S Horvath

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Gene network interconnectedness and the generalized topological overlap measure
    Andy M Yip
    Department of Mathematics, National University of Singapore, 2, Science Drive 2, Singapore 117543, Singapore
    BMC Bioinformatics 8:22. 2007
  2. ncbi request reprint Expression of transcription factor Yin Yang 1 in prostate cancer
    David Seligson
    Department of Pathology and Laboratory Medicine, University of California, Los Angeles, 90095, USA
    Int J Oncol 27:131-41. 2005
  3. pmc When is hub gene selection better than standard meta-analysis?
    Peter Langfelder
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 8:e61505. 2013
  4. pmc Is my network module preserved and reproducible?
    Peter Langfelder
    Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
    PLoS Comput Biol 7:e1001057. 2011
  5. pmc Cluster and propensity based approximation of a network
    John Michael Ranola
    Biomathematics, University of California, Los Angeles, CA, USA
    BMC Syst Biol 7:21. 2013
  6. pmc Network methods for describing sample relationships in genomic datasets: application to Huntington's disease
    Michael C Oldham
    Department of Neurology, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, USA
    BMC Syst Biol 6:63. 2012
  7. pmc Text-mining applied to autoimmune disease research: the Sjögren's syndrome knowledge base
    Sven Ulrik Gorr
    Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
    BMC Musculoskelet Disord 13:119. 2012
  8. pmc Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease
    Andrew J Levine
    Department of Neurology, National Neurological AIDS Bank, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
    BMC Med Genomics 6:4. 2013
  9. pmc Adipose co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes
    Blake E Haas
    Department of Human Genetics, Gonda Center, Los Angeles, California, 90095 7088, USA
    BMC Med Genomics 5:61. 2012
  10. pmc Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects
    Kristel R van Eijk
    Department of Medical Genetics, University Medical Center Utrecht, Utrecht 3584, CG, The Netherlands
    BMC Genomics 13:636. 2012

Collaborators

Detail Information

Publications100

  1. pmc Gene network interconnectedness and the generalized topological overlap measure
    Andy M Yip
    Department of Mathematics, National University of Singapore, 2, Science Drive 2, Singapore 117543, Singapore
    BMC Bioinformatics 8:22. 2007
    ..Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness...
  2. ncbi request reprint Expression of transcription factor Yin Yang 1 in prostate cancer
    David Seligson
    Department of Pathology and Laboratory Medicine, University of California, Los Angeles, 90095, USA
    Int J Oncol 27:131-41. 2005
    ..These results may also implicate YY1 as a useful diagnostic and prognostic marker...
  3. pmc When is hub gene selection better than standard meta-analysis?
    Peter Langfelder
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 8:e61505. 2013
    ..The article also reports a comparison of meta-analysis techniques applied to gene expression data and presents novel R functions for carrying out consensus network analysis, network based screening, and meta analysis...
  4. pmc Is my network module preserved and reproducible?
    Peter Langfelder
    Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
    PLoS Comput Biol 7:e1001057. 2011
    ..Data, R software and accompanying tutorials can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ModulePreservation...
  5. pmc Cluster and propensity based approximation of a network
    John Michael Ranola
    Biomathematics, University of California, Los Angeles, CA, USA
    BMC Syst Biol 7:21. 2013
    ..Multigraph networks are attractive because they support likelihood based inference. Unfortunately, it is unclear how to adjust current statistical methods to detect the clusters inherent in many data sets...
  6. pmc Network methods for describing sample relationships in genomic datasets: application to Huntington's disease
    Michael C Oldham
    Department of Neurology, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, USA
    BMC Syst Biol 6:63. 2012
    ..Consequently, the full extent of sample variation in genomic studies is often under-appreciated, complicating downstream analytical tasks such as gene co-expression network analysis...
  7. pmc Text-mining applied to autoimmune disease research: the Sjögren's syndrome knowledge base
    Sven Ulrik Gorr
    Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
    BMC Musculoskelet Disord 13:119. 2012
    ..The goal of this study was to develop a database that collects and organizes gene and protein expression data from the existing literature for comparative analysis with future gene expression and proteomic studies of Sjögren's syndrome...
