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Open Access Highly Accessed Research article

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation

Sergei A Manakov12, Seth GN Grant1 and Anton J Enright2*

Author Affiliations

1 Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

2 European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK

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BMC Genomics 2009, 10:419  doi:10.1186/1471-2164-10-419

Published: 8 September 2009

Additional files

Additional file 1:

GO terms enriched in mRNA expression clusters. Top 15 most enriched GO terms in the two largest mRNA expression clusters (i.e. with average trends continuously decreasing or increasing between any two consecutive timepoints). Types of ontologies tested (Ont.): BP - biological process; MF - molecular function; CC - cellular component. Analysis results listed: q - number of genes from a GO term present in a group of predicted targets, m - total number of genes within a GO term, P - non-adjusted p. value for a given enrichment. See Methods for details.

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Additional file 2:

miRNAs belonging to the three major expression categories (with fold change expression cutoff). List of miRNAs by type of expression with a P. value cutoff of 0.05 and magnitude of fold change cutoff of 1.5. Steady-state - highly expressed miRNAs (among top 30 most highly expressed) showing no change of abundance between any timepoints. Decreasing - miRNAs classified by MCL (see Methods) into an expression cluster with average trend decreasing between all consecutive timepoints. Increasing -miRNAs classified by MCL into an expression cluster with average trend increasing between all consecutive timepoints. Numbers in parentheses show the ranking of a miRNA among all profiled miRNAs sorted by the maximal value of expression at any timepoint.

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Additional file 3:

miRNAs belonging to the three major expression categories (with no fold change expression cutoff). List of miRNAs by type of expression with a p. value cutoff of 0.05 and no magnitude of fold change cutoff. Steady-state - highly expressed miRNAs (among top 30 most highly expressed) showing no change of abundance between any timepoints. Decreasing - miRNAs classified by MCL (see Methods) into an expression cluster with average trend decreasing between all consecutive timepoints. Increasing -miRNAs classified by MCL into an expression cluster with average trend increasing between all consecutive timepoints. Numbers in parentheses show the ranking of a miRNA among all profiled miRNAs sorted by the maximal value of expression at any timepoint.

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Additional file 4:

RT-PCR validation of the three miRNAs profiled by microarrays. (A) mmu-let-7a showed no change of abundance between the first (day 1) and the last (day 8) timepoints (-1 < ΔΔCt < 1). (B) mmu-miR-143 showed significant decrease (ΔΔCt < -4.43, P < 2e - 16) and (C) mmu-miR-370 a significant increase (ΔΔCt = 2.93, P < 2.1e - 19) in abundance levels. The error-bars are equal to two standard deviations of ΔCt values between the replicates.

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Additional file 5:

miRNAs among the top 100 most expressed with seed matching sites most enriched in the 3'UTRs of sorted genes. 3'UTR words - words enriched in 3'UTRs of sorted genes. Complementary miRNA - miRNA with seed region (positions 2..8) complementary to the enriched word. miRNA expression trend - average trend of miRNA expression category and cluster as defined by differential expression analysis and classified by MCL where applicable (see Methods): steady-state - highly expressed miRNAs (among the top 30 most highly expressed) showing no change of abundance between any timepoints; decreasing - miRNAs from an expression cluster with average trend decreasing between all consecutive timepoints; increasing - miRNAs from an expression cluster with average trend increasing between all consecutive timepoints; other - miRNAs classified into other minor MCL expression clusters. Numbers in parentheses show the ranking of a miRNA among all profiled miRNAs, sorted by the maximal value of expression at any timepoint.

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Additional file 6:

List of all miRNAs in five large genomic clusters enriched in differentially regulated miRNAs. Increasing Expression - list of miRNAs from two genomic clusters on Chromosome 12. These clusters are enriched in miRNA with an average expression trend increasing between all consecutive time-points. Decreasing Expression - list of miRNAs from a genomic cluster on Chromosome 14 and two on Chromosome X enriched in miRNA with an average expression trend decreasing between all consecutive timepoints. Numbers in parentheses show chromosomal coordinates of the first and last miRNAs in a genomic cluster. Letters in parentheses refer to the expression of a miRNA: (I) - average trend increasing between all consecutive timepoints; (D) - average trend decreasing between all consecutive timepoints; (s) -no significant differential expression; (e) - average trend is not included in the above categories. Available information concerning associated genomic features and potential regulatory sites: TSS - transcription start site; CpG - CpG island evidence; cDNA - experimental EST evidence; polyA - polyadenylation evidence; Regulatory Information - experimental evidence from functional genomics database of Ensembl.

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Additional file 7:

The edit distance between the seed regions of co-expressed miRNAs. Seed regions of co-expressed miRNAs were on average more similar than seed regions of randomly chosen miRNAs. All calculated edit distances (possible values from 1 to 7) are displayed as a histogram of percentages for pairs of co-expressed miRNAs (red bars) and randomly chosen pairs of miRNAs (grey bars). The distance distribution is shown with orange (co-expressed miRNAs) and grey (randomly chosen miRNAs) solid lines. Means of distance distributions are shown with orange (co-expressed miRNAs) and grey (randomly chosen pairs of miRNAs) dashed lines.

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Additional file 8:

GO terms most enriched (P <0.001) in highly expressed predicted targets. Types of ontology terms tested (Ont.): BP - biological process; MF - molecular function; CC - cellular component. The results for targets exclusively predicted for the two types of miRNA expression clusters (with a decreasing or increasing average trends of expression) are given separately. Analysis results listed: q - number of genes from a GO term present in a group of predicted targets, m - total number of genes in a GO term, P - not adjusted p. value for a given enrichment. See Methods for details.

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Additional file 9:

miRNA targets among post-synaptic genes. The list of genes coding for components of post-synaptic proteome (PSP) that were predicted to be targeted by miRNAs down-regulated during culture development (see Discussion for details).

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Additional file 10:

List of Reactome subnetworks for genes targeted by miRNAs. Root Reactome subnetworks significantly enriched (unadjusted p. value < 0.05) among inversely correlated predicted targets (see Methods). Subnetwork Category - the name of a Root Reactome subnetwork with any of the children significantly enriched; Enrichment P value - unadjusted enrichment p. values; Present/Total - number of genes from the subnetwork category present in the query versus total number of genes in the subnetwork category; Ensembl gene IDs - Ensembl gene IDs of present genes; Gene Symbols - gene symbols of present genes.

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Additional file 11:

Graphical representation of Reactome subnetworks of genes targeted by miRNAs. Individual Reactome events (reactions and/or pathways) with participating genes present among predicted targets of up- and down-regulated miRNAs (see Predicted targets of differentially expressed miRNAs). Every event is shown as an arrow, events with the genes present in the sets of miRNA targets are in black.

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