Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology

Wei Shi; Wanlei Zhou

doi:10.1109/GENSIPS.2006.353159

Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology

Wei Shi, Wanlei Zhou

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Other › peer-review

Abstract

This paper took advantage of phylogenetic footprinting and statistical analysis to identify putative cis-regulatory elements in the promoters of human genes. Three organisms were investigated including human, mouse and drosophila melanogaster. 124 putative regulatory elements of length 8 were yielded from this research and they were grouped into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters revealed that SP1, EGR and NRF-1 were the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene Ontology (GO) analysis revealed that many of GO categories of transcription factors binding to these elements matched the GO categories of genes whose promoters contain these elements.

Original language	English
Title of host publication	2006 IEEE International Workshop on Genomic Signal Processing and Statstics
Editors	Edward R. Dougherty
Place of Publication	Piscataway NJ USA
Publisher	IEEE, Institute of Electrical and Electronics Engineers
Pages	67-68
Number of pages	2
ISBN (Electronic)	9781424403844
ISBN (Print)	9781424403851
DOIs	https://doi.org/10.1109/GENSIPS.2006.353159
Publication status	Published - 2006
Externally published	Yes
Event	IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2006 - College Station, United States of America Duration: 28 May 2006 → 30 May 2006 https://ieeexplore.ieee.org/xpl/conhome/4161740/proceeding

Conference

Conference	IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2006
Abbreviated title	GENSIPS 2006
Country/Territory	United States of America
City	College Station
Period	28/05/06 → 30/05/06
Internet address	https://ieeexplore.ieee.org/xpl/conhome/4161740/proceeding

Access to Document

10.1109/GENSIPS.2006.353159

Cite this

Shi, W., & Zhou, W. (2006). Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology. In E. R. Dougherty (Ed.), 2006 IEEE International Workshop on Genomic Signal Processing and Statstics (pp. 67-68). IEEE, Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/GENSIPS.2006.353159

@inproceedings{9c0adaedebd94f27a2e40ab10393b56e,

title = "Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology",

abstract = "This paper took advantage of phylogenetic footprinting and statistical analysis to identify putative cis-regulatory elements in the promoters of human genes. Three organisms were investigated including human, mouse and drosophila melanogaster. 124 putative regulatory elements of length 8 were yielded from this research and they were grouped into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters revealed that SP1, EGR and NRF-1 were the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene Ontology (GO) analysis revealed that many of GO categories of transcription factors binding to these elements matched the GO categories of genes whose promoters contain these elements.",

author = "Wei Shi and Wanlei Zhou",

year = "2006",

doi = "10.1109/GENSIPS.2006.353159",

language = "English",

isbn = "9781424403851",

pages = "67--68",

editor = "Dougherty, \{Edward R. \}",

booktitle = "2006 IEEE International Workshop on Genomic Signal Processing and Statstics",

publisher = "IEEE, Institute of Electrical and Electronics Engineers",

address = "United States of America",

note = "IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2006, GENSIPS 2006 ; Conference date: 28-05-2006 Through 30-05-2006",

url = "https://ieeexplore.ieee.org/xpl/conhome/4161740/proceeding",

}

Shi, W & Zhou, W 2006, Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology. in ER Dougherty (ed.), 2006 IEEE International Workshop on Genomic Signal Processing and Statstics. IEEE, Institute of Electrical and Electronics Engineers, Piscataway NJ USA, pp. 67-68, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2006, College Station, Texas, United States of America, 28/05/06. https://doi.org/10.1109/GENSIPS.2006.353159

Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology. / Shi, Wei; Zhou, Wanlei.
2006 IEEE International Workshop on Genomic Signal Processing and Statstics. ed. / Edward R. Dougherty. Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, 2006. p. 67-68.

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Other › peer-review

TY - GEN

T1 - Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology

AU - Shi, Wei

AU - Zhou, Wanlei

PY - 2006

Y1 - 2006

N2 - This paper took advantage of phylogenetic footprinting and statistical analysis to identify putative cis-regulatory elements in the promoters of human genes. Three organisms were investigated including human, mouse and drosophila melanogaster. 124 putative regulatory elements of length 8 were yielded from this research and they were grouped into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters revealed that SP1, EGR and NRF-1 were the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene Ontology (GO) analysis revealed that many of GO categories of transcription factors binding to these elements matched the GO categories of genes whose promoters contain these elements.

AB - This paper took advantage of phylogenetic footprinting and statistical analysis to identify putative cis-regulatory elements in the promoters of human genes. Three organisms were investigated including human, mouse and drosophila melanogaster. 124 putative regulatory elements of length 8 were yielded from this research and they were grouped into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters revealed that SP1, EGR and NRF-1 were the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene Ontology (GO) analysis revealed that many of GO categories of transcription factors binding to these elements matched the GO categories of genes whose promoters contain these elements.

UR - http://www.scopus.com/inward/record.url?scp=48649103615&partnerID=8YFLogxK

U2 - 10.1109/GENSIPS.2006.353159

DO - 10.1109/GENSIPS.2006.353159

M3 - Conference Paper

AN - SCOPUS:48649103615

SN - 9781424403851

SP - 67

EP - 68

BT - 2006 IEEE International Workshop on Genomic Signal Processing and Statstics

A2 - Dougherty, Edward R.

PB - IEEE, Institute of Electrical and Electronics Engineers

CY - Piscataway NJ USA

T2 - IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2006

Y2 - 28 May 2006 through 30 May 2006

ER -

Shi W, Zhou W. Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology. In Dougherty ER, editor, 2006 IEEE International Workshop on Genomic Signal Processing and Statstics. Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers. 2006. p. 67-68 doi: 10.1109/GENSIPS.2006.353159

Using phylogenetic footprinting to discover putative cis-regulatory elements and analysing their coexistence and related gene ontology

Abstract

Conference

Access to Document

Other files and links

Cite this