Tom C Freeman

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. ncbi A logic-based diagram of signalling pathways central to macrophage activation
    Sobia Raza
    Division of Pathway Medicine, University of Edinburgh, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
    BMC Syst Biol 2:36. 2008
  2. ncbi Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling
    Paul Lacaze
    Division of Pathway Medicine, The University of Edinburgh, The Chancellor s Building, College of Medicine, Edinburgh, UK
    BMC Genomics 10:372. 2009
  3. ncbi Construction, visualisation, and clustering of transcription networks from microarray expression data
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, United Kingdom
    PLoS Comput Biol 3:2032-42. 2007
  4. ncbi Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations
    Neil A Mabbott
    The Roslin Institute and Royal Dick School of Veterinary Studies, The University of Edinburgh, Roslin Biocentre, Roslin, Midlothian, UK
    Immunobiology 215:724-36. 2010
  5. ncbi The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK
    BMC Syst Biol 4:65. 2010
  6. ncbi Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data
    Lawrence P Petalidis
    Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke s Hospital, Cambridge, United Kingdom
    Mol Cancer Ther 7:1013-24. 2008
  7. ncbi Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis
    Ella L Palmer
    MRC Rosalind Franklin Centre for Genomics Research RFCGR, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
    BMC Genomics 7:145. 2006
  8. ncbi Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SB, UK
    Genome Biol 6:R56. 2005
  9. ncbi An oligonucleotide microarray for transcriptome analysis of Schistosoma mansoni and its application/use to investigate gender-associated gene expression
    Jennifer M Fitzpatrick
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Mol Biochem Parasitol 141:1-13. 2005
  10. ncbi Bioinformatic analysis of primary endothelial cell gene array data illustrated by the analysis of transcriptome changes in endothelial cells exposed to VEGF-A and PlGF
    Jonathan Schoenfeld
    Department of Pathology, Cambridge University, Cambridge, UK
    Angiogenesis 7:143-56. 2004

Collaborators

  • Stijn van Dongen
  • Shiri Freilich
  • Sobia Raza
  • David A Hume
  • Paul Lacaze
  • Thorsten Forster
  • G C Weston
  • Paul Lyons
  • Samir A Saidi
  • Xavier Gidrol
  • Jean Marie Rouillard
  • Ella L Palmer
  • Richard W E Clarkson
  • K F Hoffmann
  • Roslin Russell
  • Brian D M Tom
  • Nicola A Johnson
  • Neil A Mabbott
  • Lawrence P Petalidis
  • Jennifer M Fitzpatrick
  • Stephen K Smith
  • Renata Almeida
  • Khashayar Lessan
  • Laurie Scott
  • Jonathan Schoenfeld
  • Richard Stephens
  • Cristin G Print
  • Dana Kramer
  • Caroline A Wallace
  • J Kenneth Baillie
  • Magnus Backlund
  • Lisa Happerfield
  • Anastasis Oulas
  • V Peter Collins
  • Karen Plant
  • Lu Liu
  • Panayiota Poirazi
  • Matthew T Wayland
  • Debbie J Williams
  • David A Johnston
  • David W Dunne
  • Gary W Williams
  • Alasdair C Ivens
  • Mark P Levick
  • Deborah F Smith
  • Amanda Evans
  • Ekaterini Vourvouhaki
  • D Stephen Charnock-Jones
  • Gareth Denyer
  • Ram Sasisekharan
  • Sharon H McCann
  • Brian J Gilmartin
  • Michael Harris
  • Peter Rogers
  • Iracilda Sampaio
  • Alan Norrish
  • Horacio Schneider
  • Jenefer M Blackwell
  • Sabrina D Dyall
  • Stephen D Charnock-Jones
  • David Vetrie
  • Mallik Sundaram
  • Danial Lawson
  • Richard M Coulson
  • Shiladitya Sengupta
  • Armando A Genazzani
  • Luigia Fresu
  • Dominique S Ashby
  • Anne E Kwitek
  • Anne M Glazier
  • Lawrence W Stanton
  • James Scott
  • Saira Ali
  • Penny J Norsworthy
  • Danilo C Carlos
  • Timothy J Aitman

