LIVIVO - Suchergebnisse -

Suchergebnis

Treffer 1 - 10 von insgesamt 11

Suchoptionen

Artikel: The genetics of type I interferon in systemic lupus erythematosus

Bronson, Paola G / Chaivorapol, Christina / Ortmann, Ward / Behrens, Timothy W / Graham, Robert R

Current Opinion in Immunology. 2012 Oct., v. 24, no. 5

2012

Abstract: The discovery that type I interferon (IFN)-inducible genes were strongly upregulated in peripheral blood in SLE over a decade ago sparked interest in understanding the relationship between type I IFN and SLE. Genome-wide association studies provide ... ...

Abstract	The discovery that type I interferon (IFN)-inducible genes were strongly upregulated in peripheral blood in SLE over a decade ago sparked interest in understanding the relationship between type I IFN and SLE. Genome-wide association studies provide strong genetic evidence that type I IFNs are important for SLE risk. Of 47 genetic variants associated with SLE, over half (27/47, 57%) can be linked to type I IFN production or signaling. The recent identification of single gene mutations for disorders that share features with SLE – Aicardi–Goutières syndrome, chilblain lupus, and spondyloenchondrodysplasia – provide additional support for the hypothesis that type I IFNs are central drivers of SLE pathogenesis. These insights provide significant focus for efforts to tackle SLE therapeutically.
Schlagwörter	blood ; gene expression regulation ; genes ; genetic variation ; genome-wide association study ; interferons ; lupus erythematosus ; mutation ; pathogenesis ; risk
Sprache	Englisch
Erscheinungsverlauf	2012-10
Umfang	p. 530-537.
Erscheinungsort	Elsevier Ltd
Dokumenttyp	Artikel
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2012.07.008
Datenquelle	NAL Katalog (AGRICOLA)

Volltext online

Zugriff für angemeldete ZB MED Nutzerinnen und Nutzer

Zusatzmaterialien

Verfügbar in ZB MED Bonn

Z 2005/713: Hefte anzeigen

Über subito bestellen

Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

Fernleihe an ZB MED

Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

Details ▾

Artikel ; Online: The genetics of type I interferon in systemic lupus erythematosus.

Bronson, Paola G / Chaivorapol, Christina / Ortmann, Ward / Behrens, Timothy W / Graham, Robert R

Current opinion in immunology

2012 Band 24, Heft 5, Seite(n) 530–537

Abstract	The discovery that type I interferon (IFN)-inducible genes were strongly upregulated in peripheral blood in SLE over a decade ago sparked interest in understanding the relationship between type I IFN and SLE. Genome-wide association studies provide strong genetic evidence that type I IFNs are important for SLE risk. Of 47 genetic variants associated with SLE, over half (27/47, 57%) can be linked to type I IFN production or signaling. The recent identification of single gene mutations for disorders that share features with SLE--Aicardi-Goutières syndrome, chilblain lupus, and spondyloenchondrodysplasia--provide additional support for the hypothesis that type I IFNs are central drivers of SLE pathogenesis. These insights provide significant focus for efforts to tackle SLE therapeutically.
Mesh-Begriff(e)	Animals ; Disease Models, Animal ; Genome-Wide Association Study/methods ; Genome-Wide Association Study/trends ; Humans ; Interferon Type I/biosynthesis ; Interferon Type I/genetics ; Interferon Type I/physiology ; Lupus Erythematosus, Systemic/etiology ; Lupus Erythematosus, Systemic/genetics ; Lupus Erythematosus, Systemic/immunology ; Mutation ; Signal Transduction/genetics ; Signal Transduction/immunology
Chemische Substanzen	Interferon Type I
Sprache	Englisch
Erscheinungsdatum	2012-10
Erscheinungsland	England
Dokumenttyp	Journal Article ; Review
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2012.07.008
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Volltext online

Zugriff für angemeldete ZB MED Nutzerinnen und Nutzer

Zusatzmaterialien

Verfügbar in ZB MED Köln/Königswinter

Zs.A 2773: Hefte anzeigen			Standort: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 13: Hefte anzeigen

Über subito bestellen

Details ▾

Artikel ; Online: fREDUCE

Li Hao / Zheng Jiashun / Chaivorapol Christina / Wu Randy Z / Liang Shoudan

BMC Bioinformatics, Vol 8, Iss 1, p

Detection of degenerate regulatory elements using correlation with expression

2007 Band 399

Abstract: Abstract Background The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor ... ...

