funpred - Function Prediction CMSC 858L Predicting Protein...

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Function Prediction CMSC 858L
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Predicting Protein Function from Networks Ultimately, we want to know how various processes in the cell work. A frst step: fgure out which proteins are involved in which biological role. What do we mean by a “biological role”? - Several diFFerent schemes: Gene Ontology (largest, most widely used) MIPS (good collection oF known protein complexes) KEGG (manually curated pathways)
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pollen tube growth Gene Ontology ( GO ) Node = manually defned Function Directed, acyclic graph Main edges are either “is a” or “part oF” Curated collection oF biological Functions
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Gene Ontology has 3 Sub-ontologies Cellular component : a part of the cell (a location, or organelle, or other structure) Biological process : a collection of steps that the cell carries out to achieve some purpose. E.g. cell division. Molecular function : a speciFc mechanism that a protein performs. E.g. - a kinase would have molecular function “phosphorylation”; - a transcription factor would have molecular function “DNA binding” Each protein may be annotated with several terms from each sub-ontology.
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Edge Types is_a : like a C++ or Java subclass relationship. - A is_a B means A is a more specifc version oF B - E.g. “nuclear chromosome” is_a “chromosome”.
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funpred - Function Prediction CMSC 858L Predicting Protein...

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