The best way is to download Cytoscape 3.2.0 or higher version (http://apps.cytoscape.org), this platform give you user friend access to view network, pathways, any kind of data genomics, RNA, sequencing data, Gene ontology etc. The second thing is you will install Plug in applications according to your need like for gene ontology (BiNGO, ClueGO etc) and for RNA-sequencing applications you can see here (http://apps.cytoscape.org/search?q=RNA+sequencing). The best option is to do operating Cytoscape for analysis, you will get in touch with totorials (www.cytoscape.org/manual/Cytoscape3_0_1Manual.pdf). Cytoscape has also various species options for your required data visualization and analysis.  

Thanks Abdul, the only problem with Cytoscape is to create an input file, which is so hard to make, for a non-computer person.

Thanks Gaurav,when I tried using Bingo it asked file in a specific format, did I miss anything? Can we just paste the list of genes and it will do?

I am not sure whether there is a "best" method. There are indeed a number of useful methods to find what GO classes and which pathways contain relatively high amounts genes. Let me mention a few others GO-Elite (a standalone program we wrote and that can do both) and TopGO an R procedure. Both do "pruning" which is relevant for GO analysis because you will otherwise get too many meaningless big classes. But... You probably don't even want the best method. You seem to be asking for the easier to use ones. Please allow me to grump a bit about this. Honestly for me that sounds a bit like it would sound to a wet lab scientist if somebody told him a pipette is too hard to use. Yes, tools can be hard, and yes we should make them easier. But they are often complex because analysis just is. Pipettes for fixed volumes are also easier but you are not going to use these all the time. Ok enough about that. Back to the enrichment analysis. You might also want a tool that is able to see the group or especially the pathway that result from your analysis. Biology is complex, and sometimes a pathway is only enriched because a larger number of isoenzymes are, or sometimes it doesn't show up at the top since it contains some genes that are irrelevant for your situation. So you only want to use the enrichment analysis to then look at the pathway and decide what you think about the biological relevance of the result. Please don't publish the pathway list as an end result. To do this you could use Cytoscape, which was mentioned before. I would also suggest PathVisio. Our pathway analysis tool and visualisation tool (and the editor for WikiPathways). It does pathway enrichment using Z-scores out of the box with an easy to use user interface (but do do the tutorials). There is also a Gene Set Enrichment plugin if you think that analysis type is more useful.

AgriGO is tecnically sound and gives you nice figures...in adidtion to that, it is a web-based serviced that takes 5 minutes to learn to use.