Abstract	Abstract Background The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs. Results We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. fREDUCE introduces several algorithmic refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC symbols. On yeast ChIP-chip benchmarks, fREDUCE correctly identified motifs and their degeneracies with accuracies greater than its predecessor REDUCE as well as other known motif-finding programs. We have also used fREDUCE to make novel motif predictions for transcription factors with poorly characterized binding sites. Conclusion We demonstrate that fREDUCE is a valuable tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude other motif detection methods.
Schlagwörter	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Thema/Rubrik (Code)	006
Sprache	Englisch
Erscheinungsdatum	2007-10-01T00:00:00Z
Verlag	BMC
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

Volltext online

Volltext online

Zusatzmaterialien

Fernleihe an ZB MED

Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

Artikel ; Online: ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

Huntley, Melanie A / Larson, Jessica L / Chaivorapol, Christina / Becker, Gabriel / Lawrence, Michael / Hackney, Jason A / Kaminker, Joshua S

Bioinformatics (Oxford, England)

2013 Band 29, Heft 24, Seite(n) 3220–3221

Abstract: Unlabelled: It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We ... ...

Abstract	Unlabelled: It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. Availability: The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.
Mesh-Begriff(e)	Algorithms ; Computational Biology ; Databases, Factual ; Gene Expression Profiling/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Software
Sprache	Englisch
Erscheinungsdatum	2013-09-29
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btt551
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Zusatzmaterialien

Verfügbar in ZB MED Köln/Königswinter

Zs.A 2374: Hefte anzeigen

Standort:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Über subito bestellen

Details ▾
- Im ZB MED-Bestand
- Kostenpflichtig bestellen

Artikel: Association of the interferon signature metric with serological disease manifestations but not global activity scores in multiple cohorts of patients with SLE.

Kennedy, William P / Maciuca, Romeo / Wolslegel, Kristen / Tew, Wei / Abbas, Alexander R / Chaivorapol, Christina / Morimoto, Alyssa / McBride, Jacqueline M / Brunetta, Paul / Richardson, Bruce C / Davis, John C / Behrens, Timothy W / Townsend, Michael J

Lupus science & medicine

2015 Band 2, Heft 1, Seite(n) e000080

Abstract: Objectives: The interferon (IFN) signature (IS) in patients with systemic lupus erythematosus (SLE) includes over 100 genes induced by type I IFN pathway activation. We developed a method to quantify the IS using three genes-the IS metric (ISM)-and ... ...

Abstract	Objectives: The interferon (IFN) signature (IS) in patients with systemic lupus erythematosus (SLE) includes over 100 genes induced by type I IFN pathway activation. We developed a method to quantify the IS using three genes-the IS metric (ISM)-and characterised the clinical characteristics of patients with SLE with different ISM status from multiple clinical trials. Methods: Blood microarray expression data from a training cohort of patients with SLE confirmed the presence of the IS and identified surrogate genes. We assayed these genes in a quantitative PCR (qPCR) assay, yielding an ISM from the IS. The association of ISM status with clinical disease characteristics was assessed in patients with extrarenal lupus and lupus nephritis from four clinical trials. Results: Three genes, HERC5, EPSTI and CMPK2, correlated well with the IS (p>0.96), and composed the ISM qPCR assay. Using the 95th centile for healthy control data, patients with SLE from different studies were classified into two ISM subsets-ISM-Low and ISM-High-that are longitudinally stable over 36 weeks. Significant associations were identified between ISM-High status and higher titres of anti-dsDNA antibodies, presence of anti extractable nuclear antigen autoantibodies, elevated serum B cell activating factor of the tumour necrosis factor family (BAFF) levels, and hypocomplementaemia. However, measures of overall clinical disease activity were similar for ISM-High and ISM-Low groups. Conclusions: The ISM is an IS biomarker that divides patients with SLE into two subpopulations-ISM-High and ISM-Low-with differing serological manifestations. The ISM does not distinguish between high and low disease activity, but may have utility in identifying patients more likely to respond to treatment(s) targeting IFN-α. Clinicaltrialsgov registration number: NCT00962832.
Sprache	Englisch
Erscheinungsdatum	2015-03-28
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	2779620-6
ISSN	2053-8790
ISSN	2053-8790
DOI	10.1136/lupus-2014-000080
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Zusatzmaterialien

