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Topic: Regulatory sequence

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	Gene Regulatory Networks
		Gene regulatory networks (GRNs) are the on-off switches and rheostats of a cell operating at the gene level.
		This was shown by microarray gene chip analyses in yeast cells, and each gene was found to possess a similar cis-regulatory DNA sequence that mediates binding of a particular transcription factor.
		A major gene regulatory network in the bacterium Caulobacter is now beginning to be mapped in a comprehensive manner based on genome-wide expression analyses coupled with genetic methods [M. Laub et al., Science 290, 214448 (2000)].
	www.doegenomestolife.org /science/generegulatorynetwork.shtml (1067 words)

	Research projects
		The sequences are being assembled currently and the result is expected to average sequence scaffolds of 20-30,000 bp.
		Previously we had identified two sequence fragments that recapitulate the temporal and spatial extent of this pattern: a 4 kb region just 5-prime of and including the transcription start site and a region about 1800 bp that occupies most of the intron between the 6th and 7th exons of this transcription unit.
		Expression of this regulatory element is enhanced by fusing it with either of two genomic regions downstream of the coding region.
	www.cco.caltech.edu /~mirsky/research.htm (8557 words)

	In Silico Identification of Putative Regulatory Sequence Elements in the 5'-Untranslated Region of Genes That Are ...
		In Silico Identification of Putative Regulatory Sequence Elements in the 5'-Untranslated Region of Genes That Are Expressed during Male Gametogenesis -- Hulzink et al.
		Schematic representation of the distribution of overrepresented sequence elements (pollen elements) in the 5'-UTR of the pollen-expressed gene ntp303.
		Hulzink RJM (2002) Post-transcriptional regulation of gene expression during male gametogenesis: regulatory and structural properties of the 5'-untranslated region of pollen-expressed genes.
	www.plantphysiol.org /cgi/content/full/132/1/75 (4002 words)

	Brassica regulatory sequence fo r root-specific or root-abundant gene
		Wong et al, which is incorporated herein by reference, discloses the DNA sequence for 999 bp of the crystal protein sequence and the 5' flanking sequence of 176 bp.
		A recombinant DNA molecule comprising an isolated polynucleotide having the nucleotide sequence of FIG.
		A recombinant DNA plasmid comprising an isolated polynucleotide having the nucleotide sequence of FIG.
	www.nal.usda.gov /bic/BTTOX/BT-patents/05401836.html (6602 words)

	Transcriptional Regulation of Kaposi's Sarcoma-associated Herpesvirus-encoded Oncogene Viral Interferon Regulatory ...
		One of the KSHV nonstructural regulatory lytic genes is the ORF-K9 that encodes the viral interferon regulatory factor (vIRF).
		A, diagram illustrating the upstream regulatory sequence of vIRF promoter and DNA fragments used to generate CAT reporter constructs.
		B, three different regions of the upstream regulatory sequences of vIRF promoter were inserted into the HindIII/BamHI sites upstream of the HSV-TK promoter (pBLCAT2) fused to the CAT gene to test their effect on TK promoter activity.
	www.jbc.org /cgi/content/full/277/14/12023 (5634 words)

	Regulatory Sequence that Controls the Expression of Allergic-Related Cytokines
		Edward Rubin and Kelly Frazer have identified and functionally characterized the conserved non-coding sequence (CNS)-1 as a potent regulator controlling the expression of three genes associated with numerous allergic and atopic diseases.
		Since regulatory sequence variation can contribute to human disorders as much as coding variation, this invention has important therapeutic and diagnostic applications.
		The newly discovered sequences can be used to diagnose altered CNS sequences that increase or decrease the expression of IL-4, IL-13, and IL-5.
	www.lbl.gov /tt/techs/lbnl1584.html (457 words)

	Candidate Regulatory Sequence Elements for Cell Cycle-Dependent Transcription in Saccharomyces cerevisiae -- Wolfsberg ...
		The number of upstream regions expected to contain that sequence element, if the element were evenly distributed among all intervals in all data sets, is marked with the pink box.
		The sequence elements that we have identified are responsible for much of the cell cycle regulation described by Cho et al.
		Dissecting the regulatory circuitry of a eukaryotic genome.
	www.genome.org /cgi/content/full/9/8/775 (6552 words)

	CABIO,96,Trifonov (Site not responding. Last check: 2007-10-22)
		Although one would normally expect a given regulatory element to perform best when it fully matches its consensus sequence, this is generally far from being the case.
		Apart from numerous individual codes (sequence patterns) specific for a given species or gene, there are many different general (universal) sequence codes all interacting with one another.
		Examples of overlapping of different codes and their interaction are discussed, as well as the role of degeneracy of the codes and the sequence complexity as a function of code density.
	www.nslij-genetics.org /gene/g-cabio96-t.html (232 words)

	Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover -- ...
		For a subset of 20 of the regulatory regions, we
		Dashed lines and dashed shapes indicate that the regulatory sequence was available, but no significant alignment was found for the respective region.
		Numbers inside the shapes for the sequences of rodent or human (for the rodent-specific sites) indicate the number of nucleotides that are different in this species' sequence from the human reference functional sequence (including gaps).
	mbe.oxfordjournals.org /cgi/content/full/19/7/1114 (4068 words)

