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Results: 1 to 20 of 83

1.

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.

Genome Biol. 2009;10(7):R79. doi: 10.1186/gb-2009-10-7-r79. Epub 2009 Jul 22.

PMID:
19624849
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference.

de Hoon M, Hayashizaki Y.

Biotechniques. 2008 Apr;44(5):627-8, 630, 632. doi: 10.2144/000112802. Review.

PMID:
18474037
[PubMed - indexed for MEDLINE]
Free Article
3.

Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity.

Yamashita R, Suzuki Y, Sugano S, Nakai K.

Gene. 2005 May 9;350(2):129-36. Epub 2005 Mar 19.

PMID:
15784181
[PubMed - indexed for MEDLINE]
4.
5.

Analysis of promoter regions of co-expressed genes identified by microarray analysis.

Veerla S, Höglund M.

BMC Bioinformatics. 2006 Aug 17;7:384.

PMID:
16916454
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genome-wide analysis of factors regulating gene expression in liver.

Teufel A, Weinmann A, Krupp M, Budinger M, Galle PR.

Gene. 2007 Mar 15;389(2):114-21. Epub 2006 Nov 7.

PMID:
17174484
[PubMed - indexed for MEDLINE]
7.

Genesis: cluster analysis of microarray data.

Sturn A, Quackenbush J, Trajanoski Z.

Bioinformatics. 2002 Jan;18(1):207-8.

PMID:
11836235
[PubMed - indexed for MEDLINE]
Free Article
8.

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.

PMID:
15790569
[PubMed - indexed for MEDLINE]
Free Article
9.

Clustering and re-clustering for pattern discovery in gene expression data.

Ma PC, Chan KC, Chiu DK.

J Bioinform Comput Biol. 2005 Apr;3(2):281-301.

PMID:
15852506
[PubMed - indexed for MEDLINE]
10.

Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.

Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P, Suzuki H.

Biotechniques. 2008 Jul;45(1):95-7. doi: 10.2144/000112814.

PMID:
18611171
[PubMed - indexed for MEDLINE]
Free Article
11.

Mass distributed clustering: a new algorithm for repeated measurements in gene expression data.

Matsumoto S, Aisaki K, Kanno J.

Genome Inform. 2005;16(2):183-94.

PMID:
16901101
[PubMed - indexed for MEDLINE]
12.

Combined analysis of expression data and transcription factor binding sites in the yeast genome.

Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM.

BMC Genomics. 2004 Aug 26;5(1):59.

PMID:
15331021
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Oligonucleotide DNA chips are useful adjuncts in epigenetic studies of glioblastomas.

Kim B, Kim H, Song BJ, Cha SH, Lee MO, Park SH.

Neuropathology. 2006 Oct;26(5):409-16.

PMID:
17080717
[PubMed - indexed for MEDLINE]
14.

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.

Ohler U.

Nucleic Acids Res. 2006;34(20):5943-50. Epub 2006 Oct 26.

PMID:
17068082
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A tool-kit for cDNA microarray and promoter analysis.

Shah NH, King DC, Shah PN, Fedoroff NV.

Bioinformatics. 2003 Sep 22;19(14):1846-8.

PMID:
14512358
[PubMed - indexed for MEDLINE]
Free Article
16.

Construction, visualisation, and clustering of transcription networks from microarray expression data.

Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ.

PLoS Comput Biol. 2007 Oct;3(10):2032-42.

PMID:
17967053
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.

Chiang DY, Brown PO, Eisen MB.

Bioinformatics. 2001;17 Suppl 1:S49-55.

PMID:
11472992
[PubMed - indexed for MEDLINE]
Free Article
18.

Genomic analysis.

Lee PS, Lee KH.

Curr Opin Biotechnol. 2000 Apr;11(2):171-5. Review.

PMID:
10753760
[PubMed - indexed for MEDLINE]
19.

Analyzing gene expression data from microarray and next-generation dna sequencing transcriptome profiling assays using GeneSifter analysis edition.

Porter S, Olson NE, Smith T.

Curr Protoc Bioinformatics. 2009 Sep;Chapter 7:Unit 7.14 7.14.1-35. doi: 10.1002/0471250953.bi0714s27.

PMID:
19728290
[PubMed - indexed for MEDLINE]
20.

Principles of gene microarray data analysis.

Mocellin S, Rossi CR.

Adv Exp Med Biol. 2007;593:19-30. Review.

PMID:
17265713
[PubMed - indexed for MEDLINE]

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