Open Access Highly Accessed Research article

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury

Li-Wei Chang1, Andreu Viader2, Nobish Varghese1, Jacqueline E Payton1, Jeffrey Milbrandt2 and Rakesh Nagarajan1*

  • * Corresponding author: Rakesh Nagarajan rakesh@wustl.edu

  • † Equal contributors

Author Affiliations

1 Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110, USA

2 Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110, USA

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BMC Genomics 2013, 14:84  doi:10.1186/1471-2164-14-84

Published: 6 February 2013

Additional files

Additional file 1: Table S1:

Known myelin genes and regulators.

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Additional file 2: Table S2:

Genes in dynamically regulated SC injury response coexpressed gene clusters.

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Additional file 3: Table S3:

miRNAs correlated with the expression of injury response gene clusters.

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Additional file 4: Table S4:

miRNAs anti-correlated with the expression of SC injury response gene clusters.

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Additional file 5: Table S5:

Dynamically regulated miRNAs cotegorized by correlation with differentiation/myelination or proliferation genes.

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Additional file 6: Table S6:

List of experimentally characterized miRNA TSS used to test miRNA TSS prediction.

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Additional file 7: Table S7:

TSS of human and mouse miRNAs predicted by TSSvote and supporting evidence.

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Additional file 8: Figure S1:

Workflow of the computational method for predicting TFs that regulate mRNAs or miRNAs. The same computational model is used to predict TFs that regulate mRNAs using NCBI’s TSS annotation and to predict TFs that regulate miRNAs using computational TSS prediction.

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Additional file 9: Table S8:

ChIP-Seq datasets used in validating computational TF target prediction.

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Additional file 10: Table S9:

Enriched TF bind sites in genes in SC injury response gene clusters.

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Additional file 11: Table S10:

Enriched miRNA binding sites in genes in SC injury response gene clusters.

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Additional file 12: Figure S2:

Luciferase assays confirm a direct interaction between miR-124 and the 3’-UTR of Egr2. Overexpression of miR-124 but not of a Ctrl miRNA in HEK293T cells expressing a luciferase reporter construct carrying the 3’-UTR of Egr2 results in significantly decreased luciferase activity (p<0.05, two-tailed Student’s t-test). Mutating the predicted landing pad for miR-124 in the 3’-UTR of Egr2 disrupts the interaction between miR-124 and the Egr2 3’-UTR luciferase construct and restores luciferase activity.

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Additional file 13: Table S11:

TF and miRNA regulatory network motifs in the SC injury response network.

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