Über subito bestellen

Details ▾
- Kostenpflichtig bestellen

Artikel ; Online: CompMoby

Ramalho-Santos Miguel / Yeh Ru-Fang / Wei Grace / Melton Collin / Chaivorapol Christina / Blelloch Robert / Li Hao

BMC Bioinformatics, Vol 9, Iss 1, p

Comparative MobyDick for detection of cis-regulatory motifs

2008 Band 455

Abstract: Abstract Background The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions ...

Abstract	Abstract Background The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions of genes while sequence elements within the 3' untranslated regions of mRNAs play important roles in post-transcriptional regulation such as mRNA stability and translation efficiency. Identifying cis-regulatory elements, or motifs, in multicellular eukaryotes is more difficult compared to unicellular eukaryotes due to the larger intergenic sequence space and the increased complexity in regulation. Experimental techniques for discovering functional elements are often time consuming and not easily applied on a genome level. Consequently, computational methods are advantageous for genome-wide cis-regulatory motif detection. To decrease the search space in metazoans, many algorithms use cross-species alignment, although studies have demonstrated that a large portion of the binding sites for the same trans-acting factor do not reside in alignable regions. Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans. Results We present CompMoby (Comparative MobyDick), software developed to identify cis-regulatory binding sites at both the transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factors. The CompMoby algorithm was previously shown to identify cis-regulatory binding sites in upstream regions of genes co-regulated in embryonic stem cells. In this paper, we extend the software to identify putative cis-regulatory motifs in 3' UTR sequences and verify our results using experimentally validated data sets in mouse and human. We also detail the implementation of CompMoby into a user-friendly tool that includes a web interface to a streamlined analysis. Our software allows detection of motifs in the following three categories: one, those that are ...
Schlagwörter	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Thema/Rubrik (Code)	570
Sprache	Englisch
Erscheinungsdatum	2008-10-01T00:00:00Z
Verlag	BMC
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

Volltext online

Volltext online

Zusatzmaterialien

Fernleihe an ZB MED

Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

Artikel: Cell- and gene-specific regulation of primary target genes by the androgen receptor.

Bolton, Eric C / So, Alex Y / Chaivorapol, Christina / Haqq, Christopher M / Li, Hao / Yamamoto, Keith R

Genes & development

2007 Band 21, Heft 16, Seite(n) 2005–2017

Abstract: The androgen receptor (AR) mediates the physiologic and pathophysiologic effects of androgens including sexual differentiation, prostate development, and cancer progression by binding to genomic androgen response elements (AREs), which influence ... ...

