • Enrichr

Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q.N., Wang, Z.C., Meirelles, G.V., Clark, N.R. & Ma'ayan, A. (2013). Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14.

  • PANTHER

Mi, H.Y., Muruganujan, A., Casagrande, J.T. & Thomas, P.D. (2013). Large-scale gene function analysis with the PANTHER classification system. Nat. Protoc. 8, 1551-1566.

  • GSEA (GSAA)

Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. & Mesirov, J.P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102, 15545-15550.

Xiong, Q., Mukherjee, S. & Furey, T.S. (2014). GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data. Sci Rep 4, 6347.

  • DAVID

Huang, D.W., Sherman, B.T. & Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57.

ADD COMMENTlink written 4.1 years ago by Gary450
2
gravatar for roalva1
4.0 years ago by
roalva180
Spain
roalva180 wrote:

If you want not just visualize but analyze I would go for these two tools:

From the same author as STRING:

SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks

http://nar.oxfordjournals.org/content/37/suppl_2/W109.abstract?sid=b02562a2-c08e-46c0-af8a-ad2ddc0bbd0c

NETWORK MINER: Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

http://nar.oxfordjournals.org/content/40/20/e158.abstract?sid=c828e255-831b-4a2e-9e30-ebae78705b8c

These tools are under Babelomics 5.0: functional interpretation for new generations of genomic data. In the menu functional

http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv384

www.babelomics.org

 

You can also use http://cellmaps.babelomics.org/ to visualize your network interactively.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by roalva180
1
gravatar for Deepak Tanwar
4.1 years ago by
Deepak Tanwar3.9k
ETH Zürich, Switzerland
Deepak Tanwar3.9k wrote:

You can use Cytoscape http://www.cytoscape.org/

http://wiki.cytoscape.org/Publications

ADD COMMENTlink written 4.1 years ago by Deepak Tanwar3.9k
1
gravatar for jeffk8900
4.1 years ago by
jeffk8900120
United States
jeffk8900120 wrote:

Double check on DAVID. I believe that resource has not been updated in a couple of years. 

ADD COMMENTlink written 4.1 years ago by jeffk8900120
1

You are totally right, jeffk8900. The last updated time of DAVID is in 2009. Even though, sometimes it is still very helpful depends on our NGS data and biological question. Another very useful but not perfect tool for your information as the below.

 

STRING

Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J.Y., Minguez, P., Bork, P., von Mering, C. & Jensen, L.J. (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808-D815.

Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L.J. & von Mering, C. (2011). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39, D561-D568.

ADD REPLYlink written 4.1 years ago by Gary450

I think they've a recent update like at the end of 2017

ADD REPLYlink written 14 months ago by pablo6199170

Hi pablo61991,

Please let me know where did you find that information (about update in end of 2017)?

ADD REPLYlink modified 14 months ago • written 14 months ago by EagleEye6.2k

Sorry I missed the year, as you said it comes from 2016

DAVID 6.8 (current beta release) May. 2016

-- The DAVID Knowledgebase completely rebuilt -- Entrez Gene integrated as the central identifier to allow for more timely updates while still incorporating Ensembl and Uniprot as integral data sources -- New GO category (GO Direct) provides GO mappings directly annotated by the source database (no parent terms included) -- New annotation categories -- New list identifier systems added for list uploading and conversion -- A few bugs fixed

ADD REPLYlink written 14 months ago by pablo6199170

Sorry I forgot to attach this link in above reply, https://david.ncifcrf.gov/content.jsp?file=update.html

ADD REPLYlink modified 14 months ago • written 14 months ago by EagleEye6.2k
1
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe41k
London, England
Kevin Blighe41k wrote:

igraph in R can now do everything and has many common metrics integrated, such as hub score, vertex degree, BC, etc.: Network plot from expression data in R using igraph

ADD COMMENTlink modified 14 months ago • written 14 months ago by Kevin Blighe41k
0
gravatar for mahnazkiani
4.1 years ago by
mahnazkiani40
United States
mahnazkiani40 wrote:

I thought that Cytoscape will help me to visualize the network analysis results not doing the analysis?

ADD COMMENTlink written 4.1 years ago by mahnazkiani40
1

You are both right and not totally right. Cytoscape alone cannot do too many things. Please go to the Cytoscape APP Store (http://apps.cytoscape.org/apps/all#downloads). There are a lot of APPs can help you to perform gene set enrichment analysis based on most popular databases, e.g. GO, Wikipathways, KEGG, Reactome, and so on. There are also other many amazing functions performed by other APPs. 

ADD REPLYlink written 4.0 years ago by Gary450
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