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Results: 1 to 20 of 117

1.

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.

Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.

Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19.

PMID:
19374773
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO.

Nucleic Acids Res. 2011 Jan;39(Database issue):D856-60. doi: 10.1093/nar/gkq1112. Epub 2010 Nov 12.

PMID:
21075797
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Macrophages.com: an on-line community resource for innate immunity research.

Robert C, Lu X, Law A, Freeman TC, Hume DA.

Immunobiology. 2011 Nov;216(11):1203-11. doi: 10.1016/j.imbio.2011.07.025. Epub 2011 Jul 23.

PMID:
21924793
[PubMed - indexed for MEDLINE]
4.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

Lepoivre C, Bergon A, Lopez F, Perumal NB, Nguyen C, Imbert J, Puthier D.

BMC Bioinformatics. 2012 Jan 31;13:19. doi: 10.1186/1471-2105-13-19.

PMID:
22292669
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model.

Le Béchec A, Portales-Casamar E, Vetter G, Moes M, Zindy PJ, Saumet A, Arenillas D, Theillet C, Wasserman WW, Lecellier CH, Friederich E.

BMC Bioinformatics. 2011 Mar 4;12:67. doi: 10.1186/1471-2105-12-67.

PMID:
21375730
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.

Ghedira K, Hornischer K, Konovalova T, Jenhani AZ, Benkahla A, Kel A.

Infect Genet Evol. 2011 Jun;11(4):769-77. doi: 10.1016/j.meegid.2010.10.015. Epub 2010 Nov 18.

PMID:
21093613
[PubMed - indexed for MEDLINE]
7.

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury.

Chang LW, Viader A, Varghese N, Payton JE, Milbrandt J, Nagarajan R.

BMC Genomics. 2013 Feb 6;14:84. doi: 10.1186/1471-2164-14-84.

PMID:
23387820
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.

Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.

PMID:
19377474
[PubMed - indexed for MEDLINE]
9.

Comparative promoter region analysis powered by CORG.

Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M.

BMC Genomics. 2005 Feb 21;6:24.

PMID:
15723697
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

CRSD: a comprehensive web server for composite regulatory signature discovery.

Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W571-7.

PMID:
16845073
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human.

Re A, Corá D, Taverna D, Caselle M.

Mol Biosyst. 2009 Aug;5(8):854-67. doi: 10.1039/b900177h. Epub 2009 Jun 19.

PMID:
19603121
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.

Baumbach J, Wittkop T, Kleindt CK, Tauch A.

Nat Protoc. 2009;4(6):992-1005. doi: 10.1038/nprot.2009.81.

PMID:
19498379
[PubMed - indexed for MEDLINE]
13.

FishMap Zv8 update--a genomic regulatory map of zebrafish.

Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S.

Zebrafish. 2010 Jun;7(2):179-80. doi: 10.1089/zeb.2009.0624.

PMID:
20528264
[PubMed - indexed for MEDLINE]
14.

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO.

Genome Biol. 2009;10(4):R40. doi: 10.1186/gb-2009-10-4-r40. Epub 2009 Apr 19.

PMID:
19374775
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.

Yeh HY, Cheng SW, Lin YC, Yeh CY, Lin SF, Soo VW.

BMC Med Genomics. 2009 Dec 21;2:70. doi: 10.1186/1755-8794-2-70.

PMID:
20025723
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. Epub 2007 Dec 23.

PMID:
18158297
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.

Huang H, Wu X, Sonachalam M, Mandape SN, Pandey R, MacDorman KF, Wan P, Chen JY.

BMC Bioinformatics. 2012;13 Suppl 15:S2. doi: 10.1186/1471-2105-13-S15-S2. Epub 2012 Sep 11.

PMID:
23046413
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.

PMID:
15113405
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

PMID:
15723693
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.

J Mol Biol. 2001 May 25;309(1):99-120.

PMID:
11491305
[PubMed - indexed for MEDLINE]

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