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TFCat: the curated catalog of mouse and human transcription factors
Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek
Genome Biol. 2009; 10(3): R29. Published online 2009 March 12. doi: 10.1186/gb-2009-10-3-r29
PMCID:
PMC2691000
Abstract Full Text PDF–295K Supplementary Material

Is Cited by the Following 15 Articles in this Archive:

Novel Insights into the Downstream Pathways and Targets Controlled by Transcription Factors CREM in the Testis
Rok Kosir, Peter Juvan, Martina Perse, Tomaz Budefeld, Gregor Majdic, Martina Fink, Paolo Sassone-Corsi, Damjana Rozman
PLoS One. 2012; 7(2): e31798. Published online 2012 February 22. doi: 10.1371/journal.pone.0031798
PMCID:
PMC3285179
Abstract Full Text PDF–1.7M Supplementary Material
AnimalTFDB: a comprehensive animal transcription factor database
Hong-Mei Zhang, Hu Chen, Wei Liu, Hui Liu, Jing Gong, Huili Wang, An-Yuan Guo
Nucleic Acids Res. 2012 January; 40(D1): D144–D149. Published online 2011 November 12. doi: 10.1093/nar/gkr965
PMCID:
PMC3245155
Abstract Full Text PDF–4.9M
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
John S Reece-Hoyes, A Rasim Barutcu, Rachel Patton McCord, Jun Seop Jeong, Lizhi Jiang, Andrew MacWilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E Hill, Seth Blackshaw, Heng Zhu, Job Dekker, Albertha J M Walhout
Nat Methods. Author manuscript; available in PMC 2012 June 1.
Published in final edited form as: Nat Methods. 2011 October 30; 8(12): 1050–1052. doi: 10.1038/nmeth.1764
PMCID:
PMC3263363
Free in PMC on 2012/06/01
Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection
Konstantina Dimitrakopoulou, Charalampos Tsimpouris, George Papadopoulos, Claudia Pommerenke, Esther Wilk, Kyriakos N Sgarbas, Klaus Schughart, Anastasios Bezerianos
J Clin Bioinforma. 2011; 1: 27. Published online 2011 October 21. doi: 10.1186/2043-9113-1-27
PMCID:
PMC3219564
Abstract Full Text PDF–705K Supplementary Material
Transcriptional Networks in Epithelial-Mesenchymal Transition
Christo Venkov, David Plieth, Terri Ni, Amitava Karmaker, Aihua Bian, Alfred L. George, Jr, Eric G. Neilson
PLoS One. 2011; 6(9): e25354. Published online 2011 September 30. doi: 10.1371/journal.pone.0025354
PMCID:
PMC3184133
Abstract Full Text PDF–1.2M Supplementary Material
Conserved and differential gene interactions in dynamical biological systems
Zhengyu Ouyang, Mingzhou Song, Robert Güth, Thomas J. Ha, Matt Larouche, Dan Goldowitz
Bioinformatics. 2011 October 15; 27(20): 2851–2858. Published online 2011 August 11. doi: 10.1093/bioinformatics/btr472
PMCID:
PMC3187649
Free in PMC on 2012/10/15
Towards resolving the transcription factor network controlling myelin gene expression
Debra L. Fulton, Eric Denarier, Hana C. Friedman, Wyeth W. Wasserman, Alan C. Peterson
Nucleic Acids Res. 2011 October; 39(18): 7974–7991. Published online 2011 July 5. doi: 10.1093/nar/gkr326
PMCID:
PMC3185407
Abstract Full Text PDF–6.0M Supplementary Material
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays
Kathy N. Lam, Harm van Bakel, Atina G. Cote, Anton van der Ven, Timothy R. Hughes
Nucleic Acids Res. 2011 June; 39(11): 4680–4690. Published online 2011 February 14. doi: 10.1093/nar/gkq1303
PMCID:
PMC3113560
Abstract Full Text PDF–4.2M Supplementary Material
Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes
Ji-Hoon Cho, Richard Gelinas, Kai Wang, Alton Etheridge, Melissa G Piper, Kara Batte, Duaa Dakhallah, Jennifer Price, Dan Bornman, Shile Zhang, Clay Marsh, David Galas
BMC Med Genomics. 2011; 4: 8. Published online 2011 January 17. doi: 10.1186/1755-8794-4-8
PMCID:
PMC3035594
Abstract Full Text PDF–3.9M Supplementary Material
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins
Ulf Schaefer, Sebastian Schmeier, Vladimir B. Bajic
Nucleic Acids Res. 2011 January; 39(Database issue): D106–D110. Published online 2010 October 21. doi: 10.1093/nar/gkq945
PMCID:
PMC3013796
Abstract Full Text PDF–82K
High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina Leslie
PLoS Comput Biol. 2010 September; 6(9): e1000916. Published online 2010 September 9. doi: 10.1371/journal.pcbi.1000916
PMCID:
PMC2936517
Abstract Full Text PDF–759K Supplementary Material
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
Morana Vitezic, Timo Lassmann, Alistair R. R. Forrest, Masanori Suzuki, Yasuhiro Tomaru, Jun Kawai, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, Carsten O. Daub
Nucleic Acids Res. 2010 December; 38(22): 8141–8148. Published online 2010 August 19. doi: 10.1093/nar/gkq729
PMCID:
PMC3001087
Abstract Full Text PDF–4.0M Supplementary Material
Genomic repertoires of DNA-binding transcription factors across the tree of life
Varodom Charoensawan, Derek Wilson, Sarah A. Teichmann
Nucleic Acids Res. 2010 November; 38(21): 7364–7377. Published online 2010 July 30. doi: 10.1093/nar/gkq617
PMCID:
PMC2995046
Abstract Full Text PDF–2.4M Supplementary Material
Mechano-transduction in periodontal ligament cells identifies activated states of MAP-kinases p42/44 and p38-stress kinase as a mechanism for MMP-13 expression
Nelli Ziegler, Angel Alonso, Thorsten Steinberg, Dale Woodnutt, Annette Kohl, Eva Müssig, Simon Schulz, Pascal Tomakidi
BMC Cell Biol. 2010; 11: 10. Published online 2010 January 28. doi: 10.1186/1471-2121-11-10
PMCID:
PMC2824740
Abstract Full Text PDF–1.2M
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin
Nucleic Acids Res. 2010 January; 38(Database issue): D105–D110. Published online 2010 January. doi: 10.1093/nar/gkp950
PMCID:
PMC2808906
Abstract Full Text PDF–1.1M
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