Skip to main content
SpringerLink
Log in

Introduction to “A Handbook of Transcription Factors”

  • Chapter
  • First Online:
A Handbook of Transcription Factors

Part of the book series: Subcellular Biochemistry ((SCBI,volume 52))

Abstract

This chapter briefly summarizes the topics in this volume.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Joshi R, et al. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131:530–543

    Article  PubMed  CAS  Google Scholar 

  2. Hu S, et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139:610–622

    Article  PubMed  CAS  Google Scholar 

  3. Fulton DL, et al. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol 10:R29

    Article  PubMed  Google Scholar 

  4. Benos PV, Bulyk ML, Stormo GD (2002) Additivity in protein–DNA interactions: how good an approximation is it? Nucleic Acids Res 30:4442–4451

    Article  PubMed  CAS  Google Scholar 

  5. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315:233–237

    Article  PubMed  CAS  Google Scholar 

  6. Badis G, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720–1723

    Article  PubMed  CAS  Google Scholar 

  7. Tompa M, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23:137–144

    Article  PubMed  CAS  Google Scholar 

  8. Granek JA, Clarke ND (2005) Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol 6:R87

    Article  PubMed  Google Scholar 

  9. Arnosti DN, Kulkarni MM (2005) Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J Cell Biochem 94:890–898

    Article  PubMed  CAS  Google Scholar 

  10. Berman BP, et al. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 99:757–762

    Article  PubMed  CAS  Google Scholar 

  11. Wunderlich Z, Mirny LA (2009) Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet 25:434–440

    Article  PubMed  CAS  Google Scholar 

  12. Segal E, Widom, J (2009) DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet 10:443–456

    Article  PubMed  CAS  Google Scholar 

  13. Wasson T, Hartemink AJ (2009) An ensemble model of competitive multi-factor binding of the genome. Genome Res 19:2101–2112

    Google Scholar 

  14. Davidson EH (2006) The Regulatory Genome. Academic Press, London

    Google Scholar 

  15. Rice PA, Correll CC (2008) Protein-nucleic acid interactions: structural biology. Royal Society of Chemistry, Cambridge, UK

    Book  Google Scholar 

  16. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705

    Article  PubMed  CAS  Google Scholar 

  17. Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447:407–412

    Article  PubMed  CAS  Google Scholar 

  18. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669–681

    Article  PubMed  CAS  Google Scholar 

  19. Bonneau R (2008) Learning biological networks: from modules to dynamics. Nat Chem Biol 4:658–664

    Article  PubMed  CAS  Google Scholar 

  20. Alon U (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, Boca Raton, FL

    Google Scholar 

  21. Junker BH, Schreiber F (2008) Analysis of Biological Networks, Wiley Series on Bioinformatics. Wiley, Hoboken, NJ

    Book  Google Scholar 

  22. Moazed D (2009) RNAs in transcriptional gene silencing and genome defence. Nature 457:413–420

    Article  PubMed  CAS  Google Scholar 

  23. Nagano T, Fraser P (2009) Emerging similarities in epigenetic gene silencing by long noncoding RNAs. Mamm Genome 20:557–562

    Article  PubMed  CAS  Google Scholar 

  24. Latchman DS (2008) Eukaryotic Transcription Factors, Fifth Edition. Academic Press, London

    Google Scholar 

  25. Locker J (2000) Transcription Factors, Human Molecular Genetics Series. BIOS Scientific Publication, Oxford

    Google Scholar 

  26. Ghosh D, Locker J (1996) Transcription Factors: Essential Data. Wiley, New York, NY

    Google Scholar 

  27. Pabo CO, Sauer RT (1984) Protein-DNA recognition. Annu Rev Biochem 53:293–321

    Article  PubMed  CAS  Google Scholar 

  28. Michelson AM, Bulyk ML (2006) Biological code breaking in the 21st century. Mol Syst Biol 2:2006 0018

    Article  PubMed  Google Scholar 

  29. Liu LA, Bader JS (2007) Ab initio prediction of transcription factor binding sites. Pac Symp Biocomput 2007:484–495

    Google Scholar 

  30. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117:185–198

    Article  PubMed  CAS  Google Scholar 

  31. Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C (2004) Predicting genetic regulatory response using classification. Bioinformatics 20(Suppl 1):i232–40

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada

    T.R. Hughes

Authors
  1. T.R. Hughes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to T.R. Hughes .

Editor information

Editors and Affiliations

  1. , Centre for Cellular and Biomolecular Res, University of Toronto, College St. 160, Toronto, M5S 3E1, Canada

    Timothy R. Hughes

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Hughes, T. (2011). Introduction to “A Handbook of Transcription Factors”. In: Hughes, T. (eds) A Handbook of Transcription Factors. Subcellular Biochemistry, vol 52. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9069-0_1

Download citation

Publish with us

Policies and ethics

Search

Navigation