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Items: 1 to 20 of 131

1.

CisView: a browser and database of cis-regulatory modules predicted in the mouse genome.

Sharov AA, Dudekula DB, Ko MS.

DNA Res. 2006 Jun 30;13(3):123-34. Epub 2006 Sep 15.

PMID:
16980320
2.
3.

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.

4.

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

Ferretti V, Poitras C, Bergeron D, Coulombe B, Robert F, Blanchette M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D122-6. Epub 2006 Dec 5.

6.

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.

Lee TY, Chang WC, Hsu JB, Chang TH, Shien DM.

BMC Genomics. 2012;13 Suppl 1:S3. doi: 10.1186/1471-2164-13-S1-S3. Epub 2012 Jan 17.

7.

CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.

Navarro C, Lopez FJ, Cano C, Garcia-Alcalde F, Blanco A.

PLoS One. 2014 Sep 30;9(9):e108065. doi: 10.1371/journal.pone.0108065. eCollection 2014.

8.

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.

9.

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.

PMID:
24042128
10.

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.

Yang TH, Wang CC, Hung PC, Wu WS.

BMC Syst Biol. 2014;8 Suppl 4:S8. doi: 10.1186/1752-0509-8-S4-S8. Epub 2014 Dec 8.

11.

INSECT: IN-silico SEarch for Co-occurring Transcription factors.

Rohr CO, Parra RG, Yankilevich P, Perez-Castro C.

Bioinformatics. 2013 Nov 15;29(22):2852-8. doi: 10.1093/bioinformatics/btt506. Epub 2013 Sep 4.

PMID:
24008418
12.

AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana.

Chen YA, Wen YC, Chang WC.

BMC Genomics. 2012 Mar 8;13:85. doi: 10.1186/1471-2164-13-85.

13.

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

Marinescu VD, Kohane IS, Riva A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D91-7.

14.

CREME: Cis-Regulatory Module Explorer for the human genome.

Sharan R, Ben-Hur A, Loots GG, Ovcharenko I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W253-6.

15.

Selective constraints in experimentally defined primate regulatory regions.

Gaffney DJ, Blekhman R, Majewski J.

PLoS Genet. 2008 Aug 15;4(8):e1000157. doi: 10.1371/journal.pgen.1000157.

16.

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.

Acevedo-Luna N, Mariño-Ramírez L, Halbert A, Hansen U, Landsman D, Spouge JL.

BMC Bioinformatics. 2016 Nov 21;17(1):479.

17.

Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.

Rouault H, Mazouni K, Couturier L, Hakim V, Schweisguth F.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14615-20. doi: 10.1073/pnas.1002876107. Epub 2010 Jul 29.

18.

Computation-based discovery of cis-regulatory modules by hidden Markov model.

Wu J, Xie J.

J Comput Biol. 2008 Apr;15(3):279-90. doi: 10.1089/cmb.2008.0024.

PMID:
18333759
19.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

20.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Jegga AG, Chen J, Gowrisankar S, Deshmukh MA, Gudivada R, Kong S, Kaimal V, Aronow BJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D116-21. Epub 2006 Dec 18.

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