Have you enabled your application for transaction analytics as given in this docs
If yes, can you cross check in your app agent logs if there's any exception related to analytics or connectivity issue between your app agent and the analytic agent process.
We have AppDynamics 4.2 & also configured Analytic agent 4.2 as a standalone machine agent for java application.
As we have trying to create new analytic search,UI doesn’t show any application in Add criteria field.
Machine agent log :
[system-thread-0] 16 Mar 2017 10:25:42,750 INFO SystemAgent - Started AppDynamics Machine Agent Successfully.
[ExtensionStarter-ServerMonitoring] 16 Mar 2017 10:26:03,635 INFO SimAgentRepetitiveLoggingModule - The turnover time for the SIM agent repetitive logger is 5 minutes
[ConfigExecutor-0] 16 Mar 2017 10:26:03,813 INFO CrashGuardRunner - Not starting crash guard extension because it is disabled.To enable, please update the configuration enabled in CrashGuardConfig.yml