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Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression.

Mullany LE, Wolff RK, Slattery ML - Cancer Inform (2015)

Bottom Line: We used 13 criteria to evaluate effectiveness and usability of existing bioinformatics tools.MiRPath performed the best of all the tools in linking miRNAs, with 92% of all miRNAs linked as well as the highest based on our established criteria followed by Ingenuity (58% linked).Hopefully, this evaluation will help guide the development of new tools.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT, USA.

ABSTRACT
MiRNAs are small, nonprotein-coding RNA molecules involved in gene regulation. While bioinformatics help guide miRNA research, it is less clear how they perform when studying biological pathways. We used 13 criteria to evaluate effectiveness and usability of existing bioinformatics tools. We evaluated the performance of six bioinformatics tools with a cluster of 12 differentially expressed miRNAs in colorectal tumors and three additional sets of 12 miRNAs that are not part of a known cluster. MiRPath performed the best of all the tools in linking miRNAs, with 92% of all miRNAs linked as well as the highest based on our established criteria followed by Ingenuity (58% linked). Other tools, including Empirical Gene Ontology, miRó, miRMaid, and PhenomiR, were limited by their lack of available tutorials, lack of flexibility and interpretability, and/or difficulty using the tool. In summary, we observed a lack of standardization across bioinformatic tools and a general lack of specificity in terms of pathways identified between groups of miRNAs. Hopefully, this evaluation will help guide the development of new tools.

No MeSH data available.


Related in: MedlinePlus

Coordinated expression with miRNAs.
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Related In: Results  -  Collection


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f1-cin-14-2015-121: Coordinated expression with miRNAs.

Mentions: MiRNAs are small, nonprotein-coding RNA molecules, ∼22 nucleotides in length,1–5 which are complementary to messenger RNA (mRNA) molecules. The mature miRNAs are generated from the cleavage of larger precursor RNA molecules by the enzymes Drosha and Dicer.6 The resulting mature miRNA then binds with an RNA-induced silencing complex, which has the ability to bind to mRNA molecules and alter gene expression by either inhibiting mRNA translation into protein or by promoting mRNA degradation,7 usually by mRNA cleavage or deadenylation.4 MiRNAs are thought to be involved in the carcinogenetic process given their ability to act as tumor suppressors and oncogenes.4 A single miRNA may regulate many different genes, and a single gene may be cooperatively regulated by different miR-NAs.7–9 Since the relationships between miRNAs and their products are numerous, and participate in several different biological processes, it is imperative to look at combinations of miRNAs and genes being expressed to better understand the role of miRNAs in the carcinogenic process. Coordinated gene expression involves the transcription of many genes that work together in specific cellular functions and biological pathways to create a required response.10Figure 1 depicts this process for miRNAs. It has been suggested, “The recognition of coordinated expression profiles… enables inferences about biological pathways and genes functions to be made”.11 It has also been suggested that there are two classes of clustered miRNAs, those with similar sequences that work on a group of genes together, and those of a dissimilar sequence that produce a biological response by regulating different genes involved in that process at the same time.1 MiRNAs are seen as regulators of cell phenotypes6 and are being considered as potential biomarkers that can be used to help diagnosis, stage, and target cancer treatments.12


Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression.

Mullany LE, Wolff RK, Slattery ML - Cancer Inform (2015)

Coordinated expression with miRNAs.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4629629&req=5

f1-cin-14-2015-121: Coordinated expression with miRNAs.
Mentions: MiRNAs are small, nonprotein-coding RNA molecules, ∼22 nucleotides in length,1–5 which are complementary to messenger RNA (mRNA) molecules. The mature miRNAs are generated from the cleavage of larger precursor RNA molecules by the enzymes Drosha and Dicer.6 The resulting mature miRNA then binds with an RNA-induced silencing complex, which has the ability to bind to mRNA molecules and alter gene expression by either inhibiting mRNA translation into protein or by promoting mRNA degradation,7 usually by mRNA cleavage or deadenylation.4 MiRNAs are thought to be involved in the carcinogenetic process given their ability to act as tumor suppressors and oncogenes.4 A single miRNA may regulate many different genes, and a single gene may be cooperatively regulated by different miR-NAs.7–9 Since the relationships between miRNAs and their products are numerous, and participate in several different biological processes, it is imperative to look at combinations of miRNAs and genes being expressed to better understand the role of miRNAs in the carcinogenic process. Coordinated gene expression involves the transcription of many genes that work together in specific cellular functions and biological pathways to create a required response.10Figure 1 depicts this process for miRNAs. It has been suggested, “The recognition of coordinated expression profiles… enables inferences about biological pathways and genes functions to be made”.11 It has also been suggested that there are two classes of clustered miRNAs, those with similar sequences that work on a group of genes together, and those of a dissimilar sequence that produce a biological response by regulating different genes involved in that process at the same time.1 MiRNAs are seen as regulators of cell phenotypes6 and are being considered as potential biomarkers that can be used to help diagnosis, stage, and target cancer treatments.12

Bottom Line: We used 13 criteria to evaluate effectiveness and usability of existing bioinformatics tools.MiRPath performed the best of all the tools in linking miRNAs, with 92% of all miRNAs linked as well as the highest based on our established criteria followed by Ingenuity (58% linked).Hopefully, this evaluation will help guide the development of new tools.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT, USA.

ABSTRACT
MiRNAs are small, nonprotein-coding RNA molecules involved in gene regulation. While bioinformatics help guide miRNA research, it is less clear how they perform when studying biological pathways. We used 13 criteria to evaluate effectiveness and usability of existing bioinformatics tools. We evaluated the performance of six bioinformatics tools with a cluster of 12 differentially expressed miRNAs in colorectal tumors and three additional sets of 12 miRNAs that are not part of a known cluster. MiRPath performed the best of all the tools in linking miRNAs, with 92% of all miRNAs linked as well as the highest based on our established criteria followed by Ingenuity (58% linked). Other tools, including Empirical Gene Ontology, miRó, miRMaid, and PhenomiR, were limited by their lack of available tutorials, lack of flexibility and interpretability, and/or difficulty using the tool. In summary, we observed a lack of standardization across bioinformatic tools and a general lack of specificity in terms of pathways identified between groups of miRNAs. Hopefully, this evaluation will help guide the development of new tools.

No MeSH data available.


Related in: MedlinePlus