Computational analysis reveals 43% antisense transcription in 1182 transcripts in mouse muscle

András Györffy, Z. Tulassay, Pawel Surowiak, B. Györffy

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

It is increasingly evident that there is a widespread antisense transcription in the human and other eukaryotic genomes. However, the concept of general antisense expression is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence of antisense transcription. We contrasted 20 Affymetrix MGU74A version 1 mouse genome chips to 12 MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contained the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database. As the Affymetrix data is semi quantitative, the relative levels of antisense partners were analysed. We detected antisense transcription with an overall magnitude of 43% relative to sense transcription in the investigated transcripts. The average MGU74A version 1 expression is shifted towards smaller expression values (MGU74A version 1: 525.1; version 2: 1219.1; t-test: p <0.001). A direct correlation between sense and antisense expression values could not be observed. Genes with high inverse expression values may be correlated to the investigated condition: genes where sense/control and control/antisense ratios were above two may be included in the pathogenetic pathways associated with dystrophin deficiency. The ratio of sense to antisense transcription varied between different chromosomes. We conclude that antisense transcription is a common phenomenon in the mouse genome and may have indirect regulatory functions.

Original languageEnglish
Pages (from-to)422-430
Number of pages9
JournalDNA Sequence - Journal of DNA Sequencing and Mapping
Volume17
Issue number6
DOIs
Publication statusPublished - Dec 2006

Fingerprint

Transcription
Muscle
Genome
Genes
Muscles
Dystrophin
Chromosomes
Databases

Keywords

  • Antisense expression
  • Complementary transcripts
  • Dystrophin deficiency
  • Mouse genome

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Endocrinology
  • Molecular Biology

Cite this

Computational analysis reveals 43% antisense transcription in 1182 transcripts in mouse muscle. / Györffy, András; Tulassay, Z.; Surowiak, Pawel; Györffy, B.

In: DNA Sequence - Journal of DNA Sequencing and Mapping, Vol. 17, No. 6, 12.2006, p. 422-430.

Research output: Contribution to journalArticle

@article{063dedabb7a24f95bdb09fb0c641a40f,
title = "Computational analysis reveals 43{\%} antisense transcription in 1182 transcripts in mouse muscle",
abstract = "It is increasingly evident that there is a widespread antisense transcription in the human and other eukaryotic genomes. However, the concept of general antisense expression is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence of antisense transcription. We contrasted 20 Affymetrix MGU74A version 1 mouse genome chips to 12 MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contained the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database. As the Affymetrix data is semi quantitative, the relative levels of antisense partners were analysed. We detected antisense transcription with an overall magnitude of 43{\%} relative to sense transcription in the investigated transcripts. The average MGU74A version 1 expression is shifted towards smaller expression values (MGU74A version 1: 525.1; version 2: 1219.1; t-test: p <0.001). A direct correlation between sense and antisense expression values could not be observed. Genes with high inverse expression values may be correlated to the investigated condition: genes where sense/control and control/antisense ratios were above two may be included in the pathogenetic pathways associated with dystrophin deficiency. The ratio of sense to antisense transcription varied between different chromosomes. We conclude that antisense transcription is a common phenomenon in the mouse genome and may have indirect regulatory functions.",
keywords = "Antisense expression, Complementary transcripts, Dystrophin deficiency, Mouse genome",
author = "Andr{\'a}s Gy{\"o}rffy and Z. Tulassay and Pawel Surowiak and B. Gy{\"o}rffy",
year = "2006",
month = "12",
doi = "10.1080/10425170600986761",
language = "English",
volume = "17",
pages = "422--430",
journal = "DNA Sequence - Journal of DNA Sequencing and Mapping",
issn = "1940-1736",
publisher = "Informa Healthcare",
number = "6",

}

TY - JOUR

T1 - Computational analysis reveals 43% antisense transcription in 1182 transcripts in mouse muscle

AU - Györffy, András

AU - Tulassay, Z.

AU - Surowiak, Pawel

AU - Györffy, B.

PY - 2006/12

Y1 - 2006/12

N2 - It is increasingly evident that there is a widespread antisense transcription in the human and other eukaryotic genomes. However, the concept of general antisense expression is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence of antisense transcription. We contrasted 20 Affymetrix MGU74A version 1 mouse genome chips to 12 MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contained the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database. As the Affymetrix data is semi quantitative, the relative levels of antisense partners were analysed. We detected antisense transcription with an overall magnitude of 43% relative to sense transcription in the investigated transcripts. The average MGU74A version 1 expression is shifted towards smaller expression values (MGU74A version 1: 525.1; version 2: 1219.1; t-test: p <0.001). A direct correlation between sense and antisense expression values could not be observed. Genes with high inverse expression values may be correlated to the investigated condition: genes where sense/control and control/antisense ratios were above two may be included in the pathogenetic pathways associated with dystrophin deficiency. The ratio of sense to antisense transcription varied between different chromosomes. We conclude that antisense transcription is a common phenomenon in the mouse genome and may have indirect regulatory functions.

AB - It is increasingly evident that there is a widespread antisense transcription in the human and other eukaryotic genomes. However, the concept of general antisense expression is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence of antisense transcription. We contrasted 20 Affymetrix MGU74A version 1 mouse genome chips to 12 MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contained the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database. As the Affymetrix data is semi quantitative, the relative levels of antisense partners were analysed. We detected antisense transcription with an overall magnitude of 43% relative to sense transcription in the investigated transcripts. The average MGU74A version 1 expression is shifted towards smaller expression values (MGU74A version 1: 525.1; version 2: 1219.1; t-test: p <0.001). A direct correlation between sense and antisense expression values could not be observed. Genes with high inverse expression values may be correlated to the investigated condition: genes where sense/control and control/antisense ratios were above two may be included in the pathogenetic pathways associated with dystrophin deficiency. The ratio of sense to antisense transcription varied between different chromosomes. We conclude that antisense transcription is a common phenomenon in the mouse genome and may have indirect regulatory functions.

KW - Antisense expression

KW - Complementary transcripts

KW - Dystrophin deficiency

KW - Mouse genome

UR - http://www.scopus.com/inward/record.url?scp=33847212142&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33847212142&partnerID=8YFLogxK

U2 - 10.1080/10425170600986761

DO - 10.1080/10425170600986761

M3 - Article

C2 - 17381043

AN - SCOPUS:33847212142

VL - 17

SP - 422

EP - 430

JO - DNA Sequence - Journal of DNA Sequencing and Mapping

JF - DNA Sequence - Journal of DNA Sequencing and Mapping

SN - 1940-1736

IS - 6

ER -