Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Abstract Text:

Inhan Lee,Subramanian S Ajay,Haiming Chen,Atsushi Maruyama,Nulang Wang,Melvin G McInnis,Brian D Athey,

MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched sequences (previously yielding only noise levels in microarray experiments) for genome-wide microarray "signal" probes to discriminate single nucleotide differences and to improve probe qualities. Our probes for the entire let-7 family are both homogeneous and specific, verified using microarray signals from fluorescent dye-tagged oligonucleotides corresponding to the let-7 family, demonstrating the power of our algorithm. In addition, false let-7c signals from conventional perfectly-matched probes were identified in lymphoblastoid cell-line samples through comparison with our probe-set signals, raising concerns about false let-7 family signals in conventional microarray platform.

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Publishing Authors By Initials

I Lee,SS Ajay,H Chen,A Maruyama,N Wang,MG McInnis,BD Athey,

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Nucleic acids research

VOLUME: 36

Page Numbers: e27

Journal Abbreviation: Nucleic Acids Res.

ISSN: 1362-4962

DAY: 21

MONTH: 01

YEAR: 2008

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 411011

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Keywords Mesh Terms:

KEYWORDS: Reverse Transcriptase Polymerase Chain R

MESH TERMS: chemistry

Chemical & Substance for Abstract: Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Information

Substance Name: let-7 microRNA, human

Registry Number: 0

Grant and Affiliation Information for Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).

AFFILIATION: Department of Psychiatry, University of Michigan, Ann Arbor, Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA. inhan@umich.edu

Country: England

AGENCY: United States NIDA

GRANT: U54-DA021519

ACRONYM: DA

MEDLINETA: Nucleic Acids Res

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru ProDeG Related Publications

• Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
• Sonography in the diagnosis of branchial cysts.