PubMed

Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system.

Tsai HK, Su CP, Lu MY, Shih CH, Wang D.

BMC Genomics. 2007 Oct 3;8:352.PMID: 17910772 [PubMed - indexed for MEDLINE]Related articlesFree article

Two non-homologous brain diseases-related genes, SERPINI1 and PDCD10, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner.

Chen PY, Chang WS, Chou RH, Lai YK, Lin SC, Chi CY, Wu CW.

BMC Mol Biol. 2007 Jan 9;8:2.PMID: 17212813 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae.

Sudarsanam P, Pilpel Y, Church GM.

Genome Res. 2002 Nov;12(11):1723-31.PMID: 12421759 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification.

Lin LH, Lee HC, Li WH, Chen BS.

BMC Bioinformatics. 2005 Oct 18;6:258.PMID: 16232312 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ.

PLoS One. 2008 Sep 3;3(9):e3112.PMID: 18769540 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.

Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB.

Genome Biol. 2003;4(7):R43. Epub 2003 Jun 26.PMID: 12844359 [PubMed - indexed for MEDLINE]Related articlesFree article

Inter- and intra-combinatorial regulation by transcription factors and microRNAs.

Zhou Y, Ferguson J, Chang JT, Kluger Y.

BMC Genomics. 2007 Oct 30;8:396.PMID: 17971223 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying combinatorial regulation of transcription factors and binding motifs.

Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ.

Genome Biol. 2004;5(8):R56. Epub 2004 Jul 28.PMID: 15287978 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of transcription factor cooperativity via stochastic system model.

Chang YH, Wang YC, Chen BS.

Bioinformatics. 2006 Sep 15;22(18):2276-82. Epub 2006 Jul 14.PMID: 16844711 [PubMed - indexed for MEDLINE]Related articlesFree article

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.

Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L.

J Mol Biol. 2006 Jun 30;360(1):213-27. Epub 2006 May 3.PMID: 16762362 [PubMed - indexed for MEDLINE]Related articles

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

Yu X, Lin J, Zack DJ, Qian J.

BMC Bioinformatics. 2007 Nov 9;8:437.PMID: 17996093 [PubMed - indexed for MEDLINE]Related articlesFree article

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.

Tsai HK, Chou MY, Shih CH, Huang GT, Chang TH, Li WH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W221-6. Epub 2007 May 30.PMID: 17537814 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer.

Eisermann K, Tandon S, Bazarov A, Brett A, Fraizer G, Piontkivska H.

BMC Genomics. 2008 Jul 16;9:337.PMID: 18631392 [PubMed - indexed for MEDLINE]Related articlesFree article

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

Zhu J, Zhang MQ.

Bioinformatics. 1999 Jul-Aug;15(7-8):607-11.PMID: 10487868 [PubMed - indexed for MEDLINE]Related articlesFree article

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.

Tanay A, Regev A, Shamir R.

Proc Natl Acad Sci U S A. 2005 May 17;102(20):7203-8. Epub 2005 May 9.PMID: 15883364 [PubMed - indexed for MEDLINE]Related articlesFree article

A systematic approach to detecting transcription factors in response to environmental stresses.

Lin LH, Lee HC, Li WH, Chen BS.

BMC Bioinformatics. 2007 Dec 8;8:473.PMID: 18067669 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

Guzmán-Vargas L, Santillán M.

BMC Syst Biol. 2008 Jan 31;2:13.PMID: 18237429 [PubMed - indexed for MEDLINE]Related articlesFree article

Conservation and evolution of cis-regulatory systems in ascomycete fungi.

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB.

PLoS Biol. 2004 Dec;2(12):e398. Epub 2004 Nov 9.PMID: 15534694 [PubMed - indexed for MEDLINE]Related articlesFree article

Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion.

Byrnes JK, Morris GP, Li WH.

Mol Biol Evol. 2006 Jun;23(6):1136-43. Epub 2006 Mar 9.PMID: 16527865 [PubMed - indexed for MEDLINE]Related articlesFree article

The determinants of gene order conservation in yeasts.

Poyatos JF, Hurst LD.

Genome Biol. 2007;8(11):R233.PMID: 17983469 [PubMed - indexed for MEDLINE]Related articlesFree article