BioMed Central | Articles which cite: Identification of conserved regulatory elements by comparative genome analysis.

Log on / register
Feedback | Support | My details

home journals A-Z subject areas advanced search authors reviewers libraries about my BioMed Central

Identification of conserved regulatory elements by comparative genome analysis.
Lenhard B, Sandelin A, Mendoza L, Engström P, Jareborg N, Wasserman WW
J Biol 2003, 2:13
[Full text] [PubMed] [Related articles] [Cited on BioMed Central]

printer friendly

to [Help]

PubMed Central articles that cite the above article:

1.	JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B Nucleic Acids Res 2004 Jan 1, 32:D91-4 [PubMed Central] [PubMed] [Related articles]
2.	Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli. Brown CT, Callan CG Proc Natl Acad Sci U S A 2004 Feb 24, 101:2404-9 [PubMed Central] [PubMed] [Related articles]
3.	RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites. Hu Y, Wang T, Stormo GD, Gordon JI Proc Natl Acad Sci U S A 2004 Apr 13, 101:5559-64 [PubMed Central] [PubMed] [Related articles]
4.	CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets. Karanam S, Moreno CS Nucleic Acids Res 2004 Jul 1, 32:W475-84 [PubMed Central] [PubMed] [Related articles]
5.	ConSite: web-based prediction of regulatory elements using cross-species comparison. Sandelin A, Wasserman WW, Lenhard B Nucleic Acids Res 2004 Jul 1, 32:W249-52 [PubMed Central] [PubMed] [Related articles]
6.	Evaluation of myc E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays. Kim JW, Zeller KI, Wang Y, Jegga AG, Aronow BJ, O'Donnell KA, Dang CV Mol Cell Biol 2004 Jul, 24:5923-36 [PubMed Central] [PubMed] [Related articles]
7.	DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. Barta E, Sebestyén E, Pálfy TB, Tóth G, Ortutay CP, Patthy L Nucleic Acids Res 2005 Jan 1, 33:D86-90 [PubMed Central] [PubMed] [Related articles]
8.	Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W Genome Res 2005 Jan, 15:184-94 [PubMed Central] [PubMed] [Related articles]
9.	cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. Kulkarni MM, Arnosti DN Mol Cell Biol 2005 May, 25:3411-20 [PubMed Central] [PubMed] [Related articles]
10.	Charting gene regulatory networks: strategies, challenges and perspectives. Wei GH, Liu DP, Liang CC Biochem J 2004 Jul 1, 381:1-12 [PubMed Central] [PubMed] [Related articles]
11.	oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP, Wasserman WW Nucleic Acids Res 2005, 33:3154-64 [PubMed Central] [PubMed] [Related articles]
12.	Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. Corcoran DL, Feingold E, Dominick J, Wright M, Harnaha J, Trucco M, Giannoukakis N, Benos PV Genome Res 2005 Jun, 15:840-7 [PubMed Central] [PubMed] [Related articles]
13.	FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Corcoran DL, Feingold E, Benos PV Nucleic Acids Res 2005 Jul 1, 33:W442-6 [PubMed Central] [PubMed] [Related articles]
14.	Exploring hepatic hormone actions using a compilation of gene expression profiles. Ståhlberg N, Merino R, Hernández LH, Fernández-Pérez L, Sandelin A, Engström P, Tollet-Egnell P, Lenhard B, Flores-Morales A BMC Physiol 2005, 5:8 [PubMed Central] [PubMed] [Related articles]
15.	Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. Mustonen V, Lässig M Proc Natl Acad Sci U S A 2005 Nov 1, 102:15936-41 [PubMed Central] [PubMed] [Related articles]
16.	Core promoter sequences contribute to ovo-B regulation in the Drosophila melanogaster germline. Bielinska B, Lü J, Sturgill D, Oliver B Genetics 2005 Jan, 169:161-72 [PubMed Central] [PubMed] [Related articles]
17.	Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D Proc Natl Acad Sci U S A 2006 Apr 25, 103:6605-10 [PubMed Central] [PubMed] [Related articles]
18.	Practical strategies for discovering regulatory DNA sequence motifs. MacIsaac KD, Fraenkel E PLoS Comput Biol 2006 Apr, 2:e36 [PubMed Central] [PubMed] [Related articles]
19.	Phylogenetic analysis of 5'-noncoding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules. Buchanan CD, Klein PE, Mullet JE Genetics 2004 Nov, 168:1639-54 [PubMed Central] [PubMed] [Related articles]
20.	Heterotachy in mammalian promoter evolution. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA PLoS Genet 2006 Apr, 2:e30 [PubMed Central] [PubMed] [Related articles]
21.	Transcription factor map alignment of promoter regions. Blanco E, Messeguer X, Smith TF, Guigó R PLoS Comput Biol 2006 May, 2:e49 [PubMed Central] [PubMed] [Related articles]
