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
Cytoscape is a wonderful tool. There are other great tools I also used for your reference.
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.
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.
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.
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.
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
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.
You can use Cytoscape.
Double check on DAVID. I believe that resource has not been updated in a couple of years.
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
I thought that Cytoscape will help me to visualize the network analysis results not doing the analysis?
You are both right and not totally right. Cytoscape alone cannot do too many things. Please go to the Cytoscape APP Store. 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.
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version 2.3.6
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.
I think they've a recent update like at the end of 2017
Hi pablo61991,
Please let me know where did you find that information (about update in end of 2017)?
All I can see is recent update on DAVID 6.8 is Oct 2016 (https://david.ncifcrf.gov/content.jsp?file=release.html) and if I look at individual knowledge-base it looks like KEGG version is from December 2015 and Gene Ontology version is from April 2016 (https://david.ncifcrf.gov/content.jsp?file=update.html).
And previously I tested/compared other tools with DAVID 6.8-beta version, I could see some problems associated with the update. It is possible that the problem was rectified later but still the database is not up-to-date according to information from DAVID website.
My suggestion is to use more than one tool for enrichment analysis and compare the results. Or else simply go for the updated tools. Also check out the tool we developed to overcome this issue, GeneSCF.
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
Sorry I forgot to attach this link in above reply, https://david.ncifcrf.gov/content.jsp?file=update.html