  8. pmc Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease
    Andrew J Levine
    Department of Neurology, National Neurological AIDS Bank, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
    BMC Med Genomics 6:4. 2013
    ..Additionally, we compare these data to those derived from brains of individuals with Alzheimer's disease (AD) in order to identify common pathways of neuropathogenesis...
  9. pmc Adipose co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes
    Blake E Haas
    Department of Human Genetics, Gonda Center, Los Angeles, California, 90095 7088, USA
    BMC Med Genomics 5:61. 2012
    ..Fat is stored in the form of TGs in human adipose tissue. We hypothesized that gene co-expression networks in human adipose tissue may be correlated with serum TG levels and help reveal novel genes involved in TG regulation...
  10. pmc Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects
    Kristel R van Eijk
    Department of Medical Genetics, University Medical Center Utrecht, Utrecht 3584, CG, The Netherlands
    BMC Genomics 13:636. 2012
    ..However, recent studies suggest that the relationship between genetic variation, DNA methylation and expression is more complex...
  11. pmc Random generalized linear model: a highly accurate and interpretable ensemble predictor
    Lin Song
    Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
    BMC Bioinformatics 14:5. 2013
    ..Since limited evaluations suggested that these ensemble predictors were less accurate than alternative predictors, they have found little attention in the literature...
  12. pmc Comparison of co-expression measures: mutual information, correlation, and model based indices
    Lin Song
    Human Genetics, David Geffen School of Medicine, University of California, California, Los Angeles, USA
    BMC Bioinformatics 13:328. 2012
    ..Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes)...
  13. pmc Weighted gene coexpression network analysis strategies applied to mouse weight
    Tova F Fuller
    Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
    Mamm Genome 18:463-72. 2007
    ..These examples provide evidence that integration of network properties may well help chart the path across the gene-trait chasm...
  14. pmc Air-pollutant chemicals and oxidized lipids exhibit genome-wide synergistic effects on endothelial cells
    Ke Wei Gong
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Genome Biol 8:R149. 2007
    ..We hypothesize that these pro-oxidative chemicals could synergize with oxidized lipid components generated in low-density lipoprotein particles to enhance vascular inflammation and atherosclerosis...
  15. pmc Understanding network concepts in modules
    Jun Dong
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 1:24. 2007
    ..Dozens of potentially useful network concepts are known from graph theory...
  16. pmc Gene networks associated with conditional fear in mice identified using a systems genetics approach
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 5:43. 2011
    ..To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution...
  17. pmc Eigengene networks for studying the relationships between co-expression modules
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 1:54. 2007
    ..Ample literature exists on how to detect biologically meaningful modules in networks but there is a need for methods that allow one to study the relationships between modules...
  18. pmc Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome
    Angela P Presson
    Biostatistics, University of California, Los Angeles, CA, USA
    BMC Syst Biol 2:95. 2008
    ..Here we show that the additional inclusion of genetic marker data allows one to characterize network relationships as causal or reactive in a chronic fatigue syndrome (CFS) data set...
  19. pmc Using genetic markers to orient the edges in quantitative trait networks: the NEO software
    Jason E Aten
    Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
    BMC Syst Biol 2:34. 2008
    ....
  20. pmc Is human blood a good surrogate for brain tissue in transcriptional studies?
    Chaochao Cai
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
    BMC Genomics 11:589. 2010
    ..We tested this hypothesis by relating three human brain expression data sets (from cortex, cerebellum and caudate nucleus) to two large human blood expression data sets (comprised of 1463 individuals)...
  21. pmc Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks
    Marc R J Carlson
    Gonda Goldschmied Neuroscience and Genetics Research Center, Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 7088, USA
    BMC Genomics 7:40. 2006
    ..Highly connected hub proteins, largely responsible for maintaining network connectivity, have been found to be much more likely to be essential for yeast survival...
  22. pmc Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
    Mike J Mason
    Statistics, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 10:327. 2009
    ..To that end, we investigated the use of unsigned and signed network analysis to identify pluripotency and differentiation related genes...
  23. pmc Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients
    Christiaan G J Saris
    Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
    BMC Genomics 10:405. 2009
    ..Since access to spinal cord tissue is not possible at disease onset, we investigated changes in gene expression profiles in whole blood of ALS patients...
