Predicting post-synaptic activity in proteins with data mining.
The bioinformatics problem being addressed in this paper is to predict whether or not a protein has post-synaptic activity. This problem is of great intrinsic interest because proteins with post-synaptic activities are connected with functioning of the nervous system. Indeed, many proteins having post-synaptic activity have been functionally characterized by biochemical, immunological and proteomic exercises. They represent a wide variety of proteins with functions in extracellular signal reception and propagation through intracellular apparatuses, cell adhesion molecules and scaffolding proteins that link them in a web. The challenge is to automatically discover features of the primary sequences of proteins that typically occur in proteins with post-synaptic activity but rarely (or never) occur in proteins without post-synaptic activity, and vice-versa. In this context, we used data mining to automatically discover classification rules that predict whether or not a protein has post-synaptic activity. The discovered rules were analysed with respect to their predictive accuracy (generalization ability) and with respect to their interestingness to biologists (in the sense of representing novel, unexpected knowledge).
Pappa
Gisele L
GL
Computing Laboratory, University of Kent, Canterbury, UK.
Baines
Anthony J
AJ
Freitas
Alex A
AA
D003628:Database Management Systems; D030562:Databases, Protein; D019706:Excitatory Postsynaptic Potentials / Q000502:physiology; D016247:Information Storage and Retrieval / Q000379:methods; D009411:Nerve Endings / Q000737:chemistry / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism*; D018377:Neurotransmitter Agents / Q000737:chemistry / Q000378:metabolism; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship; D013569:Synapses / Q000737:chemistry* / Q000378:metabolism*
D009419:Nerve Tissue Proteins; D018377:Neurotransmitter Agents