I like GeneMANIA a lot. It is a web based open source tool which takes gene list as input. It is also available as a Cytoscape plugin. To use GeneMANIA you'll need to create your gene list. Typically, I create two list of genes: (1) up regulated, and (2) down regulated. I feed them separately to GeneMANIA to identify networks and pathways that are either down regulated or up regulated.

There are a lot of other similar tools. I am listing a few of them that I have used. PANTHER, String-db, ToppFun (it is part of Toppgene suite), and gProfiler.

In addition, you can use Cytoscape. I do most of my analysis in cytoscape because I can integrate information from a lot different sources/plugins. It has a nice collection of plugins that'll allow you to do a lot of downstream analyses, which you are looking for.

Finding out "what is going on" is intelectual work and not provided by software. You already profiled the NFkB related genes. Based on this, a screen for other pathways that might play a role using this data is strange and unlikely to give any reasonable result (if you were talking about possibly performing gene set analyses, gene enrichment analyses or overrepresentation analyses). I would suggest to take a map of the NFkB pathway with interactions, indicated activations and repressions and so on and to add the information from the qPCR experiment. Then try to find out what parts of this pathway may seem to be activated or repressed and how the changes might reflect the changes in the signal input from the environment and the output (cellular rection) as response to that.

Ingenuity Pathways Analysis is a interesting tool to integrate several data of gene expression. Also KEGG Pathway Database is useful to look several related pathway.

Jochen Wilchelm: Yes I did and can do some more intellectual work on NFkB pathway but I wanted to find some information from the broader context. I do not think the program will do extra results without my involvement but it can bring some data that could be a nice foundation for my intellectual work. Some proteins related to NFkB are involved in plenty of processes and maybe for example the level of fold regulation could be a clue to find out what is responsible for the differential regulation

I was also looking for a suggestions for the tools that may help to also present the results in a interesting way not only to "find out what is going on" . Thank you for sharing your thoughts - some question on researchgate may seem ignorant for experts but sometimes it is hard to find even basic information in the net or pubmed. I work in the chemistry Institute and have little scientific support in a lot of areas in biology....but fortunately we got ResearchGate and a lot of people that are will to help.

Regards

Tomasz

I like GeneMANIA a lot. It is a web based open source tool which takes gene list as input. It is also available as a Cytoscape plugin. To use GeneMANIA you'll need to create your gene list. Typically, I create two list of genes: (1) up regulated, and (2) down regulated. I feed them separately to GeneMANIA to identify networks and pathways that are either down regulated or up regulated.

There are a lot of other similar tools. I am listing a few of them that I have used. PANTHER, String-db, ToppFun (it is part of Toppgene suite), and gProfiler.

In addition, you can use Cytoscape. I do most of my analysis in cytoscape because I can integrate information from a lot different sources/plugins. It has a nice collection of plugins that'll allow you to do a lot of downstream analyses, which you are looking for.

Sorry Tomasz, I did not want to be offensive in any way. Maybe I have chose the wrong wording. It was not meant in a bad way. I wanted to be constructive. I kindly ask pardon!

I am not a fan of Ingenuity Analysis because it gives a crazy score that has no statistical relevance (not an FDR, Q-value, P-value or anything) - so when we get manuscripts to review that use this we generally tell them to go and repeat the analysis using a different approach. ToppFun is probably the easiest to use hypergeometric enrichment site right now that gives tidy results. However, I'm not sure that you're going to get too much from a hypergeometric enrichment analysis because your gene list is already biased towards NFkB related genes, so this pathway is definitely going to come up and that is probably all. It seems like this panel is dedicated to measuring components of NFkB signaling and inferring activity of the pathway. So if I were you, I would probably just put the genes and their fold-changes into a ".rnk" file and run a pre-ranked GSEA using GSEA-P software and your panel as the gene set (http://www.broadinstitute.org/gsea/index.jsp). This will tell you whether there is significant enrichment in your condition of interest. Alternatively, you could create different .rnk files for each condition using the reciprocal of the dCt value, which will enable you to assess changes in enrichment.

My suggestion is GeneMANIA Networks from GeneMANIA, 19 july 2012, version 3.1.2

Http://www.genemania.org

Thank you a lot for your suggestions - you presented possibilities to analyse my data that I was not aware of - now I have a lot try.

P.S Jochen Wilhelm - I did not found your comment as offensive but did not want to be perceived as being ignorant or a person that believe in software generated data as a bible - also beg a pardon if you found yourself confused by my comment.

All fine, Tomasz. I am glad that you found some help.

Very welcome Tomasz

To Michael Green, I am quite intrigued by your comments on IPA. As I understand it, the platform uses p-values for Fisher's Exact Test to calculate their scores. Is this something that is perhaps not up to scratch ? This is one of the few databases that are manually curated instead of being assembled from free text searches, do you perceive this to be less reliable or biased in any way ? I would be very interested in hearing your views on this. Thanks very much !

This is a great discussion and learning us all and Genemania seems to be used by many. I still have a few suggestions as reading material for Tomasz as its also good to get an idea for basic knowledge AS SOME MAY BE GOOD FOR METABOLIC AND REGULATORY PATHWAYS, OTHERS FOR CELL SIGNALLING networks and TRANSCRIPTION FACTORS. So, here I have a few tools and sites for suggestive reading.

1. http://cgap.nci.nih.gov/Tools

2. http://www.biobase.de/pages/products/databases.html.

3. Brief Bioinform. 2003 Dec;4(4):315-24.

In silico tools for signal transduction research.

Lindvall JM, Blomberg KE, Smith CI.

4. BMC Sys Biol. 2013 Feb 21;7:15. doi: 10.1186/1752-0509-7-15.

Precise generation of systems biology models from KEGG pathways.

Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A.

you may also want to look at insilico gene expression data on the UCSC golden path, loads of gene expression studies have been carried out and data submitted on the golden path. I am sure you are likely to find a scenario of NF-kB that is similar to yours and the work would have been done on different celllines, if your data is comparable, it might strengthen your argument on the biological inference of your results- hope this helps