  24. pmc Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background
    Simone de Jong
    Department of Medical Genetics and Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
    BMC Genomics 11:20. 2010
    ..We performed a whole-genome gene expression experiment and applied a systems biology approach using weighted gene co-expression network analysis...
  25. pmc Multivariate variance-components analysis of longitudinal blood pressure measurements from the Framingham Heart Study
    Peter Kraft
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    BMC Genet 4:S55. 2003
    ..2 and 2.4, respectively). In this study, multivariate analysis provides no increase in power; this is likely due to the strong positive correlation in systolic blood pressure measured at different ages...
  26. pmc Protein expression based multimarker analysis of breast cancer samples
    Angela P Presson
    Department of Biostatistics, UCLA, Los Angeles, CA 90095, USA
    BMC Cancer 11:230. 2011
    ..Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups...
  27. pmc Expression of phosphorylated raf kinase inhibitor protein (pRKIP) is a predictor of lung cancer survival
    Sara Huerta-Yepez
    Unidad de Investigacion en Enferemedades Oncologicas, Hospital Infantil de Mexico, Federico Gomez, SSA, Mexico
    BMC Cancer 11:259. 2011
    ..The prognostic power has typically been based on total RKIP expression and has not considered the significance of phospho-RKIP...
  28. pmc Differential expression of anterior gradient gene AGR2 in prostate cancer
    Erin L Maresh
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
    BMC Cancer 10:680. 2010
    ..In particular, AGR2 has previously been found to be one of several genes that encode secreted proteins showing increased expression in prostate cancer cells compared to normal prostatic epithelium...
  29. pmc Elevated MED28 expression predicts poor outcome in women with breast cancer
    Nam K Yoon
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
    BMC Cancer 10:335. 2010
    ..MED28 has also been associated with tumor progression in in vitro and in vivo models. Here we examined the association of MED28 expression with human breast cancer progression...
  30. pmc Strategies for aggregating gene expression data: the collapseRows R function
    Jeremy A Miller
    Interdepartmental Program for Neuroscience, UCLA, Los Angeles, California, USA
    BMC Bioinformatics 12:322. 2011
    ..Several standard statistical summary techniques can be used, but network methods also provide useful alternative methods to find representatives. Currently few collapsing functions are developed and widely applied...
  31. pmc WGCNA: an R package for weighted correlation network analysis
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 9:559. 2008
    ..While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial...
  32. ncbi request reprint Family-based tests for associating haplotypes with general phenotype data: application to asthma genetics
    Steve Horvath
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genet Epidemiol 26:61-9. 2004
    ..00005) and the measure of bronchodilator responsiveness (P value =0.016)...
  33. pmc Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target
    S Horvath
    Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 103:17402-7. 2006
    ....
  34. ncbi request reprint The family based association test method: strategies for studying general genotype--phenotype associations
    S Horvath
    Institute for Medical Statistics and Genetic Epidemiology, University of Bonn, Bonn, Germany
    Eur J Hum Genet 9:301-6. 2001
    ..This result allows us to generalise the RC-TDT to dominant, recessive and multi-allelic marker codings. Simulations compare the resulting FBAT tests to the RC-TDT and the S-TDT. The FBAT software is freely available...
  35. pmc Network module detection: Affinity search technique with the multi-node topological overlap measure
    Ai Li
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Res Notes 2:142. 2009
    ..CONCLUSION: Our flexible module detection method is implemented in the MTOM software which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/MTOM/..
  36. ncbi request reprint Family-based association test method: age of onset traits and covariates
    S Horvath
    Department of Human Genetics, UCLA School of Medicine, Gonda Neuroscience and Genetics Research Center, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
    Genet Epidemiol 21:S403-8. 2001
    ..We find only weak evidence (p = 0.0002) that marker D06G032 is associated with the affectation status...
  37. ncbi request reprint Network neighborhood analysis with the multi-node topological overlap measure
    Ai Li
    Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095 1772, USA
    Bioinformatics 23:222-31. 2007
    ..g. the topological overlap measure. Since the use of multiple nodes in the seed set may lead to more informative neighborhoods, it can be advantageous to define multi-node similarity measures...