Detail Information

Publications16

  1. ncbi A logic-based diagram of signalling pathways central to macrophage activation
    Sobia Raza
    Division of Pathway Medicine, University of Edinburgh, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
    BMC Syst Biol 2:36. 2008
    ..However, these pathways are commonly viewed as separate entities rather than an integrated network of molecular interactions...
  2. ncbi Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling
    Paul Lacaze
    Division of Pathway Medicine, The University of Edinburgh, The Chancellor s Building, College of Medicine, Edinburgh, UK
    BMC Genomics 10:372. 2009
    ..Genome-wide changes in transcript abundance caused by siRNA activity were measured using exon-level microarrays in the presence or absence of IFNgamma...
  3. ncbi Construction, visualisation, and clustering of transcription networks from microarray expression data
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, United Kingdom
    PLoS Comput Biol 3:2032-42. 2007
    ..This work has been implemented in a freely available open-source application named BioLayout Express(3D)...
  4. ncbi Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations
    Neil A Mabbott
    The Roslin Institute and Royal Dick School of Veterinary Studies, The University of Edinburgh, Roslin Biocentre, Roslin, Midlothian, UK
    Immunobiology 215:724-36. 2010
    ....
  5. ncbi The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK
    BMC Syst Biol 4:65. 2010
    ..However, implementing and agreeing how best to do this is currently the subject of some debate...
  6. ncbi Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data
    Lawrence P Petalidis
    Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke s Hospital, Cambridge, United Kingdom
    Mol Cancer Ther 7:1013-24. 2008
    ..Finally, 11 gene classifiers that differentiate between primary and secondary glioblastomas were also identified...
  7. ncbi Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis
    Ella L Palmer
    MRC Rosalind Franklin Centre for Genomics Research RFCGR, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
    BMC Genomics 7:145. 2006
    ....
  8. ncbi Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SB, UK
    Genome Biol 6:R56. 2005
    ..In this study, mouse proteins were assigned into functional and phyletic groups and the gene expression patterns of the different protein groupings were examined by microarray analysis in various mouse tissues...
  9. ncbi An oligonucleotide microarray for transcriptome analysis of Schistosoma mansoni and its application/use to investigate gender-associated gene expression
    Jennifer M Fitzpatrick
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Mol Biochem Parasitol 141:1-13. 2005
    ..These data demonstrate the power of this new resource to facilitate a greater understanding into the biological complexities of schistosome development and maturation useful for identifying novel intervention strategies...
  10. ncbi Bioinformatic analysis of primary endothelial cell gene array data illustrated by the analysis of transcriptome changes in endothelial cells exposed to VEGF-A and PlGF
    Jonathan Schoenfeld
    Department of Pathology, Cambridge University, Cambridge, UK
    Angiogenesis 7:143-56. 2004
    ..In contrast to some previous studies, we found that VEGF-A and PlGF consistently regulated only small, non-overlapping and culture media-dependant sets of HUVEC transcripts, despite causing significant cell biological changes...
  11. ncbi Expression profiling of the Leishmania life cycle: cDNA arrays identify developmentally regulated genes present but not annotated in the genome
    Renata Almeida
    Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2XY, UK
    Mol Biochem Parasitol 136:87-100. 2004
    ..Careful annotation of cDNAs onto the Leishmania genome will be important before producing the next generation of oligonucleotide arrays based on annotated genes of the genomic sequencing project...
  12. ncbi Endothelial cells preparing to die by apoptosis initiate a program of transcriptome and glycome regulation
    Nicola A Johnson
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    FASEB J 18:188-90. 2004
    ..We propose that the transcriptome and glycome regulation presented here synergize with previously described protein-based changes to guide the apoptotic program...
  13. ncbi The genes induced by signal transducer and activators of transcription (STAT)3 and STAT5 in mammary epithelial cells define the roles of these STATs in mammary development
    Richard W E Clarkson
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
    Mol Endocrinol 20:675-85. 2006
    ....
  14. ncbi Calcineurin controls the expression of numerous genes in cerebellar granule cells
    Dana Kramer
    Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
    Mol Cell Neurosci 23:325-30. 2003
    ....
  15. ncbi Radiation hybrid mapping of 70 rat genes from a data set of differentially expressed genes
    Caroline A Wallace
    Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
    Mamm Genome 13:194-7. 2002
    ..The data provide new map locations for rat genes and will aid efforts to advance the rat genome map. The data may also be used to prioritize candidate QTL genes in SHR and other rat strains on the basis of their map location...