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Series GSE14794 Query DataSets for GSE14794
Status Public on Jun 25, 2009
Title Genome-wide Transcriptional Profiling Reveals MicroRNA-correlated Genes and Pathways in Human Lymphoblastoid Cell Lines
Organism Homo sapiens
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Summary Background: Expression level of many genes shows abundant natural variation in human populations. The variations in gene expression are believed to contribute to phenotypic differences. Emerging evidence has shown that microRNAs (miRNAs) are one of the key regulators of gene expression. However, past studies have focused on the miRNA target genes and use loss- or gain-of-function approach that may not reflect natural association between miRNA and mRNAs. Methodology/Principal Findings: To examine miRNA regulatory effect on global gene expression under endogenous condition, we performed pair-wise correlation coefficient analysis on expression levels of 366 miRNAs and 14,174 messenger RNAs (mRNAs) in 90 immortalized lymphoblastoid cell lines, and observed significant correlations between the two species of RNA transcripts. We identified a total of 7,207 significantly correlated miRNA-mRNA pairs (false discovery rate q <0.01). Of those, 4,085 pairs showed positive correlations while 3,122 pairs showed negative correlations. Gene ontology analyses on the miRNA-correlated genes revealed significant enrichments in several biological pathways related to cell cycle, cell communication and signal transduction. Individually, each of three miRNAs (miR-331, -98 and -33b) demonstrated significant correlation with the genes in cell cycle-related biological processes, which is consistent with important role of miRNAs in cell cycle regulation. Surprisingly, most miRNA-correlated genes were not direct targets predicted by mRNA target prediction program, TargetScan, suggesting indirect endogenous relationship between miRNAs and their correlated mRNAs. Conclusions/Significance: This study demonstrates feasibility of using naturally expressed transcript profiles to identify endogenous correlation between miRNA and miRNA. By applying this genome-wide approach, we have identified thousands of miRNA-correlated genes and revealed potential role of miRNAs in several important cellular functions. The study results along with accompanying data sets will provide a wealth of high-throughput data to further evaluate the miRNA-regulated genes and eventually in phenotypic variations of human populations.

Keywords: correlation coefficient analysis, gene ontology analysis
Overall design to correlate miRNA expression levels with microRNA expression at genome-wide scale in 90 cell lines.
Contributor(s) Wang L
Citation(s) 19517021
Submission date Feb 11, 2009
Last update date Feb 15, 2013
Contact name LIANG WANG
Organization name MAYO CLINIC
Department LAB MED PATH
Street address 200 FIRST ST SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
Platforms (2)
GPL6102 Illumina human-6 v2.0 expression beadchip
GPL8178 Illumina Human v1 MicroRNA expression beadchip
Samples (180)
GSM369900 EBV transformed lymphoblastoid cell line (microRNA, Sample 1)
GSM369901 EBV transformed lymphoblastoid cell line (microRNA, Sample 2)
GSM369902 EBV transformed lymphoblastoid cell line (microRNA, Sample 3)
BioProject PRJNA112077

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE14794_180_mRNA profiles_no_normalization.txt 240.7 Mb (ftp)(http) TXT
GSE14794_192_microRNA profiles_no_normalization.txt 4.3 Mb (ftp)(http) TXT
GSE14794_RAW.tar 5.9 Mb (http)(custom) TAR
GSE14794_ReadMe.txt 14.7 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Raw data are available on Series record
Processed data included within Sample table

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