You can do pathway analysis on those genes. There are several commercial available tools like Ingenuity IPA, Metacore. See if your institute already have the license for those. If not, there are free pathway analysis tools as well that may be similar to IPA and Matacore, such as iPathwayGuide: https://apps.advaitabio.com/oauth-provider/login

These software can provide you a lot of information like canonical pathway analysis, network, regulators, biofunction, etc..However, each of those software have their own bias toward specific field. For example, IPA is more toward cancer and cardiovascular.

I hope this help! 

I agree with Chio-Ling. If you do not have licence for IPA, you can also use DAVID website: http://david.abcc.ncifcrf.gov/

Are you working with microarray or NGS data? 

Here is a paper that may be of interest:

http://www.nature.com/nprot/journal/v8/n9/abs/nprot.2013.099.html 

In addition to the use of DAVID proposed by Guillaume, the output provided by DAVID should be represented and analyzed by REVIGO. It takes long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds.

http://revigo.irb.hr/

 Thankyou all for your answers...

 and thanks Sir(Alexander Zhavoronkov for the paper)

ipathway have license related issues so i prefer to do the analysis using David as you people have suggested.

Sir i am working on huge EST data..

with Revigo we are only able to view geneotology terms not the genes..

Is there any relevant tool other than revigo to view upregulated and downregulated genes??

You are right, revigo is only able to view geneontology terms, but it is really useful when DAVID provides you with redundant ontology terms. In addition, it provides nice charts to use in a further functional analysis.

I think you should also look for metabolic information. In that case, Pahtway projector and ipath2 provides additional information by mapping your overexpressed genes in metabolic KEGG maps. You can also define the color and the width of your overexpressed genes related to their levels of expression.

http://www.g-language.org/PathwayProjector/

http://pathways.embl.de/

Unfortunately, for a proper mapping you should translate your set of differentially expressed genes according KEGG Orthology code. 

For that purpose, I reccomend you to "translate" your gene nomenclature by using Uniprot website.

http://www.uniprot.org/proteomes/

In that webpage, you can organize and personalize a table which displays all the features you can find in almost all the databases. Among them, of course, you can find the KEGG orthology number (KO, in the phylogenomic headland) assigned to the genes of your genome.

I hope that will be useful for you.

Best regards.

Thankyou Sir..i will follow this..