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Results: 1 to 20 of 79

1.

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
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.

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.

Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE.

Bioinformatics. 2007 Mar 15;23(6):771-3. Epub 2007 Jan 17.

PMID:
17234641
[PubMed - indexed for MEDLINE]
Free Article
4.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.

PMID:
23161675
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Cistrome: an integrative platform for transcriptional regulation studies.

Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS.

Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83.

PMID:
21859476
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

BMC Immunol. 2008 Mar 5;9:7. doi: 10.1186/1471-2172-9-7.

PMID:
18321385
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation.

Kubosaki A, Tomaru Y, Tagami M, Arner E, Miura H, Suzuki T, Suzuki M, Suzuki H, Hayashizaki Y.

Genome Biol. 2009;10(4):R41. doi: 10.1186/gb-2009-10-4-r41. Epub 2009 Apr 19.

PMID:
19374776
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.

Cesaroni M, Cittaro D, Brozzi A, Pelicci PG, Luzi L.

Bioinformatics. 2008 Dec 15;24(24):2918-20. doi: 10.1093/bioinformatics/btn542. Epub 2008 Oct 21.

PMID:
18945685
[PubMed - indexed for MEDLINE]
Free Article
9.

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
10.

[Analysis of the transcriptional regulatory network in the model organisms: yeast and sea urchin].

Takamatsu K, Takeda T.

Tanpakushitsu Kakusan Koso. 2004 Dec;49(17 Suppl):2742-50. Review. Japanese. No abstract available.

PMID:
15669249
[PubMed - indexed for MEDLINE]
11.

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

Chen J, Zhao P, Massaro D, Clerch LB, Almon RR, DuBois DC, Jusko WJ, Hoffman EP.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D578-81.

PMID:
14681485
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

[ChIP on chip for transcriptional regulatory network analysis].

Miura H, Tomaru Y.

Tanpakushitsu Kakusan Koso. 2004 Dec;49(17 Suppl):2710-6. Review. Japanese. No abstract available.

PMID:
15669244
[PubMed - indexed for MEDLINE]
13.

Integration of cap analysis of gene expression and chromatin immunoprecipitation analysis on array reveals genome-wide androgen receptor signaling in prostate cancer cells.

Takayama K, Tsutsumi S, Katayama S, Okayama T, Horie-Inoue K, Ikeda K, Urano T, Kawazu C, Hasegawa A, Ikeo K, Gojyobori T, Ouchi Y, Hayashizaki Y, Aburatani H, Inoue S.

Oncogene. 2011 Feb 3;30(5):619-30. doi: 10.1038/onc.2010.436. Epub 2010 Oct 4.

PMID:
20890304
[PubMed - indexed for MEDLINE]
14.

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]
15.

GeneCruiser: a web service for the annotation of microarray data.

Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov JP.

Bioinformatics. 2005 Sep 15;21(18):3681-2. Epub 2005 Jul 19.

PMID:
16030072
[PubMed - indexed for MEDLINE]
Free Article
16.

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D98-103.

PMID:
16381984
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

BarleyExpress: a web-based submission tool for enriched microarray database annotations.

Tang X, Shen L, Dickerson JA.

Bioinformatics. 2005 Feb 1;21(3):399-401. Epub 2004 Sep 3.

PMID:
15347571
[PubMed - indexed for MEDLINE]
Free Article
18.

Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation.

Tummala P, Mali RS, Guzman E, Zhang X, Mitton KP.

Mol Vis. 2010 Feb 17;16:252-71.

PMID:
20161818
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database.

Shah JK, Garner HR, White MA, Shames DS, Minna JD.

BMC Bioinformatics. 2007 May 31;8:178.

PMID:
17540034
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Bloader--a batch loader application for MIAMExpress.

Schwager C, Blake J.

Bioinformatics. 2005 Apr 15;21(8):1727-9. Epub 2004 Dec 21.

PMID:
15613394
[PubMed - indexed for MEDLINE]
Free Article

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