  38. ncbi request reprint Gene expression profiling identifies molecular subtypes of gliomas
    Ruty Shai
    Department of Human Genetics, Henry E Singleton Brain Tumor Program, UCLA School of Medicine, Los Angeles, CA 90095, USA
    Oncogene 22:4918-23. 2003
    ..These results further define molecular subsets of gliomas which may potentially be used for patient stratification, and suggest potential targets for treatment...
  39. ncbi request reprint Gene expression profiling of gliomas strongly predicts survival
    William A Freije
    Department of Human Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
    Cancer Res 64:6503-10. 2004
    ....
  40. ncbi request reprint Global histone modification patterns predict risk of prostate cancer recurrence
    David B Seligson
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Nature 435:1262-6. 2005
    ..Thus, widespread changes in specific histone modifications indicate previously undescribed molecular heterogeneity in prostate cancer and might underlie the broad range of clinical behaviour in cancer patients...
  41. ncbi request reprint Correlation of Ki-67 and gelsolin expression to clinical outcome in renal clear cell carcinoma
    Harri Visapaa
    Department of Pathology and Laboratory Medicine, University of California, Los Angeles, School of Medicine, USA
    Urology 61:845-50. 2003
    ....
  42. ncbi request reprint Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo
    Gheeyoung Choe
    Departments of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
    Cancer Res 63:2742-6. 2003
    ..These results provide the first dissection of the PI3K pathway in glioblastoma in vivo and suggest an approach to stratifying patients for targeted kinase inhibitor therapy...
  43. ncbi request reprint Ki67, gelsolin and PTEN expression in sarcomatoid renal tumors
    Harri Visapaa
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, 695 Charles E Young Drive South, Box 957088, Los Angeles, CA 90095 7088, USA
    Urol Res 30:387-9. 2003
    ..We also show that gelsolin expression differs between the studied tumor types, suggesting different roles for gelsolin in the carcinogenesis of different renal tumor types...
  44. ncbi request reprint Expression of X-linked inhibitor of apoptosis protein is a strong predictor of human prostate cancer recurrence
    David B Seligson
    Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California 90095 1747, USA
    Clin Cancer Res 13:6056-63. 2007
    ..We examined the expression patterns of XIAP with regard to human prostate cancer, predicting that XIAP status may predict cancer recurrence and/or clinical outcome...
  45. ncbi request reprint Loss of CD10 (neutral endopeptidase) is a frequent and early event in human prostate cancer
    Stephen J Freedland
    Department of Urology, UCLA School of Medicine, Los Angeles, CA 90095 1738, USA
    Prostate 55:71-80. 2003
    ....
  46. ncbi request reprint Statistical methods for analyzing tissue microarray data
    Xueli Liu
    Department of Biostatistics, School of Public Health, UCLA, Los Angeles, California, USA
    J Biopharm Stat 14:671-85. 2004
    ..We also use bump hunting (patient rule induction method), which we adapt to the use with survival data. The proposed methods are applied to a kidney cancer tissue microarray data set...
  47. pmc Global levels of histone modifications predict prognosis in different cancers
    David B Seligson
    Departments of Pathology and Laboratory Medicine, Human Genetics, David GeffenSchool of Medicine, University of California, Los Angeles, California 90095 1737, USA
    Am J Pathol 174:1619-28. 2009
    ....
  48. pmc A family-based test for correlation between gene expression and trait values
    Peter Kraft
    Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90095 1772, USA
    Am J Hum Genet 72:1323-30. 2003
    ....
  49. pmc Geometric interpretation of gene coexpression network analysis
    Steve Horvath
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
    PLoS Comput Biol 4:e1000117. 2008
    ..The unification of coexpression network methods with traditional data mining methods can inform the application and development of systems biologic methods...
  50. pmc Functional organization of the transcriptome in human brain
    Michael C Oldham
    Interdepartmental Program for Neuroscience, University of California Los Angeles, Los Angeles, California 90095, USA
    Nat Neurosci 11:1271-82. 2008
    ..Our findings provide a new foundation for neurogenetic inquiries by revealing a robust and previously unrecognized organization to the human brain transcriptome...
