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Analysis of the NCI-60 dataset for cancer-related microRNA and mRNA using expression profiles.

Abstract：

BACKGROUND:Recent studies have indicated that microRNA (miRNA) may play an oncogenic or tumor suppressor role in human cancer. To study the regulatory role of miRNAs in tumorigenesis, an integrated platform has been set up to provide a user friendly interface for query. The main advantage of the present platform is that all the miRNA target genes' information and disease records are drawn from experimentally verified or high confidence records. RESULTS:MiRNA target gene results are annotated with reference to the disease gene as well as the pathway database. The correlation strength between miRNA and target gene expression profile is quantified by computing the correlation coefficient using the NCI-60 expression profiling data. Comprehensive analysis of the NCI-60 data found that the cumulative percentage of negative correlation coefficients for cleavage regulation is slightly higher than its positive counterpart; which indicated that the mRNA degradation mechanism is slightly dominant. In addition, the RNAHybrid and TargetScans scores are computed which potentially served as quantitative estimators for miRNA-mRNA binding events. Three scores are defined for each miRNA-mRNA pair, which are based on the disease gene and pathway information. These three scores allow user to sort out high confidence cancer-related miRNA-mRNA pairs. Statistical tests were applied to investigate the relations of three chromosomal features, i.e., CpG island, fragile site, and miRNA cluster, with cancer-related miRNAs. A web-based interface has been set up for query, which can be accessed at: http://ppi.bioinfo.asia.edu.tw/mirna_target/ CONCLUSIONS:The main advantage of the present platform on miRNA-mRNA targeting information is that all the target genes' information and disease records are experimentally verified. Although this may limit the number of miRNA-mRNA relationships, the results provided here are more solid and have fewer false positive events. Certain novel cancer-related miRNA-mRNA pairs are identified and confirmed in the literature. Fisher's exact test suggests that CpG island and fragile site associated miRNAs tend to associate with cancer formation. In summary, the present platform provides an easy means of investigating cancer-related miRNAs.

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Weng CW,Lee SC,Lee YL,Ng KL

doi

10.1016/j.compbiolchem.2013.02.001

subject

Has Abstract

pub_date

2013-06-01 00:00:00

pages

15-21

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(13)00014-5

journal_volume

44

pub_type

杂志文章

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