Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed

A Arora

A Cimmino

A Esquela-Kerscher

A Essaghir

A Grimson

A Krek

AJ Enright

B Boyerinas

C Cheng

C Welch

CE Ott

CJ Braun

D Baek

D Barh

D Betel

DC Corney

DP Bartel

DW Huang

E Bell

E Grönroos

F Sohler

F Xiao

Fatah Kashanchi

GE Liu

GL Papadopoulos

H Hermeking

H Naeem

Haroon Naeem

HI Suzuki

J Gsponer

J Liu

J Lu

JC Huang

JM Kim

JS Wei

K Tu

KK Farh

L He

L Ma

LJ Jensen

LP Lim

M Gironella

M Kertesz

M Li

M Selbach

MP Tschan

MW Rhoades

O Ben-Ami

O Hobert

P Alexiou

P Brodersen

P Sood

PA Pappas

Q Jiang

Q Liu

R Goni

Ralf Zimmer

RC Friedman

Robert Küffner

S Bai

S Griffiths-Jones

S Nam

S Sassen

S Subramanian

S Volinia

SA Georges

SF Wotton

Siegel

T Otto

TC Chang

TS Keshava Prasad

V Matys

Y Benjamini

PLoS ONE

English

PubMed

Naeem, Haroon

Küffner, Robert

Zimmer, Ralf

Universität München: Elektronischen Publikationen

MIRTFnet: analysis of miRNA regulated transcription factors.

Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed.MIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably.The consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis

Naeem Haroon

Küffner Robert

Zimmer Ralf

Public Library of Science (PLOS)

MIRTFnet: Analysis of miRNA Regulated Transcription Factors

Open Access LMU

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BACKGROUND: Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed. METHODOLOGY/PRINCIPAL FINDINGS: MIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably. CONCLUSIONS/SIGNIFICANCE: The consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis

Naeem, H

Küffner, R

Zimmer, R

University of Melbourne Institutional Repository

BackgroundSeveral expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed.Methodology/principal findingsMIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably.Conclusions/significanceThe consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis

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MIRTFnet: Analysis of miRNA Regulated Transcription Factors

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Universität München: Elektronischen Publikationen

Public Library of Science (PLOS)

Open Access LMU

University of Melbourne Institutional Repository

Directory of Open Access Journals

Crossref

Public Library of Science (PLOS)