22.	Evolutionary turnover of mammalian transcription start sites. Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Hayshizaki Y, Sandelin A Genome Res 2006 Jun, 16:713-22 [PubMed Central] [PubMed] [Related articles]
23.	Mammalian genomes ease location of human DNA functional segments but not their description. Newberg LA, Lawrence CE Stat Appl Genet Mol Biol 2004, 3:Article23 [PubMed Central] [PubMed] [Related articles]
24.	PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Lardenois A, Chalmel F, Bianchetti L, Sahel JA, Léveillard T, Poch O Nucleic Acids Res 2006 Jul 1, 34:W578-83 [PubMed Central] [PubMed] [Related articles]
25.	A male-specific quantitative trait locus on 1p21 controlling human stature. Sammalisto S, Hiekkalinna T, Suviolahti E, Sood K, Metzidis A, Pajukanta P, Lilja HE, Soro-Paavonen A, Taskinen MR, Tuomi T, Almgren P, Orho-Melander M, Groop L, Peltonen L, Perola M J Med Genet 2005 Dec, 42:932-9 [PubMed Central] [PubMed] [Related articles]
26.	GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. Jegga AG, Chen J, Gowrisankar S, Deshmukh MA, Gudivada R, Kong S, Kaimal V, Aronow BJ Nucleic Acids Res 2007 Jan, 35:D116-21 [PubMed Central] [PubMed] [Related articles]
27.	Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey JR, MacDonald CC, Graber JH Nucleic Acids Res 2007, 35:234-46 [PubMed Central] [PubMed] [Related articles]
28.	Transposable elements donate lineage-specific regulatory sequences to host genomes. Mariño-Ramírez L, Lewis KC, Landsman D, Jordan IK Cytogenet Genome Res 2005, 110:333-41 [PubMed Central] [PubMed] [Related articles]
29.	Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages. Timmons JA, Wennmalm K, Larsson O, Walden TB, Lassmann T, Petrovic N, Hamilton DL, Gimeno RE, Wahlestedt C, Baar K, Nedergaard J, Cannon B Proc Natl Acad Sci U S A 2007 Mar 13, 104:4401-6 [PubMed Central] [PubMed] [Related articles]
30.	Yct1p, a novel, high-affinity, cysteine-specific transporter from the yeast Saccharomyces cerevisiae. Kaur J, Bachhawat AK Genetics 2007 Jun, 176:877-90 [PubMed Central] [PubMed] [Related articles]
31.	In silico detection of sequence variations modifying transcriptional regulation. Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J PLoS Comput Biol 2008 Jan, 4:e5 [PubMed Central] [PubMed] [Related articles]
32.	* Unable to retrieve article 18208319 * [PubMed Central] [PubMed] [Related articles]
33.	JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A Nucleic Acids Res 2008 Jan, 36:D102-6 [PubMed Central] [PubMed] [Related articles]
34.	Associating transcription factor-binding site motifs with target GO terms and target genes. Bodén M, Bailey TL Nucleic Acids Res 2008 Jul, 36:4108-17 [PubMed Central] [PubMed] [Related articles]
35.	Connections Between ETV6-Modulated Genes: Identification of Shared Features. Boily G, Beaulieu P, Healy J, Sinnett D Cancer Inform 2008, 6:183-201 [PubMed Central] [PubMed] [Related articles]
36.	High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Whitington T, Perkins AC, Bailey TL Nucleic Acids Res 2009 Jan, 37:14-25 [PubMed Central] [PubMed] [Related articles]
37.	Multiple whole-genome alignments without a reference organism. Dubchak I, Poliakov A, Kislyuk A, Brudno M Genome Res 2009 Apr, 19:682-9 [PubMed Central] [PubMed] [Related articles]
38.	COTRASIF: conservation-aided transcription-factor-binding site finder. Tokovenko B, Golda R, Protas O, Obolenskaya M, El'skaya A Nucleic Acids Res 2009 Apr, 37:e49 [PubMed Central] [PubMed] [Related articles]
39.	The Drosophila Pax6 paralogs have different functions in head development but can partially substitute for each other. Jacobsson L, Kronhamn J, Rasmuson-Lestander A Mol Genet Genomics 2009 Sep, 282:217-31 [PubMed Central] [PubMed] [Related articles]
40.	The complex spatio-temporal regulation of the Drosophila myoblast attractant gene duf/kirre. Guruharsha KG, Ruiz-Gomez M, Ranganath HA, Siddharthan R, Vijayraghavan K PLoS One 2009, 4:e6960 [PubMed Central] [PubMed] [Related articles]
41.	Discovery of regulatory elements is improved by a discriminatory approach. Valen E, Sandelin A, Winther O, Krogh A PLoS Comput Biol 2009 Nov, 5:e1000562 [PubMed Central] [PubMed] [Related articles]

This article is also cited by 35 articles in BioMed Central

printer friendly

to [Help]

Terms and Conditions Privacy statement Information for advertisers Jobs at BMC Contact us