public static Pattern controlsStateChangeThroughDegradation ( ) { Pattern p = new Pattern ( SequenceEntityReference . class , "upstream ER" ) ; p . add ( linkedER ( true ) , "upstream ER" , "upstream generic ER" ) ; p . add ( erToPE ( ) , "upstream generic ER" , "upstream SPE" ) ; p . add ( linkToComplex ( ) , "upstream SPE" , "upstream PE" ) ; p . add ( peToControl ( ) , "upstream PE" , "Control" ) ; p . add ( controlToConv ( ) , "Control" , "Conversion" ) ; p . add ( new NOT ( participantER ( ) ) , "Conversion" , "upstream ER" ) ; p . add ( new Empty ( new Participant ( RelType . OUTPUT ) ) , "Conversion" ) ; p . add ( new Participant ( RelType . INPUT ) , "Conversion" , "input PE" ) ; p . add ( linkToSpecific ( ) , "input PE" , "input SPE" ) ; p . add ( peToER ( ) , "input SPE" , "downstream generic ER" ) ; p . add ( type ( SequenceEntityReference . class ) , "downstream generic ER" ) ; p . add ( linkedER ( false ) , "downstream generic ER" , "downstream ER" ) ; return p ; }
Finds cases where proteins affect their degradation .