Peggy Farnham

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes
    Henriette O'Geen
    Genome Center, University of California at Davis, Davis, CA 95616, USA
    BMC Genomics 11:689. 2010
  2. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
  3. pmc Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
    Kimberly R Blahnik
    Department of Computer Science, University of California Davis, Davis, CA 95616, USA
    Nucleic Acids Res 38:e13. 2010
  4. pmc Suz12 binds to silenced regions of the genome in a cell-type-specific manner
    Sharon L Squazzo
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 16:890-900. 2006
  5. pmc Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
    Dag H Yasui
    Department of Medical Microbiology and Immunology, Rowe Program in Human Genetics, School of Medicine, University of California, 1 Shields Avenue, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 104:19416-21. 2007
  6. pmc E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites
    Alina Rabinovich
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 18:1763-77. 2008
  7. doi request reprint Using ChIP-seq technology to identify targets of zinc finger transcription factors
    Henriette O'Geen
    Department of Pharmacology, Genome Center, University of California at Davis, Davis, CA, USA
    Methods Mol Biol 649:437-55. 2010
  8. pmc Comparison of sample preparation methods for ChIP-chip assays
    Henriette O'Geen
    University of California Davis, Davis, CA 95616, USA
    Biotechniques 41:577-80. 2006
  9. pmc Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263
    Seth Frietze
    Department of Pharmacology and the Genome Center, University of California, Davis, California 95616, USA
    J Biol Chem 285:1393-403. 2010
  10. pmc Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
    Vitalina M Komashko
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 18:521-32. 2008

Collaborators

  • Janine LaSalle
  • John L Rinn
  • Howard Chang
  • Ian F Korf
  • AMBER R HOGART
  • Henriette O'Geen
  • Roland Green
  • Xiaoqin Xu
  • Victor X Jin
  • Alina Rabinovich
  • Sharon L Squazzo
  • Seth Frietze
  • Vitalina M Komashko
  • Mark Bieda
  • Kimberly R Blahnik
  • Sushma Iyengar
  • Charles M Nicolet
  • Dag H Yasui
  • Kim Blahnik
  • Bertram Ludäscher
  • Daniel He
  • Lihong Shi
  • Yu Hsuan Lin
  • Xun Lan
  • Osamu Tanabe
  • Timothy McPhillips
  • Alina R Cao
  • Maureen A Sartor
  • Lorigail Echipare
  • Lei Dou
  • James D Engel
  • Sushma S Iyengar
  • Roman Rabinovich
  • Luis G Acevedo
  • Roxanne O Vallero
  • Sailaja Peddada
  • Mathew J Oberley
  • Karen N Thatcher
  • Mark C Bieda
  • Raman P Nagarajan
  • Michael A Singer
  • Sung Wook Jang
  • Danny Reinberg
  • Raphael Margueron
  • Sheryl R Krig

