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Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles.

Calura E, Martini P, Sales G, Beltrame L, Chiorino G, D'Incalci M, Marchini S, Romualdi C - Nucleic Acids Res. (2014)

Bottom Line: However, with the benefit of hindsight we can assert that, since we completely ignored the non-coding part of the transcriptome, we spent the last decade to study cell mechanisms having few data in our hands.In this scenario, microRNAs, which are key post-trascriptional regulators, deserve special attention.To fill these gaps, we present 'micrographite' a new pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Padova, via U. Bassi 58/B, 35121 Padova, Italy.

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Mucinous ovarian cancer circuit and qRT-PCR validations. (A) The path with the maximum score: the mucinous path. As described in the legend, miRNA–target validated interactions can be achieved from both manual curation (literature mining) and public databases. Predicted interactions are obtained from Targetscan predictions filtered by expression correlations. (B) qRT-PCR boxplot for specific genes and miRNA of the best path. Mucinous (M), clear cell (C), serous (S), endometrioid (E): ***≤0.005, **≤0.05, *≤0.1.
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Figure 2: Mucinous ovarian cancer circuit and qRT-PCR validations. (A) The path with the maximum score: the mucinous path. As described in the legend, miRNA–target validated interactions can be achieved from both manual curation (literature mining) and public databases. Predicted interactions are obtained from Targetscan predictions filtered by expression correlations. (B) qRT-PCR boxplot for specific genes and miRNA of the best path. Mucinous (M), clear cell (C), serous (S), endometrioid (E): ***≤0.005, **≤0.05, *≤0.1.

Mentions: All the significant pathways listed in Table 3 were analyzed looking for the best scored path inside each pathway (portion of the whole pathway see Supplementary Material S2). All the main paths of each pathway were then combined into a new non-redundant meta–pathway (Supplementary Material S3). As mentioned before, this path combination reduces redundant information due to pathway overlaps and connects disjoint paths due to the artificial subdivision of cellular processes into discrete entities (paths that start in a pathway and end in another one). The union of all the paths has produced two separated networks (Supplementary Material S4 Figure 1), in which the color of edges represents the pathways of origin. The meta–pathway was then analyzed in order to identify and rank its paths (See Supplementary Material S4 Figure 2 and Supplementary Material S5). This procedure allows the finding of chains of genes and miRNAs that are differentially involved in the mucinous compared to other histotypes. Figure 2A shows the meta–pathways that contains the maximum scored path hereafter called the mucEOC pathway.


Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles.

Calura E, Martini P, Sales G, Beltrame L, Chiorino G, D'Incalci M, Marchini S, Romualdi C - Nucleic Acids Res. (2014)

Mucinous ovarian cancer circuit and qRT-PCR validations. (A) The path with the maximum score: the mucinous path. As described in the legend, miRNA–target validated interactions can be achieved from both manual curation (literature mining) and public databases. Predicted interactions are obtained from Targetscan predictions filtered by expression correlations. (B) qRT-PCR boxplot for specific genes and miRNA of the best path. Mucinous (M), clear cell (C), serous (S), endometrioid (E): ***≤0.005, **≤0.05, *≤0.1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4066781&req=5

Figure 2: Mucinous ovarian cancer circuit and qRT-PCR validations. (A) The path with the maximum score: the mucinous path. As described in the legend, miRNA–target validated interactions can be achieved from both manual curation (literature mining) and public databases. Predicted interactions are obtained from Targetscan predictions filtered by expression correlations. (B) qRT-PCR boxplot for specific genes and miRNA of the best path. Mucinous (M), clear cell (C), serous (S), endometrioid (E): ***≤0.005, **≤0.05, *≤0.1.
Mentions: All the significant pathways listed in Table 3 were analyzed looking for the best scored path inside each pathway (portion of the whole pathway see Supplementary Material S2). All the main paths of each pathway were then combined into a new non-redundant meta–pathway (Supplementary Material S3). As mentioned before, this path combination reduces redundant information due to pathway overlaps and connects disjoint paths due to the artificial subdivision of cellular processes into discrete entities (paths that start in a pathway and end in another one). The union of all the paths has produced two separated networks (Supplementary Material S4 Figure 1), in which the color of edges represents the pathways of origin. The meta–pathway was then analyzed in order to identify and rank its paths (See Supplementary Material S4 Figure 2 and Supplementary Material S5). This procedure allows the finding of chains of genes and miRNAs that are differentially involved in the mucinous compared to other histotypes. Figure 2A shows the meta–pathways that contains the maximum scored path hereafter called the mucEOC pathway.

Bottom Line: However, with the benefit of hindsight we can assert that, since we completely ignored the non-coding part of the transcriptome, we spent the last decade to study cell mechanisms having few data in our hands.In this scenario, microRNAs, which are key post-trascriptional regulators, deserve special attention.To fill these gaps, we present 'micrographite' a new pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Padova, via U. Bassi 58/B, 35121 Padova, Italy.

Show MeSH
Related in: MedlinePlus