  51. ncbi request reprint Extreme skewing of X chromosome inactivation in mothers of homosexual men
    Sven Bocklandt
    Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
    Hum Genet 118:691-4. 2006
    ..Our findings support a role for the X chromosome in regulating sexual orientation in a subgroup of gay men...
  52. ncbi request reprint Identification of molecular subtypes of glioblastoma by gene expression profiling
    Paul S Mischel
    Department of Pathology, UCLA School of Medicine, Los Angeles, CA 90095, USA
    Oncogene 22:2361-73. 2003
    ..These results define distinct molecular subtypes of GBMs that may be important in disease stratification, and in the discovery and assessment of GBM treatment strategies...
  53. pmc Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids
    Peter S Gargalovic
    Department of Medicine, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 103:12741-6. 2006
    ....
  54. pmc Integrating genetic and network analysis to characterize genes related to mouse weight
    Anatole Ghazalpour
    Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e130. 2006
    ..Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest...
  55. ncbi request reprint Tissue microarray analysis of cytoskeletal actin-associated biomarkers gelsolin and E-cadherin in urothelial carcinoma
    JianYu Rao
    Department of Pathology and Laboratory Medicine, University of California at Los Angeles, 90095, USA
    Cancer 95:1247-57. 2002
    ..However, it is not clear how these altered expressions associate with tumor progression, nor is it clear how these protein markers provide prognostic value for urothelial carcinomas...
  56. ncbi request reprint Flap endonuclease 1 is overexpressed in prostate cancer and is associated with a high Gleason score
    John S Lam
    Department of Urology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095 1738, USA
    BJU Int 98:445-51. 2006
    ..1, the most aggressive clone generated from the hormone-refractory prostate cancer cell line CL1...
  57. ncbi request reprint Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma
    Tao Shi
    Department of Human Genetics, University of California, Los Angeles, CA 90095 7088, USA
    Mod Pathol 18:547-57. 2005
    ....
  58. ncbi request reprint Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity
    Nicole K Maclennan
    Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 7088, USA
    Hum Mol Genet 15:405-15. 2006
    ..These studies show that Gyk deletion causes alterations in expression of genes in several regulatory networks and is the first time NCA has been used to expand on microarray data from a mouse KO model of a human disease...
  59. ncbi request reprint Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
    Peter Langfelder
    Department of Human Genetics, University of California at Los Angeles, CA 90095 7088, USA
    Bioinformatics 24:719-20. 2008
    ..We illustrate the use of these methods by applying them to protein-protein interaction network data and to a simulated gene expression data set...
  60. ncbi request reprint Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells
    Ichiro Nakano
    Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
    J Neurosci Res 86:48-60. 2008
    ..These results demonstrate a critical role for MELK in the proliferation of brain tumors, including their stem cells, and suggest that MELK may be a compelling molecular target for treatment of high-grade brain tumors...
  61. ncbi request reprint Carbonic anhydrase IX is an independent predictor of survival in advanced renal clear cell carcinoma: implications for prognosis and therapy
    Matthew H T Bui
    Department of Urology, University of California, Los Angeles, California 90095 1738, USA
    Clin Cancer Res 9:802-11. 2003
    ..To date, there are no molecular markers which can reliably predict RCC outcome. We investigated whether a novel kidney cancer marker, carbonic anhydrase IX (CAIX), is associated with progression and survival...
  62. pmc Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors
    Brandon H Le
    Department of Molecular, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:8063-70. 2010
    ..Collectively, these seed-specific TF genes should facilitate the identification of regulatory networks that are important for programming seed development...
  63. pmc High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes
    Elena Allen
    Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 100:9940-5. 2003
    ..The sequence characteristics that distinguished the high-LINE-1 category were used to identify more than 1,000 additional genes from the human and mouse genomes as candidate genes for monoallelic expression...
  64. ncbi request reprint Using protein expressions to predict survival in clear cell renal carcinoma
    Hyung L Kim
    Department of Urology, University of California School of Medicine, Los Angeles, California 90095 1738, USA
    Clin Cancer Res 10:5464-71. 2004
    ....