Abstract	The androgen receptor (AR) mediates the physiologic and pathophysiologic effects of androgens including sexual differentiation, prostate development, and cancer progression by binding to genomic androgen response elements (AREs), which influence transcription of AR target genes. The composition and context of AREs differ between genes, thus enabling AR to confer multiple regulatory functions within a single nucleus. We used expression profiling of an immortalized human prostate epithelial cell line to identify 205 androgen-responsive genes (ARGs), most of them novel. In addition, we performed chromatin immunoprecipitation to identify 524 AR binding regions and validated in reporter assays the ARE activities of several such regions. Interestingly, 67% of our AREs resided within approximately 50 kb of the transcription start sites of 84% of our ARGs. Indeed, most ARGs were associated with two or more AREs, and ARGs were sometimes themselves linked in gene clusters containing up to 13 AREs and 12 ARGs. AREs appeared typically to be composite elements, containing AR binding sequences adjacent to binding motifs for other transcriptional regulators. Functionally, ARGs were commonly involved in prostate cell proliferation, communication, differentiation, and possibly cancer progression. Our results provide new insights into cell- and gene-specific mechanisms of transcriptional regulation of androgen-responsive gene networks.
Mesh-Begriff(e)	Base Sequence ; Binding Sites/genetics ; Cell Line ; Cell Line, Tumor ; Cell Proliferation ; Cell Transformation, Neoplastic/genetics ; Chromatin Immunoprecipitation ; DNA/genetics ; DNA/metabolism ; Epithelial Cells/metabolism ; Gene Expression Regulation ; Humans ; Male ; Multigene Family ; Prostate/cytology ; Prostate/metabolism ; Prostatic Neoplasms/etiology ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; Receptors, Androgen/genetics ; Receptors, Androgen/metabolism
Chemische Substanzen	AR protein, human ; Receptors, Androgen ; DNA (9007-49-2)
Sprache	Englisch
Erscheinungsdatum	2007-08-15
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.1564207
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Zusatzmaterialien

Verfügbar in ZB MED Köln/Königswinter

Zs.A 2292: Hefte anzeigen			Standort: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 54: Hefte anzeigen

Über subito bestellen

Details ▾
- Im ZB MED-Bestand
- Kostenpflichtig bestellen

Artikel ; Online: Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.

Grskovic, Marica / Chaivorapol, Christina / Gaspar-Maia, Alexandre / Li, Hao / Ramalho-Santos, Miguel

PLoS genetics

2007 Band 3, Heft 8, Seite(n) e145

Abstract: Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES) cells or reprogramming somatic cells. We first analyzed the ... ...

Abstract	Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES) cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species.
Mesh-Begriff(e)	Animals ; CCAAT-Binding Factor/genetics ; CCAAT-Binding Factor/physiology ; Cell Line ; Cell Proliferation ; Cells, Cultured ; Computational Biology/methods ; Embryonic Stem Cells/chemistry ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/metabolism ; Embryonic Stem Cells/physiology ; Humans ; Mice ; Mice, Transgenic ; Multigene Family ; NIH 3T3 Cells ; Oligonucleotide Array Sequence Analysis ; Regulatory Sequences, Nucleic Acid
Chemische Substanzen	CCAAT-Binding Factor
Sprache	Englisch
Erscheinungsdatum	2007-08
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Validation Studies
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.0030145
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Volltext online

Volltext online

Zusatzmaterialien

Über subito bestellen

Details ▾
- Volltext online
- Kostenpflichtig bestellen

Artikel ; Online: Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor.

So, Alex Yick-Lun / Chaivorapol, Christina / Bolton, Eric C / Li, Hao / Yamamoto, Keith R

PLoS genetics

2007 Band 3, Heft 6, Seite(n) e94

Abstract: The glucocorticoid receptor (GR) associates with glucocorticoid response elements (GREs) and regulates selective gene transcription in a cell-specific manner. Native GREs are typically thought to be composite elements that recruit GR as well as other ... ...

