Bioinformatic identification and characterization of human endothelial cell-restricted genes

Manoj Bhasin, Lei Yuan, Derin B. Keskin, Hasan H. Otu, Towia A. Libermann, Peter Oettgen

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

Background: In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential biological role.Results: Using a high throughput microarray platform, a primary set of 1,191 transcripts that are enriched in different primary ECs compared to non-ECs was identified (LCB >3, FDR <2%). Further refinement of this initial subset of transcripts, using published data, yielded 152 transcripts (representing 109 genes) with different degrees of EC-specificity. Several interesting patterns emerged among these genes: some were expressed in all ECs and several were restricted to microvascular ECs. Pathway analysis and gene ontology demonstrated that several of the identified genes are known to be involved in vasculature development, angiogenesis, and endothelial function (P < 0.01). These genes are enriched in cardiovascular diseases, hemorrhage and ischemia gene sets (P < 0.001). Most of the identified genes are ubiquitously expressed in many different tissues. Analysis of the proximal promoter revealed the enrichment of conserved binding sites for 26 different transcription factors and analysis of the untranslated regions suggests that a subset of the EC-restricted genes are targets of 15 microRNAs. While many of the identified genes are known for their regulatory role in ECs, we have also identified several novel EC-restricted genes, the function of which have yet to be fully defined.Conclusion: The study provides an initial catalogue of EC-restricted genes most of which are ubiquitously expressed in different endothelial cells.

Original languageEnglish (US)
Article number342
JournalBMC genomics
Volume11
Issue number1
DOIs
StatePublished - May 28 2010

Fingerprint

Forensic Anthropology
Computational Biology
Endothelial Cells
Genes
Untranslated Regions
Gene Ontology
Tissue Distribution
MicroRNAs
Statistical Factor Analysis
Transcription Factors
Cardiovascular Diseases
Ischemia
Binding Sites
Hemorrhage

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Bioinformatic identification and characterization of human endothelial cell-restricted genes. / Bhasin, Manoj; Yuan, Lei; Keskin, Derin B.; Otu, Hasan H.; Libermann, Towia A.; Oettgen, Peter.

In: BMC genomics, Vol. 11, No. 1, 342, 28.05.2010.

Research output: Contribution to journalArticle

Bhasin, Manoj ; Yuan, Lei ; Keskin, Derin B. ; Otu, Hasan H. ; Libermann, Towia A. ; Oettgen, Peter. / Bioinformatic identification and characterization of human endothelial cell-restricted genes. In: BMC genomics. 2010 ; Vol. 11, No. 1.
@article{2c9e4f4fa5bf4146aa5ae7ca45944aab,
title = "Bioinformatic identification and characterization of human endothelial cell-restricted genes",
abstract = "Background: In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential biological role.Results: Using a high throughput microarray platform, a primary set of 1,191 transcripts that are enriched in different primary ECs compared to non-ECs was identified (LCB >3, FDR <2{\%}). Further refinement of this initial subset of transcripts, using published data, yielded 152 transcripts (representing 109 genes) with different degrees of EC-specificity. Several interesting patterns emerged among these genes: some were expressed in all ECs and several were restricted to microvascular ECs. Pathway analysis and gene ontology demonstrated that several of the identified genes are known to be involved in vasculature development, angiogenesis, and endothelial function (P < 0.01). These genes are enriched in cardiovascular diseases, hemorrhage and ischemia gene sets (P < 0.001). Most of the identified genes are ubiquitously expressed in many different tissues. Analysis of the proximal promoter revealed the enrichment of conserved binding sites for 26 different transcription factors and analysis of the untranslated regions suggests that a subset of the EC-restricted genes are targets of 15 microRNAs. While many of the identified genes are known for their regulatory role in ECs, we have also identified several novel EC-restricted genes, the function of which have yet to be fully defined.Conclusion: The study provides an initial catalogue of EC-restricted genes most of which are ubiquitously expressed in different endothelial cells.",
author = "Manoj Bhasin and Lei Yuan and Keskin, {Derin B.} and Otu, {Hasan H.} and Libermann, {Towia A.} and Peter Oettgen",
year = "2010",
month = "5",
day = "28",
doi = "10.1186/1471-2164-11-342",
language = "English (US)",
volume = "11",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Bioinformatic identification and characterization of human endothelial cell-restricted genes

AU - Bhasin, Manoj

AU - Yuan, Lei

AU - Keskin, Derin B.

AU - Otu, Hasan H.

AU - Libermann, Towia A.

AU - Oettgen, Peter

PY - 2010/5/28

Y1 - 2010/5/28

N2 - Background: In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential biological role.Results: Using a high throughput microarray platform, a primary set of 1,191 transcripts that are enriched in different primary ECs compared to non-ECs was identified (LCB >3, FDR <2%). Further refinement of this initial subset of transcripts, using published data, yielded 152 transcripts (representing 109 genes) with different degrees of EC-specificity. Several interesting patterns emerged among these genes: some were expressed in all ECs and several were restricted to microvascular ECs. Pathway analysis and gene ontology demonstrated that several of the identified genes are known to be involved in vasculature development, angiogenesis, and endothelial function (P < 0.01). These genes are enriched in cardiovascular diseases, hemorrhage and ischemia gene sets (P < 0.001). Most of the identified genes are ubiquitously expressed in many different tissues. Analysis of the proximal promoter revealed the enrichment of conserved binding sites for 26 different transcription factors and analysis of the untranslated regions suggests that a subset of the EC-restricted genes are targets of 15 microRNAs. While many of the identified genes are known for their regulatory role in ECs, we have also identified several novel EC-restricted genes, the function of which have yet to be fully defined.Conclusion: The study provides an initial catalogue of EC-restricted genes most of which are ubiquitously expressed in different endothelial cells.

AB - Background: In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential biological role.Results: Using a high throughput microarray platform, a primary set of 1,191 transcripts that are enriched in different primary ECs compared to non-ECs was identified (LCB >3, FDR <2%). Further refinement of this initial subset of transcripts, using published data, yielded 152 transcripts (representing 109 genes) with different degrees of EC-specificity. Several interesting patterns emerged among these genes: some were expressed in all ECs and several were restricted to microvascular ECs. Pathway analysis and gene ontology demonstrated that several of the identified genes are known to be involved in vasculature development, angiogenesis, and endothelial function (P < 0.01). These genes are enriched in cardiovascular diseases, hemorrhage and ischemia gene sets (P < 0.001). Most of the identified genes are ubiquitously expressed in many different tissues. Analysis of the proximal promoter revealed the enrichment of conserved binding sites for 26 different transcription factors and analysis of the untranslated regions suggests that a subset of the EC-restricted genes are targets of 15 microRNAs. While many of the identified genes are known for their regulatory role in ECs, we have also identified several novel EC-restricted genes, the function of which have yet to be fully defined.Conclusion: The study provides an initial catalogue of EC-restricted genes most of which are ubiquitously expressed in different endothelial cells.

UR - http://www.scopus.com/inward/record.url?scp=77952690956&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77952690956&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-11-342

DO - 10.1186/1471-2164-11-342

M3 - Article

C2 - 20509943

AN - SCOPUS:77952690956

VL - 11

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 342

ER -