Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

A gene function prediction method suitable for the design of targeted RNAi libraries is described and used to predict chromosome condensation genes. Systematic experimental validation of candidate genes in a focused RNAi screen by automated microscopy and quantitative image analysis reveals many new chromosome condensation factors.

[1]  J. Butler,et al.  Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity , 2013, Wiley interdisciplinary reviews. RNA.

[2]  Jean-Karim Hériché,et al.  Quantitative Analysis of Chromosome Condensation in Fission Yeast , 2012, Molecular and Cellular Biology.

[3]  J. Ellenberg,et al.  Mitotic lamin disassembly is triggered by lipid-mediated signaling , 2012, The Journal of cell biology.

[4]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[5]  Alfonso Valencia,et al.  Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology , 2012, PloS one.

[6]  John Quackenbush,et al.  Genome-wide siRNA screen for mediators of NF-κB activation , 2012, Proceedings of the National Academy of Sciences.

[7]  Jun Li,et al.  MIP-T3 Is a Negative Regulator of Innate Type I IFN Response , 2011, The Journal of Immunology.

[8]  Nicholas W. Kin,et al.  Mutations in Traf3ip1 reveal defects in ciliogenesis, embryonic development, and altered cell size regulation. , 2011, Developmental biology.

[9]  T. Hirano,et al.  MCPH1 regulates chromosome condensation and shaping as a composite modulator of condensin II , 2011, The Journal of cell biology.

[10]  C. Haering,et al.  Deciphering condensin action during chromosome segregation. , 2011, Trends in cell biology.

[11]  M. Oyama,et al.  The initial phase of chromosome condensation requires Cdk1-mediated phosphorylation of the CAP-D3 subunit of condensin II. , 2011, Genes & development.

[12]  B. Neumann,et al.  53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress , 2011, Nature Cell Biology.

[13]  Jesse Gillis,et al.  The Impact of Multifunctional Genes on "Guilt by Association" Analysis , 2011, PloS one.

[14]  R. King,et al.  Vigilance and validation: Keys to success in RNAi screening. , 2011, ACS chemical biology.

[15]  Bart De Moor,et al.  A guide to web tools to prioritize candidate genes , 2011, Briefings Bioinform..

[16]  Anastasia A Samsonova,et al.  False negative rates in Drosophila cell-based RNAi screens: a case study , 2011, BMC Genomics.

[17]  C. Orengo,et al.  Assessment of protein domain fusions in human protein interaction networks prediction: application to the human kinetochore model. , 2010, New biotechnology.

[18]  J. Ellenberg,et al.  The protein phosphatase 1 regulator PNUTS is a new component of the DNA damage response , 2010, EMBO reports.

[19]  E. Marcotte,et al.  It's the machine that matters: Predicting gene function and phenotype from protein networks. , 2010, Journal of proteomics.

[20]  Bernd Fischer,et al.  CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging , 2010, Nature Methods.

[21]  J. J. Ward,et al.  Condensins Promote Chromosome Recoiling during Early Anaphase to Complete Sister Chromatid Separation , 2010, Developmental cell.

[22]  Johan A. K. Suykens,et al.  L2-norm multiple kernel learning and its application to biomedical data fusion , 2010, BMC Bioinformatics.

[23]  A. Shevchenko,et al.  A Genome-Scale DNA Repair RNAi Screen Identifies SPG48 as a Novel Gene Associated with Hereditary Spastic Paraplegia , 2010, PLoS biology.

[24]  Andrew B. Clegg,et al.  CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion , 2010, PloS one.

[25]  Quaid Morris,et al.  Fast integration of heterogeneous data sources for predicting gene function with limited annotation , 2010, Bioinform..

[26]  R. Durbin,et al.  Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes , 2010, Nature.

[27]  R. Kolde,et al.  Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods , 2009, Genome Biology.

[28]  A. Emili,et al.  Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins , 2009, PLoS biology.

[29]  Tao Liu,et al.  Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology , 2009, Genome Biology.

[30]  J. Bader,et al.  Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. , 2008, Genome research.

[31]  Junjie Chen,et al.  Microcephalin/MCPH1 Associates with the Condensin II Complex to Function in Homologous Recombination Repair* , 2008, Journal of Biological Chemistry.

[32]  Ian M. Donaldson,et al.  iRefIndex: A consolidated protein interaction database with provenance , 2008, BMC Bioinformatics.

[33]  Holger Erfle,et al.  Work Flow for Multiplexing siRNA Assays by Solid-Phase Reverse Transfection in Multiwell Plates , 2008, Journal of biomolecular screening.

[34]  David Warde-Farley,et al.  GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function , 2008, Genome Biology.

[35]  Michael I. Jordan,et al.  A critical assessment of Mus musculus gene function prediction using integrated genomic evidence , 2008, Genome Biology.

