Open Access Highly Accessed Research article

miRNeye: a microRNA expression atlas of the mouse eye

Marianthi Karali1, Ivana Peluso1, Vincenzo A Gennarino13, Marchesa Bilio1, Roberta Verde14, Giampiero Lago1, Pascal Dollé2 and Sandro Banfi1*

  • * Corresponding author: Sandro Banfi banfi@tigem.it

  • † Equal contributors

Author Affiliations

1 Telethon Institute for Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy

2 IGBMC (Institute de Génétique et de Biologie Moléculaire et Cellulaire); UMR 7104 CNRS; U 964 INSERM; BP 10142, 67404 Illkirch, France

3 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA

4 ICB (Istituto di Chimica Biomolecolare), CNR, Via Campi Flegrei 34, 80078 Naples, Italy

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BMC Genomics 2010, 11:715  doi:10.1186/1471-2164-11-715

Published: 20 December 2010

Additional files

Additional file 1:

miRNA profiling of the adult mouse retina, RPE, cornea and lens. Heat-map of two-way hierarchical clustering analysis for 285 miRNAs with Delta Log2 median ratio ΔLMR ≥ 0.5 in at least one of the samples (panel A). Only miRNAs with values across all samples were considered for the analysis. Colors indicate relative expression compared to the mean for each miRNA in the entire eye: red color represents an expression level above mean, green color represents expression lower than the mean. The complete set of nodes can be seen. The 5 clusters (A-E) obtained at the five-node level are delimited by green brackets. The 25 miRNA sub-clusters selected are highlighted with blue lines. The clustering of the tissues analyzed based on their miRNA content is shown by the horizontal dendrogram in panel B. sc: sub-cluster.

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Additional file 2:

Complete dataset of the Gene Ontology analysis. The worksheet 'gsea_results_intersection' includes all the enriched GO/KEGG terms in biological processes and pathways for each of the predicted targets of the miRNAs present within each selected sub-cluster. The worksheet 'gsea_results_occurencies' summarizes the occurrence of each GO/KEGG term among the miRNA members of each selected node. The number of the miRNA members of each sub-cluster considered in the analysis is given in the last column.

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Additional file 3:

Gene Ontology analysis of the predicted targets of selected sub-clusters of miRNAs with comparable expression profiles. Schematic representation of selected GO/KEGG categories relevant to eye development and function that were enriched among the targets of at least 70% of the miRNAs present within each sub-cluster. The miRNAs within each sub-cluster considered for functional analysis of their predicted targets are listed on the last column of the table. The tissues in which each cluster was predominantly expressed are listed in the column labeled "Expression". For each GO/KEGG category the percentage of representation of this term among the miRNAs analyzed is reported within the cell. The terms of BP Biological Processes and KEGG pathways that relate to similar cellular functions are arbitrarily coloured for readers' clarity. The exact reference numbers that correspond to the GO Biological Processes and KEGG pathways of the table are the following: cell adhesion (GO:0007155); axonogenesis (GO:0007409); morphogenesis of a branching structure (GO:0001763); modification-dependent macromolecule catabolic process (GO:0043632); epithelium development (GO:0060429); transmission of nerve impulse (GO:0019226); cell migration (GO:0016477); cell motion (GO:0006928); neuron development (GO:0048666); neuron differentiation (GO:0030182); neuron projection development (GO:0031175); pattern specification process (GO:0007389); cell-cell signaling (GO:0007267); synaptic transmission (GO:0007268); vesicle-mediated transport (GO:0016192); vasculature development (GO:0001944); Wnt signaling pathway (GO:0016055); regulation of actin cytoskeleton (KEGG: mmu04810); Adherens junction (KEGG: mmu04520); Axon guidance (KEGG: mmu04360); Focal adhesion (KEGG: mmu04510); Glioma (KEGG: mmu05214); GnRH signaling pathway (KEGG: mmu04912); Melanogenesis (KEGG: mmu04916); Melanoma (KEGG: mmu05218); Neurotrophin signaling pathway (KEGG: mmu04722); Wnt signaling pathway (KEGG: mmu04310); MAPK signaling pathway (KEGG: mmu04010); TGF-beta signaling pathway (KEGG: mmu04350). Abbreviations are, cor: cornea; ret: retina; RPE: retinal pigment epithelium.

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Additional file 4:

Detailed annotation of the miRNA expression patterns obtained at all developmental stages analyzed. The table presents the overall pattern of expression (e.g. ubiquitous, ubiquitous with pattern, regional, not detected) at each developmental stage and a brief annotation of the structures that were positive for miRNA expression at each stage. Abbreviations are as follows: Developmental stage: E = Embryonic day; P = Postnatal day. Overall signal: nd = not detected; reg/1-2-3 = regional; ubi/1-2-3 = ubiquitous; uwp/1-2-3 = ubiquitous with pattern; 1-2-3 = signal intensity level Anatomical structures: BR = Brain; CB = Ciliary body; EOM = Extraocular muscles; GCL = Ganglion Cell Layer; INBL = Inner Neuroblastic Layer; INL = Inner Nuclear Layer; IR = Iris; OLF = Olfactory epithelium; ONBL = Outer Neuroblastic Layer; ONL = Outer Nuclear Layer; PHOT = Photoreceptors; RPE = Retinal Pigment Epithelium.

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Additional file 5:

Complete list of differential expression values [Log2 median ratios and Delta Log2 median ratios between each sample group (average) versus EYE1 sample]. This page contains an expression matrix for all 9 samples analyzed by microarray. Only miRNAs with 9 values (no 'NA's accepted) across samples have been included in the analysis (see column named 'count'). In column 'M' to 'P' the difference in Log2 median ratios (ΔLMR) between each sample group (average) has been calculated to the 'entire eye' common reference sample named 'EYE1'. The miRNAs have been sorted on the basis of the values in column 'Q' with the highest differential expression on top (see column named MAX). The acronym 'NA' indicates miRNAs that did not yield reliable read-outs (see Methods for further details). The numbers are all log2(Hy3/Hy5) ratios.

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Additional file 6:

Probes used for RNA in situ hybridization. The table summarizes information on probe sequence, miRBase accession number and hybridization (Thyb) temperatures.

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