Detail Information

Publications14

  1. pmc Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes
    Henriette O'Geen
    Genome Center, University of California at Davis, Davis, CA 95616, USA
    BMC Genomics 11:689. 2010
    ..The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear...
  2. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
    ..It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions...
  3. pmc Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
    Kimberly R Blahnik
    Department of Computer Science, University of California Davis, Davis, CA 95616, USA
    Nucleic Acids Res 38:e13. 2010
    ..We demonstrate the utility of our software by collecting, analyzing and comparing ChIP-seq data for six different human transcription factors/cell line combinations...
  4. pmc Suz12 binds to silenced regions of the genome in a cell-type-specific manner
    Sharon L Squazzo
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 16:890-900. 2006
    ..Finally, we have shown that some Suz12 target genes are bound by OCT4 in embryonal cells and suggest that OCT4 maintains stem cell self-renewal, in part, by recruiting PRC complexes to certain genes that promote differentiation...
  5. pmc Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
    Dag H Yasui
    Department of Medical Microbiology and Immunology, Rowe Program in Human Genetics, School of Medicine, University of California, 1 Shields Avenue, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 104:19416-21. 2007
    ..These results indicate that the primary function of MeCP2 is not the silencing of methylated promoters...
  6. pmc E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites
    Alina Rabinovich
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 18:1763-77. 2008
    ..Our findings suggest that in vivo (1) a consensus motif is not sufficient to recruit E2Fs, (2) E2Fs can bind to isolated regions that lack a consensus motif, and (3) binding can require regions other than the best match to the E2F motif...
  7. doi request reprint Using ChIP-seq technology to identify targets of zinc finger transcription factors
    Henriette O'Geen
    Department of Pharmacology, Genome Center, University of California at Davis, Davis, CA, USA
    Methods Mol Biol 649:437-55. 2010
    ....
  8. pmc Comparison of sample preparation methods for ChIP-chip assays
    Henriette O'Geen
    University of California Davis, Davis, CA 95616, USA
    Biotechniques 41:577-80. 2006
    ..Importantly, the signal-to-noise ratio using the GenomePlex WGA method is superior to the LM-PCR amplification method...
  9. pmc Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263
    Seth Frietze
    Department of Pharmacology and the Genome Center, University of California, Davis, California 95616, USA
    J Biol Chem 285:1393-403. 2010
    ..Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes...
  10. pmc Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
    Vitalina M Komashko
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 18:521-32. 2008
    ..In contrast, changes in chromatin silencing were critical for the permanent changes in gene expression in cells undergoing differentiation...
  11. pmc A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
    Xiaoqin Xu
    Department of Pharmacology, University of California Davis, Davis, California 95616, USA
    Genome Res 17:1550-61. 2007
    ..Our results support the concept of functional redundancy in the E2F family and suggest that E2F6 is not critical for histone methylation...
  12. pmc Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs
    Henriette O'Geen
    Department of Pharmacology, University of California Davis, Davis, California, United States of America
    PLoS Genet 3:e89. 2007
    ..Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1...
  13. pmc A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1
    Victor X Jin
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 16:1585-95. 2006
    ..Finally, we have used our ChIPModules approach to develop a database that includes thousands of computationally identified and/or experimentally verified E2F1 target promoters...
  14. pmc Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
    Mark Bieda
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 16:595-605. 2006
    ....

Research Grants25

  1. Mechanisms of Transcriptional Regulation in Stem Cells
    Peggy Farnham; Fiscal Year: 2007
    ..inactive chromatin will be critical for these studies. In Aim 2B, we will characterize the molecular mechanisms responsible for the stem cell-specific regulation of the Oct4 gene. ..
  2. Transcriptional Regulation of Growth related Genes
    Peggy Farnham; Fiscal Year: 2007
    ..Relevance: An understanding of the transcriptional mechanisms that drive tumor cells into a less differentiated phenotype may provide insight into the development of new therapeutic agents. ..
  3. Scaling the ChIP-chip assay to improve analysis of clinical biospecimens
    Peggy Farnham; Fiscal Year: 2007
    ..Such modifications would be a great advance in the molecular characterization of the cancer genome. ..
  4. Transcriptional Regulation of Growth related Genes
    Peggy Farnham; Fiscal Year: 2005
    ..Finally, in Aim III, we propose to modify our chromatin immunoprecipitation assay to identify novel target genes regulated by the E2F, Myc, and TCF factors in normal and cancer cells. ..
  5. TRANSCRIPTIONAL REGULATION OF GROWTH-RELATED GENES
    Peggy Farnham; Fiscal Year: 1993
    ....
  6. TRANSCRIPTIONAL REGULATION OF GROWTH-RELATED GENES
    Peggy Farnham; Fiscal Year: 2000
    ....
  7. Transcriptional Regulation of Growth related Genes
    Peggy J Farnham; Fiscal Year: 2010
    ..Relevance: An understanding of the transcriptional mechanisms that drive tumor cells into a less differentiated phenotype may provide insight into the development of new therapeutic agents. ..