  65. pmc EGFR signaling through an Akt-SREBP-1-dependent, rapamycin-resistant pathway sensitizes glioblastomas to antilipogenic therapy
    Deliang Guo
    1Department of Pathology and Laboratory Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA 90095, USA
    Sci Signal 2:ra82. 2009
    ..These results identify a previously undescribed EGFR-mediated prosurvival metabolic pathway and suggest new therapeutic approaches to treating EGFR-activated glioblastomas...
  66. ncbi request reprint Weighted gene co-expression network analysis identifies biomarkers in glycerol kinase deficient mice
    Nicole K Maclennan
    Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 1752, USA
    Mol Genet Metab 98:203-14. 2009
    ..This first application of WGCNA to mouse knockout data provides insights into the molecular mechanisms of GKD pathogenesis. The resulting systems-genetic gene screening method identifies candidate biomarkers for GKD...
  67. ncbi request reprint Relationship between survival and edema in malignant gliomas: role of vascular endothelial growth factor and neuronal pentraxin 2
    Marc R J Carlson
    Department of Human Genetics, University of California at Los Angeles and David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California 90095 1271, USA
    Clin Cancer Res 13:2592-8. 2007
    ..VEGF inhibition reduces edema and tumor burden in some patients with malignant glioma, whereas others show no response. The role of VEGF expression in edema production and the relationship to survival is not well understood...
  68. ncbi request reprint Antibody-based profiling of the phosphoinositide 3-kinase pathway in clinical prostate cancer
    George V Thomas
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
    Clin Cancer Res 10:8351-6. 2004
    ..Prostate cancers also present unique organ-specific challenges, in that tumors are heterogeneous and diagnostic tissue is extremely limited...
  69. ncbi request reprint p53 is an independent predictor of tumor recurrence and progression after nephrectomy in patients with localized renal cell carcinoma
    Oleg Shvarts
    Department of Urology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California 90095 1738, USA
    J Urol 173:725-8. 2005
    ..We determined which clinical and molecular variables can predict cancer recurrence in patients following surgical management for localized renal cell carcinoma (RCC)...
  70. pmc Conservation and evolution of gene coexpression networks in human and chimpanzee brains
    Michael C Oldham
    Interdepartmental Program for Neuroscience, Program in Neurogenetics, and Semel Institute, David Geffen School of Medicine, Los Angeles, CA 90095 6814, USA
    Proc Natl Acad Sci U S A 103:17973-8. 2006
    ..Our results provide insights into the molecular bases of primate brain organization and demonstrate the general utility of weighted gene coexpression network analysis...
  71. pmc Repetitive sequence environment distinguishes housekeeping genes
    C Daniel Eller
    UCLA Department of Human Genetics, David Geffen School of Medicine, Gonda Center, 695 E Young Drive South, Los Angeles, California 90095 7088, USA
    Gene 390:153-65. 2007
    ..Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes...
  72. ncbi request reprint Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors
    Ingo K Mellinghoff
    Department of Molecular and Medical Pharmacology and Medicine, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles 90095 1732, USA
    N Engl J Med 353:2012-24. 2005
    ..The mechanism of responsiveness of glioblastomas to these inhibitors is unknown...
  73. pmc Expression of colony-stimulating factor 1 receptor during prostate development and prostate cancer progression
    Hisamitsu Ide
    Howard Hughes Medical Institute, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 99:14404-9. 2002
    ..These observations correlate CSF-1R expression with changes in the growth and development of the normal and neoplastic prostate...
  74. ncbi request reprint Clinicopathologic and molecular correlations of necrosis in the primary tumor of patients with renal cell carcinoma
    John S Lam
    Department of Urology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California 90095 1738, USA
    Cancer 103:2517-25. 2005
    ..The authors investigated the relation of tumor necrosis to other clinicopathologic factors known to be important prognostic indicators for patients with RCC...
  75. ncbi request reprint Na,K-adenosine triphosphatase alpha1-subunit predicts survival of renal clear cell carcinoma
    David B Seligson
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
    J Urol 179:338-45. 2008
    ..We determined the clinical association of protein expression patterns of the Na,K-adenosine triphosphatase alpha1 and beta1-subunits in renal clear cell carcinoma using tissue microarrays with linked clinicopathological data...
