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I have an Xperia U[GB] and there are certain apps which do not work on it[device is not rooted shows up everytime I try to open these apps]. So what exactly does it mean by rooted device. Should I root my device? Does it have any negative implications? Also I still haven't updated it to ICS,since I've been told that Xperia U doesn't perform well with ICS.So should I upgrade it?

trouble_006
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Rooting” your device means obtaining “superuser” rights and permissions to your Android’s software. With these elevated user privileges, you gain the ability to load custom software (ROM’s), install custom themes, increase performance, increase battery life, and the ability to install software that would otherwise cost extra money (ex: WiFi tethering). Rooting is essentially “hacking” your Android device. In the iPhone world, this would be the equivalent to “Jailbreaking” your phone.

Disadvantages of Rooting

Bricking

The number one reason not to root your device is the potential risk of “bricking” it. As mentioned earlier, “bricking” your device means screwing up your phone software so badly that your phone can no longer function properly and is pretty much as useless as a brick. You would likely need to purchase a new Android device since the manufacturer of your device will void the warranty after any attempts at rooting.

Security

There is an increased risk of unknowingly installing malicious software when you root an Android device. Root access circumvents the security restrictions that are put in place by the Android OS. There isn’t really an effective way to tell just what the application intends to do with that “superuser” power. You are putting a lot of trust into the developer’s hands. In most cases, these applications are open source and the community can take a look at the source code to assess the risk. But, nevertheless, the risk is there. Fortunately, malicious software on rooted devices hasn’t really been a problem as of yet. But I thought it was worth mentioning since this could be a potential risk in the future. I’d recommend installing an Anti-Virus and Security App just to be safe. Lookout Mobile Security seems to be one of the best ones available at the moment

If you want to Root your Xperia U follow this link rooting explained on XDA http://forum.xda-developers.com/wiki/Sony_Xperia_U

The L
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    Really "bricking" your device by rooting it is a very rare case. And what you describe for "increased security risk" would only affect apps requiring root access. Last, Antivirus stuff is only to be recommended if you like to be scared by false alerts and want your device to be slowed down, sorry. See e.g. Android Antivirus: 6 truths about smartphone malware. Using some "common sense" is much more effective, and doesn't have negative impact on device performance :) – Izzy May 21 '14 at 14:54