Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Locating potential enhancer elements by comparative genomics using the EEL software.

Literature DB >> 17406258

Locating potential enhancer elements by comparative genomics using the EEL software.

Kimmo Palin¹, Jussi Taipale, Esko Ukkonen.

Abstract

This protocol describes the use of Enhancer Element Locator (EEL), a computer program that was designed to locate distal enhancer elements in long mammalian sequences. EEL will predict the location and structure of conserved enhancers after being provided with two orthologous DNA sequences and binding specificity matrices for the transcription factors (TFs) that are expected to contribute to the function of the enhancers to be identified. The freely available EEL software can analyze two 1-Mb sequences with 100 TF motifs in about 15 min on a modern Windows, Linux or Mac computer. The output provides several hypotheses about enhancer location and structure for further evaluation by an expert on enhancer function.

Entities: Species

Mesh：

Substances：
Transcription Factors

Year: 2006 PMID： 17406258 DOI： 10.1038/nprot.2006.56

Source DB: PubMed Journal: Nat Protoc ISSN： 1750-2799 Impact factor: 13.491

Keyword Cloud
Cited

19 in total

1. Role of canonical Wnt signaling/ß-catenin via Dermo1 in cranial dermal cell development.

Authors: Thu H Tran; Andrew Jarrell; Gabriel E Zentner; Adrienne Welsh; Isaac Brownell; Peter C Scacheri; Radhika Atit
Journal: Development Date: 2010-10-27 Impact factor: 6.868

2. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.

Authors: Sari Tuupanen; Mikko Turunen; Rainer Lehtonen; Outi Hallikas; Sakari Vanharanta; Teemu Kivioja; Mikael Björklund; Gonghong Wei; Jian Yan; Iina Niittymäki; Jukka-Pekka Mecklin; Heikki Järvinen; Ari Ristimäki; Mariachiara Di-Bernardo; Phil East; Luis Carvajal-Carmona; Richard S Houlston; Ian Tomlinson; Kimmo Palin; Esko Ukkonen; Auli Karhu; Jussi Taipale; Lauri A Aaltonen
Journal: Nat Genet Date: 2009-06-28 Impact factor: 38.330

3. D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements.

Authors: Josef Laimer; Clemens J Zuzan; Tobias Ehrenberger; Monika Freudenberger; Simone Gschwandtner; Carina Lebherz; Peter Lackner
Journal: BMC Bioinformatics Date: 2013-04-24 Impact factor: 3.169

4. Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H.

Authors: Alan M Pittman; Silvia Naranjo; Sanni E Jalava; Philip Twiss; Yussanne Ma; Bianca Olver; Amy Lloyd; Jayaram Vijayakrishnan; Mobshra Qureshi; Peter Broderick; Tom van Wezel; Hans Morreau; Sari Tuupanen; Lauri A Aaltonen; M Eva Alonso; Miguel Manzanares; Angela Gavilán; Tapio Visakorpi; José Luis Gómez-Skarmeta; Richard S Houlston
Journal: PLoS Genet Date: 2010-09-16 Impact factor: 5.917

Locating potential enhancer elements by comparative genomics using the EEL software.

1. Role of canonical Wnt signaling/ß-catenin via Dermo1 in cranial dermal cell development.

2. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.

3. D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements.

4. Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H.

5. Prediction and experimental validation of novel STAT3 target genes in human cancer cells.

Review 6. Decoding development in Xenopus tropicalis.

Review 7. Identification and computational analysis of gene regulatory elements.

Review 8. Analytical methods for inferring functional effects of single base pair substitutions in human cancers.

9. Genome-wide prediction of transcription factor binding sites using an integrated model.

Review 10. Integrating sequence, evolution and functional genomics in regulatory genomics.