  76. pmc Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma
    Tim F Cloughesy
    Department of Neurology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Med 5:e8. 2008
    ..Small, molecularly focused clinical studies offer the promise of the early definition of optimal biologic dose and patient population...
  77. doi request reprint Development of a real-time RT-PCR assay for detecting EGFRvIII in glioblastoma samples
    Koji Yoshimoto
    Departments of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 1732, USA
    Clin Cancer Res 14:488-93. 2008
    ..Further, frozen tissue is not routinely available, particularly for patients treated in the community. Thus, detection of EGFRvIII in formalin-fixed paraffin-embedded (FFPE) clinical samples is a major challenge...
  78. pmc An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association
    Charles R Farber
    Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California, USA
    J Bone Miner Res 24:105-16. 2009
    ..Integration of multiple genetic and genomic data sets can substantially improve the efficiency of QTL fine-mapping and candidate gene identification...
  79. pmc Insulin growth factor-binding protein 2 is a candidate biomarker for PTEN status and PI3K/Akt pathway activation in glioblastoma and prostate cancer
    R Mehrian-Shai
    Institute for Genetic Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 104:5563-8. 2007
    ....
  80. ncbi request reprint The genetics of gene expression and gene mapping
    Peter Kraft
    Department of Biostatistics, UCLA School of Public Health, Box 951772 51 236C CHS, Los Angeles, CA 90095 1772, USA
    Trends Biotechnol 21:377-8. 2003
    ....
  81. ncbi request reprint Prostate stem cell antigen expression is associated with gleason score, seminal vesicle invasion and capsular invasion in prostate cancer
    Ken ryu Han
    Department of Urology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California 90095 1738, USA
    J Urol 171:1117-21. 2004
    ..We investigated the expression and potential clinical usefulness of prostate stem cell antigen (PSCA) in CaP using tissue microarrays...
  82. pmc Presence of a putative tumor-initiating progenitor cell population predicts poor prognosis in smokers with non-small cell lung cancer
    Aik T Ooi
    Department of Pediatrics, Division of Hematology Oncology, Mattel Children s Hospital, University of California at Los Angeles, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
    Cancer Res 70:6639-48. 2010
    ..This suggests that reparative K14+ progenitor cells may be tumor-initiating cells in this subgroup of smokers with NSCLC...
  83. pmc The organization of the transcriptional network in specific neuronal classes
    Kellen D Winden
    Interdepartmental Program for Neuroscience, University of California Los Angeles, Los Angeles, CA, USA
    Mol Syst Biol 5:291. 2009
    ..These analyses provide a basis for understanding how specific aspects of neuronal phenotypic diversity are organized at the transcriptional level...
  84. pmc Epithelial membrane protein-2 expression is an early predictor of endometrial cancer development
    Omar Habeeb
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
    Cancer 116:4718-26. 2010
    ..Here the authors validate the expression of EMP2 in EC, and further examine whether EMP2 expression within preneoplastic lesions is an early prognostic biomarker for EC development...
  85. ncbi request reprint Inhibition of Atm and/or Atr disrupts gene silencing on the inactive X chromosome
    Yan Ouyang
    Department of Human Genetics, The David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Biochem Biophys Res Commun 337:875-80. 2005
    ..Atm and Atr, therefore, not only function in responding to DNA damage but perhaps also are involved in gene silencing via the maintenance of heterochromatin...
  86. pmc A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia
    Christopher L Plaisier
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
    PLoS Genet 5:e1000642. 2009
    ..We then provide evidence from two independent datasets supporting FADS3 as a causal gene for FCHL and elevated TGs in Mexicans...
  87. pmc Higher expression levels of 14-3-3sigma in ductal carcinoma in situ of the breast predict poorer outcome
    Nam K Yoon
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 1747, USA
    Cancer Biomark 5:215-24. 2009
    ..To our knowledge this is the first published study associating 14-3-3sigma protein expression with breast cancer survival...
