Which are the basic sites or databases that one should look for to learn more about the various pathways that can lead to a disease (e.g. Epilepsy, because it is of interest to me). Are there any tools or established protocols that can help us predict the pathway by which a particular diseased condition can lead to another diseased condition?
On the expensive side I would recommend Genego Metacore (from Thomson Reuters) or Ingenuity Pathway Analysis (IPA). Also for money, GeneExplain could be a good tool, more for analysis and less to for browsing around. Less deciduous and colorful, but free is KEGG - you can brows the pathways and/or make your own tools with the API the developers provide - all at no charge and for the good of research community. A good place to start, any way.
If you want something with predictive capabilities, with a chance to make novel findings, then you can try dcGO. Your question is not very specific, so it makes it hard to give you step by step links and directions for answering your question. However, typically you can go to the main search page:
http://supfam.org/SUPERFAMILY/cgi-bin/dcsearch.cgi
Type in 'epilepsy' at the top. You can select a type of epilepsy you are interested in from the paginated list and click the PSNet logo next to the name, e.g. the most general is 'epilepsy' (from CTD diseases), which takes you here:
http://supfam.org/SUPERFAMILY/cgi-bin/dcpsnet.cgi?query_po=MESH:D004827
This cross-references epilepsy (or any other disease term) with other ontologies *including pathways*. To see pathways click on the 'UP' tab when it is available. Sadly in the general case of 'epilepsy' there is no predicted link in this database to a known pathway. There are some UniProtKB terms though such as 'ligand-gated ion channel' that might give you somewhere to start (click the KW tab).
Also on the dcGO page for the given term, at the bottom you will find specific protein domains and families and supra-domains associated with the disease:
http://supfam.org/SUPERFAMILY/cgi-bin/dcbo.cgi?type=CD;po=MESH:D004827
E.g. Proton glutamate symport protein, Neurotransmitter-gated ion-channel transmembrane pore, Voltage-gated potassium channels. This doesn't answer your scientific question directly -that would be too easy- but it gives you avenues of investigation to explore.
Thank you so much Andrey and Julian for your comments. I have started looking at the sites (KEGG, supfam.org) and they are really helpful.
Andrey, (Below) I will try my best to explain what I wish to see using the tools (if possible).
There are papers suggesting that prolonged GEFS+ (a type of epilepsy) can lead later to develop Temporal Lobe Epilepsy (TLE). But the exact signalling pathway that can possibly explain this is not yet explained. So, I wish to know if bioinformatics tools could actually be used to come up with a possible solution (by which i mean pathway) for this matter. A search on OMIM with the above titles "GEFS+" and "Temporal Lobe Epilepsy" gave names of a bunch of genes. (I did these searches separately so i have two sets of genes each associated to GEFS+ and TLE respectively.) Then, I used STRING to look for the proteins that interacted with the genes (obtained from OMIM). So, now I have the sets of genes and their interacting proteins. (This is all I have tried doing at my own.)
I wanted to know if this is a good starting point or not. Can you please make any comments or suggestions on what should be done next to meet my objective (of coming up with a signalling pathway)?
I have tried my best to explain things above. If you think some more detail would help you make a comment, please let me know.
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