I left the usa for more than 1 year with green card but had stayed for the last 25 months continiously and before that left for only 3 months, will my n400 application be denied or is there a chance I can get deported and green card revoked

You might have very well screwed yourself leaving for that long.

USCIS - Continuous Residence and Physical Presence Requirements for Naturalization (http://www.uscis.gov/portal/site/uscis/menuitem.eb1d4c2a3e5b9ac89243c6a7543f6d1a/?vgnextoid=399faf4c0adb4210VgnVCM100000082ca60aRCR D&vgnextchannel=399faf4c0adb4210VgnVCM100000082ca60a RCRD)

Even being out for 6 months now can do it... a year is even more likely... but over two years... I would be surprised if they haven't revoked it.

Without approved re-entry permit, your GC is automatically revoked.

I'm in the USA now, but that was back in 2009, my question if I apply for naturalization now, if the officer looks at this, is there a chance he/she will revoke the green card and deport me