	TOUCAN - Regulatory Sequence Analysis - Gene Regulation Bioinformatics
		Herbert Mayer's tutorial on the regulatory sequence analysis of genes involved in inflammation: TUTORIAL 1.
		Sequence retrieval from Ensembl is currently done using the ensj-core Java package of Ensembl (so not by HTTP access and export function like mentioned in the paper).
		If you have suggestions on other algorithms for regulatory sequence analysis that could be useful, please send an email.
	www.esat.kuleuven.ac.be /%7Esaerts/software/toucan.php (1919 words)

	An Algorithmic Approach to Gene Regulatory Sequence Analysis (ResearchIndex) (Site not responding. Last check: 2007-10-22)
		Long-term regulation is vital in determining the ontogeny of an individual.
		If for some reason these regulatory sequences differ from the norm, birth defects can result which may prove deleterious to the...
		20 Bayesian Models for Multiple Local Sequence Alignment and Gi..
	citeseer.ist.psu.edu /rouchka96algorithmic.html (245 words)

	Phylogenetic Analysis of 5'-Noncoding Regions From the ABA-Responsive rab16/17 Gene Family of Sorghum, Maize and Rice ...
		the importance of noncoding regulatory sequences in genome function.
		The extent of sequence alignment in the Osrab16A2
		Evolutionary distance of rab family members in sorghum, maize, and rice was calculated using protein sequences with the default settings on ClustalW (http://www.ebi.ac.uk/clustalw/index.html) and is given in parentheses next to each family member.
	www.genetics.org /cgi/content/full/168/3/1639 (7500 words)

	Identification and Characterization of a Regulatory Sequence Recognized by Mycobacterium tuberculosis Persistence ... (Site not responding. Last check: 2007-10-22)
		Alterations of this sequence, as observed with the proximal
		DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity.
		In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12.
	jb.asm.org /cgi/content/full/187/1/202 (5535 words)

	Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and ...
		Frequencies of occurrence per megabase pair are given for all possible combinations of heptad sequences in either the sequences upstream of the transcription start site for 78 pairs of orthologous maize and rice genes (promoter sequences; solid line) or the CNS identified by VISTA comparisons of these same maize-rice gene pairs (VISTA CNS; dotted line).
		the evolution of regulatory sequences in the grasses.
		Forde, B.G., Heyworth, A., Pywell, J., and Kreis, M. Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat, and maize.
	www.plantcell.org /cgi/content/full/15/5/1143 (9139 words)

	Cell cyle regulated yeast genes
		Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae.
		We have used standard statistical techniques to pr edict short sequence elements that may be involved in the expression of groups of co-regulated genes.
		All upstream region s equences are oriented in the direction of transcription, with the start of the sequence at position -600 and the end of the sequence at position -1 with respect to the start codon.
	www.ncbi.nlm.nih.gov /CBBresearch/Landsman/Cell_cycle_data (391 words)

	[No title]
		Toucan - A workbench for regulatory sequence analysis on metazoan genomes,
		SSA is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site such as a transcription initiation site for instance.
		Orthoseq - alignment and exon prediction in orthologous nucleotide sequences.
	rsat.ulb.ac.be /rsat/links.html (392 words)

	Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 ...
		Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate -- Rowitch et al.
		Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate
		Genomic Sequence Analysis of Fugu rubripes CFTR and Flanking Genes in a 60 kb Region Conserving Synteny with 800 kb of Human Chromosome 7
	dev.biologists.org /cgi/content/abstract/125/14/2735 (767 words)

	Title of Invention: Brassica regulatory sequence fo r root-specific or root-abundant gene expression
		Brassica napus root cDNA library, yielding many homologous clones, which were subsequently sequenced and characterized (Bergeron et al., in preparation), and used to aid in identifying the 5', i.e., 5 prime regulatory sequences in the genomic clones.
		In another aspect, the present invention is also directed to a composite gene comprising a promoter having the nucleotide sequence of FIG.
		In another aspect, the present invention is directed to a recombinant DNA plasmid which is capable of functioning as a vector, comprising the nucleotide sequence of FIG.
	www.nal.usda.gov /bic/Biotech_Patents/1995patents/05401836.html (6660 words)

	Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression ... (Site not responding. Last check: 2007-10-22)
		Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data - van Helden, Gilbert, Wernisch, Schroeder, Wodak (ResearchIndex)
		Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data (2000)
		Applications of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data.
	citeseer.ist.psu.edu /vanhelden00application.html (406 words)

	BioAfrica - HIV-1 TAT (Transactivating regulatory protein) sequence, structure and function information (Site not responding. Last check: 2007-10-22)
		HIV TAT acts as transcriptional regulator of viral gene expression by binding to the transactivating responsive sequence (TAR) RNA element.
		Tat is one of two viral regulatory factors (Rev is the other regulatory factor), and both are necessary for HIV gene expression
		In the absence of Tat expression, HIV generates short (less than 100 nucleotides in length) transcripts
	www.bioafrica.net /proteomics/TATprot.html (1206 words)

	Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and ...
		Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
		This article has been cited by other articles:
		Functional and Phylogenetic Analyses of a Conserved Regulatory Program in the Phloem of Minor Veins
	www.plantcell.org /cgi/content/abstract/15/5/1143 (533 words)

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