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However, the "/u01/app/oracle/oradata/XE/system.dbf" file exists.Well, the error message doesn't say it doesn't exist, but that it's corrupted. It seems that the last part of the installation, the recovery of the instance stored in the installation package, failed on your system. You could either try to repair it, or - because you probably have nothing serious in your instance as it never was online - you could just reinstall it. I'd take a look into the installation log to see what error occured and if it's likely to come up again...
Also, I don't have any XE application server running and listening on 8080 tcp, did I miss something ?Well, there is no application server, actually. The APEX instance is hosted by the so called Embedded PL/SQL Gateway, which is based on the databases internal HTTP Server (XDB HTTP Server).
You'll have it online when your database comes up properly.