[36]  Laura Diosan,et al.  Optimising Multiple Kernels for SVM by Genetic Programming , 2008, EvoCOP.

[37]  Y. Iwakura,et al.  Kid-Mediated Chromosome Compaction Ensures Proper Nuclear Envelope Formation , 2008, Cell.

[38]  A. Fraser,et al.  A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans , 2008, Nature Genetics.

[39]  P. Chebotarev Spanning forests and the golden ratio , 2006, Discret. Appl. Math..

[40]  Edwin R. Hancock,et al.  Clustering and Embedding Using Commute Times , 2007, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[41]  Tijl De Bie,et al.  Kernel-based data fusion for gene prioritization , 2007, ISMB/ECCB.

[42]  J. Ellenberg,et al.  Maximal chromosome compaction occurs by axial shortening in anaphase and depends on Aurora kinase , 2007, Nature Cell Biology.

[43]  Volker Roth,et al.  Improved functional prediction of proteins by learning kernel combinations in multilabel settings , 2007, BMC Bioinformatics.

[44]  François Fouss,et al.  Random-Walk Computation of Similarities between Nodes of a Graph with Application to Collaborative Recommendation , 2007, IEEE Transactions on Knowledge and Data Engineering.

[45]  J. Ellenberg,et al.  Live-Cell Imaging Reveals a Stable Cohesin-Chromatin Interaction after but Not before DNA Replication , 2006, Current Biology.

[46]  Pavel Yu. Chebotarev,et al.  The Matrix-Forest Theorem and Measuring Relations in Small Social Groups , 2006, ArXiv.

[47]  Leszek Rychlewski,et al.  FFAS03: a server for profile–profile sequence alignments , 2005, Nucleic Acids Res..

[48]  G. Kao,et al.  Mitotic spindle checkpoint inactivation by trichostatin A defines a mechanism for increasing cancer cell killing by microtubule-disrupting agents , 2005, Cancer biology & therapy.

[49]  Alfonso Valencia,et al.  Implementing the iHOP concept for navigation of biomedical literature , 2005, ECCB/JBI.

[50]  Hiroaki Kitano,et al.  The PANTHER database of protein families, subfamilies, functions and pathways , 2004, Nucleic Acids Res..

[51]  J. Ellenberg,et al.  Distinct functions of condensin I and II in mitotic chromosome assembly , 2004, Journal of Cell Science.

[52]  Nello Cristianini,et al.  A statistical framework for genomic data fusion , 2004, Bioinform..

[53]  A. Valencia,et al.  A gene network for navigating the literature , 2004, Nature Genetics.

[54]  C. Kervrann,et al.  Robust incremental compensation of the light attenuation with depth in 3D fluorescence microscopy , 2004, Journal of microscopy.

[55]  Keith D Robertson,et al.  Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. , 2004, Nucleic acids research.

[56]  A. F. Neuwald,et al.  Differential Contributions of Condensin I and Condensin II to Mitotic Chromosome Architecture in Vertebrate Cells , 2003, Cell.

[57]  I. Gutman,et al.  Resistance distance and Laplacian spectrum , 2003 .

[58]  D. Cimini,et al.  Histone hyperacetylation in mitosis prevents sister chromatid separation and produces chromosome segregation defects. , 2003, Molecular biology of the cell.

[59]  R. Puri,et al.  MIP‐T3 associates with IL‐13Rα1 and suppresses STAT6 activation in response to IL‐13 stimulation , 2003, FEBS letters.

[60]  R. Gassmann,et al.  Condensin is required for nonhistone protein assembly and structural integrity of vertebrate mitotic chromosomes. , 2003, Developmental cell.

[61]  Nello Cristianini,et al.  Kernel Methods for Pattern Analysis , 2004 .

[62]  C. Ke Rvra N N,et al.  Robust incremental compensation of the light attenuation with depth in 3 D fluorescence microscopy , 2003 .

[63]  M. Daly,et al.  Guilt by association , 2000, Nature Genetics.

[64]  E. Rogakou,et al.  DNA Double-stranded Breaks Induce Histone H2AX Phosphorylation on Serine 139* , 1998, The Journal of Biological Chemistry.

[65]  Michael Gribskov,et al.  Combining evidence using p-values: application to sequence homology searches , 1998, Bioinform..

[66]  P. Brzoska,et al.  Mitotic chromosome condensation in the rDNA requires TRF4 and DNA topoisomerase I in Saccharomyces cerevisiae. , 1996, Genes & development.

[67]  D. Koshland,et al.  SMC2, a Saccharomyces cerevisiae gene essential for chromosome segregation and condensation, defines a subgroup within the SMC family. , 1995, Genes & development.

[68]  T. Mitchison,et al.  A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro , 1994, Cell.