  88. ncbi request reprint Prostate stem cell antigen is overexpressed in prostate cancer metastases
    John S Lam
    Department of Urology, David Geffen School of Medicine at University of California at Los Angeles, CA 90095 1738, USA
    Clin Cancer Res 11:2591-6. 2005
    ..PSCA protein and mRNA expression was examined in prostate cancer bone, lymph node, and visceral metastases to assess the potential of PSCA as an immunotherapeutic target in advanced prostate cancer...
  89. ncbi request reprint Prognostic value of carbonic anhydrase IX and KI67 as predictors of survival for renal clear cell carcinoma
    Matthew H T Bui
    Departments of Urology, University of California Los Angeles, California 90095 1738, USA
    J Urol 171:2461-6. 2004
    ..The natural history of renal cell carcinoma (RCC) is complex and not entirely explained by conventional prognostic factors. In this study we evaluated the prognostic value of carbonic anhydrase IX (CAIX) and Ki67 to predict survival in RCC...
  90. ncbi request reprint Distinct gene expression profiles in adult mouse heart following targeted MAP kinase activation
    Scherise Mitchell
    Department of Physiology, University of Maryland Baltimore, School of Medicine, Maryland, USA
    Physiol Genomics 25:50-9. 2006
    ..These results provide an overview to both short-term and long-term effects of MAP kinase activation in heart and support some common as well as unique roles for each MAP kinase cascade in the development of heart failure...
  91. pmc Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes
    Stuart M Flechner
    Section of Renal Transplantation, Transplant Center A110, Cleveland Clinic Foundation, Cleveland, OH, USA
    Am J Transplant 4:1475-89. 2004
    ....
  92. ncbi request reprint Breast cancer molecular signatures as determined by SAGE: correlation with lymph node status
    Martin C Abba
    Department of Carcinogenesis, The University of Texas M D Anderson Cancer Center, Science Park Research Division, P O Box 389, Smithville, TX 78957, USA
    Mol Cancer Res 5:881-90. 2007
    ....
  93. ncbi request reprint Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling
    Lola Rahib
    Biomedical Engineering, Interdepartmental Program, Henry Samueli School of Engineering and Applied Science at UCLA, Los Angeles, CA 90095, USA
    Eur J Hum Genet 15:646-57. 2007
    ....
  94. ncbi request reprint Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies
    Karsten Haug
    Institut fur Humangenetik, Universitatsklinikum Bonn, Wilhelmstr 31, 53111 Bonn, Germany
    Nat Genet 33:527-32. 2003
    ..G715E alters voltage-dependent gating, which may cause membrane depolarization and hyperexcitability...
  95. ncbi request reprint Using tumor markers to predict the survival of patients with metastatic renal cell carcinoma
    Hyung L Kim
    Department of Urologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
    J Urol 173:1496-501. 2005
    ..Approximately 30% of renal cell carcinomas (RCCs) present as metastatic disease. Molecular markers have the potential to characterize accurately the biological behavior of tumors and they may be useful for determining prognosis...
  96. ncbi request reprint Analysis of the Na,K-ATPase alpha- and beta-subunit expression profiles of bladder cancer using tissue microarrays
    Cromwell Espineda
    Department of Pathology and Laboratory Medicine, University of California Los Angeles, 90095, USA
    Cancer 97:1859-68. 2003
    ....
  97. ncbi request reprint Trefoil factor 3 is overexpressed in human prostate cancer
    Isla P Garraway
    Department of Urology and The Jonsson Comprehensive Cancer Center, David Geffen UCLA School of Medicine, USA
    Prostate 61:209-14. 2004
    ..These studies validate that TFF3 is overexpressed in a subset of primary and metastic prostate cancers...
  98. pmc Variations in DNA elucidate molecular networks that cause disease
    Yanqing Chen
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, 401 Terry Avenue North, Seattle, Washington 98109, USA
    Nature 452:429-35. 2008
    ..Our analysis provides direct experimental support that complex traits such as obesity are emergent properties of molecular networks that are modulated by complex genetic loci and environmental factors...
  99. ncbi request reprint Sexually dimorphic gene expression in mouse brain precedes gonadal differentiation
    Phoebe Dewing
    Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Brain Res Mol Brain Res 118:82-90. 2003
    ..The identification of genes differentially expressed between male and female brains prior to gonadal formation suggests that genetic factors may have roles in influencing brain sexual differentiation...