title: Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.
abstract: The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted relations connecting known and putative spindle proteins. The subsequent experimental validation of a number of predicted novel proteins confirmed not only their association with the spindle apparatus but also their role in mitosis. We found that 75% of our tested proteins are localizing to the spindle apparatus compared to a success rate of 35% when expert knowledge alone was used. We compare our results to the previously published MitoCheck study and see that our approach does validate some findings by this consortium. Further, we predict so-called "hidden spindle hub", proteins whose network of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network. Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system.
authors.affiliation: Centro Nacional de Investigaciones Oncológicas, Structural Biology and Biocomputing Programme, Madrid, Spain.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Rojas
authors.forename: Anna
authors.initials: A
authors.lastname: Santamaria
authors.forename: Rainer
authors.initials: R
authors.lastname: Malik
authors.forename: Thomas Skøt
authors.initials: TS
authors.lastname: Jensen
authors.forename: Roman
authors.initials: R
authors.lastname: Körner
authors.forename: Ian
authors.initials: I
authors.lastname: Morilla
authors.forename: David
authors.initials: D
authors.lastname: de Juan
authors.forename: Martin
authors.initials: M
authors.lastname: Krallinger
authors.forename: Daniel Aaen
authors.initials: DA
authors.lastname: Hansen
authors.forename: Robert
authors.initials: R
authors.lastname: Hoffmann
authors.forename: Jonathan
authors.initials: J
authors.lastname: Lees
authors.forename: Adam
authors.initials: A
authors.lastname: Reid
authors.forename: Corin
authors.initials: C
authors.lastname: Yeats
authors.forename: Anja
authors.initials: A
authors.lastname: Wehner
authors.forename: Sabine
authors.initials: S
authors.lastname: Elowe
authors.forename: Andrew B
authors.initials: AB
authors.lastname: Clegg
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Erich A
authors.initials: EA
authors.lastname: Nigg
authors.forename: Christine
authors.initials: C
authors.lastname: Orengo
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.forename: Juan A G
authors.initials: JA
authors.lastname: Ranea
mesh_terms: D018797:Cell Cycle Proteins / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030562:Databases, Protein; D006367:HeLa Cells; D006801:Humans; D008856:Microscopy, Fluorescence; D010957:Plasmids / Q000235:genetics; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D039781:PubMed; D034741:RNA, Small Interfering / Q000235:genetics; D012680:Sensitivity and Specificity; D008941:Spindle Apparatus / Q000378:metabolism*; D014162:Transfection
chemical_list: D018797:Cell Cycle Proteins; D034741:RNA, Small Interfering