MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

Sales, Gabriele; Coppe, Alessandro; Bisognin, Andrea; Biasiolo, M.; Bortoluzzi, Stefania; Romualdi, Chiara

doi:10.1093/nar/gkq423

Cited by 149 publications

(113 citation statements)

References 41 publications

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“…Using matched transcriptomic (mRNA) data available from the same tumors (Lopez-Jimenez et al 2010), integration with miRNA profiles was performed using the MiRNA And Genes Integrative Analysis (MAGIA) web tool (Sales et al 2010), for each sample in a given experimental group. First, this integration analysis was applied to all PCCs/PGLs regardless of genetic background and nAMs and then to each genetic group, filtering those miRNAs common among all PCCs/PGLs (FDR !0.05).…”

Section: Integration Of Mrna and Mirna Expression Datamentioning

confidence: 99%

Integrative analysis of miRNA and mRNA expression profiles in pheochromocytoma and paraganglioma identifies genotype-specific markers and potentially regulated pathways

Cubas¹,

Leandro‐García²,

Schiavi³

et al. 2013

Endocrine-Related Cancer

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Pheochromocytomas (PCCs) and paragangliomas (PGLs) are rare neuroendocrine neoplasias of neural crest origin that can be part of several inherited syndromes. Although their mRNA profiles are known to depend on genetic background, a number of questions related to tumor biology and clinical behavior remain unanswered. As microRNAs (miRNAs) are key players in the modulation of gene expression, their comprehensive analysis could resolve some of these issues. Through characterization of miRNA profiles in 69 frozen tumors with germline mutations in the genes SDHD, SDHB, VHL, RET, NF1, TMEM127, and MAX, we identified miRNA signatures specific to, as well as common among, the genetic groups of PCCs/PGLs. miRNA expression profiles were validated in an independent series of 30 composed of VHL-, SDHB-, SDHD-, and RET-related formalin-fixed paraffin-embedded PCC/PGL samples using quantitative real-time PCR. Upregulation of miR-210 in VHL-and SDHB-related PCCs/PGLs was verified, while miR-137 and miR-382 were confirmed as generally upregulated in PCCs/PGLs (except in MAX-related tumors). Also, we confirmed overexpression of miR-133b as VHL-specific miRNAs, miR-488 and miR-885-5p as RET-specific miRNAs, and miR-183 and miR-96 as SDHB-specific miRNAs. To determine the potential roles miRNAs play in PCC/PGL pathogenesis, we performed bioinformatic integration and pathway analysis using matched mRNA profiling data that indicated a common enrichment Finally, global proteomic analysis in SDHB and MAX tumors allowed us to determine that miRNA regulation occurs primarily through mRNA degradation in PCCs/PGLs, which partially confirmed our miRNA-mRNA integration results.

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Section: Integration Of Mrna and Mirna Expression Datamentioning

confidence: 99%

Integrative analysis of miRNA and mRNA expression profiles in pheochromocytoma and paraganglioma identifies genotype-specific markers and potentially regulated pathways

Cubas¹,

Leandro‐García²,

Schiavi³

et al. 2013

Endocrine-Related Cancer

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“…gene ontology, pathways enrichments of target genes, etc.) such as MMIA [101], MAGIA [109] and miRconnX [119], to link miRNA to transcription factors or to analyze the efect of several miRNAs such as DIANAmirExTra v2.0 [120] and TransMIR [114]. Typically, predicted target genes are used as input for functional enrichment to infer the potential functions of miRNAs.…”

Section: Integrated Tools For Mirna Analysismentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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“…Several web servers have been developed to infer miRNA targets based on the expression profiles of miRNAs and mRNAs from the same set of biological samples (11)(12)(13)(14)(15)(16). For example, the generative model for miRNA regulation (GenMirϩϩ) uses a Bayesian model to predict miRNA targets based on both target genes' 3Ј UTR region sequence features and the correlation between expressions of miRNA and its targets (15).…”

Section: Micrornas (Mirnas)mentioning

confidence: 99%

ProteoMirExpress: Inferring MicroRNA and Protein-centered Regulatory Networks from High-throughput Proteomic and mRNA Expression Data

Qin

Plewczynski

Wang

et al. 2013

Molecular & Cellular Proteomics

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MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein level and therefore can reveal the direct effects of miRNAs' translational repression. Here, we present a web server, ProteoMirExpress, that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks. With both types of high-throughput data from the users, ProteoMirExpress is able to discover not only miRNA targets that have decreased mRNA, but also subgroups of targets with suppressed proteins whose mRNAs are not significantly changed or with decreased mRNA whose proteins are not significantly changed, which are usually ignored by most current methods. Furthermore, both direct and indirect targets of miRNAs can be detected. Therefore, ProteoMirExpress provides more comprehensive miRNA-centered regulatory networks. We used several published data to assess the quality of our inferred networks and prove the value of our server. ProteoMirExpress is available online, with free access to academic users. Molecular & Cellular

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MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

Cited by 149 publications

References 41 publications

Integrative analysis of miRNA and mRNA expression profiles in pheochromocytoma and paraganglioma identifies genotype-specific markers and potentially regulated pathways

Integrative analysis of miRNA and mRNA expression profiles in pheochromocytoma and paraganglioma identifies genotype-specific markers and potentially regulated pathways

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

ProteoMirExpress: Inferring MicroRNA and Protein-centered Regulatory Networks from High-throughput Proteomic and mRNA Expression Data

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