Abstract	The glucocorticoid receptor (GR) associates with glucocorticoid response elements (GREs) and regulates selective gene transcription in a cell-specific manner. Native GREs are typically thought to be composite elements that recruit GR as well as other regulatory factors into functional complexes. We assessed whether GR occupancy is commonly a limiting determinant of GRE function as well as the extent to which core GR binding sequences and GRE architecture are conserved at functional loci. We surveyed 100-kb regions surrounding each of 548 known or potentially glucocorticoid-responsive genes in A549 human lung cells for GR-occupied GREs. We found that GR was bound in A549 cells predominately near genes responsive to glucocorticoids in those cells and not at genes regulated by GR in other cells. The GREs were positionally conserved at each responsive gene but across the set of responsive genes were distributed equally upstream and downstream of the transcription start sites, with 63% of them >10 kb from those sites. Strikingly, although the core GR binding sequences across the set of GREs varied extensively around a consensus, the precise sequence at an individual GRE was conserved across four mammalian species. Similarly, sequences flanking the core GR binding sites also varied among GREs but were conserved at individual GREs. We conclude that GR occupancy is a primary determinant of glucocorticoid responsiveness in A549 cells and that core GR binding sequences as well as GRE architecture likely harbor gene-specific regulatory information.
Mesh-Begriff(e)	Animals ; Cell Line ; Cell Line, Tumor ; Computational Biology/methods ; DNA Primers ; Gene Expression Regulation ; Humans ; Immunoprecipitation ; Mice ; Mice, Inbred C3H ; Models, Biological ; Oligonucleotide Array Sequence Analysis ; Receptors, Glucocorticoid/metabolism ; Software ; Transcription, Genetic
Chemische Substanzen	DNA Primers ; Receptors, Glucocorticoid
Sprache	Englisch
Erscheinungsdatum	2007-06
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.0030094
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Volltext online

Volltext online

Zusatzmaterialien

Über subito bestellen

Details ▾
- Volltext online
- Kostenpflichtig bestellen

Artikel ; Online: fREDUCE: detection of degenerate regulatory elements using correlation with expression.

Wu, Randy Z / Chaivorapol, Christina / Zheng, Jiashun / Li, Hao / Liang, Shoudan

BMC bioinformatics

2007 Band 8, Seite(n) 399

Abstract: Background: The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding ... ...

Abstract	Background: The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs. Results: We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. fREDUCE introduces several algorithmic refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC symbols. On yeast ChIP-chip benchmarks, fREDUCE correctly identified motifs and their degeneracies with accuracies greater than its predecessor REDUCE as well as other known motif-finding programs. We have also used fREDUCE to make novel motif predictions for transcription factors with poorly characterized binding sites. Conclusion: We demonstrate that fREDUCE is a valuable tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude other motif detection methods.
Mesh-Begriff(e)	Algorithms ; Amino Acid Motifs ; Base Sequence ; Binding Sites ; Computational Biology ; Gene Expression Profiling ; Genomics/methods ; Hepatocytes ; Humans ; Regulatory Sequences, Nucleic Acid ; Saccharomyces cerevisiae/genetics ; Substrate Specificity ; Transcription, Genetic
Sprache	Englisch
Erscheinungsdatum	2007-10-17
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-8-399
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

Zusatzmaterialien

Über subito bestellen

Details ▾
- Kostenpflichtig bestellen

Zum Seitenanfang

Ihre letzten Suchen

Volltext online

Zusatzmaterialien

Kategorien

Verfügbar in ZB MED Bonn

Über subito bestellen

Fernleihe an ZB MED

Volltext online

Zusatzmaterialien

Kategorien

Verfügbar in ZB MED Köln/Königswinter

Über subito bestellen

Volltext online

Zusatzmaterialien

Kategorien

Fernleihe an ZB MED

Zusatzmaterialien

Kategorien

Verfügbar in ZB MED Köln/Königswinter

Über subito bestellen

Zusatzmaterialien

Kategorien

Über subito bestellen

Volltext online

Zusatzmaterialien

Kategorien

Fernleihe an ZB MED

Zusatzmaterialien

Kategorien

Verfügbar in ZB MED Köln/Königswinter

Über subito bestellen

Volltext online

Zusatzmaterialien

Kategorien

Über subito bestellen

Volltext online

Zusatzmaterialien

Kategorien

Über subito bestellen

Zusatzmaterialien

Kategorien

Über subito bestellen