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Table 4 Putative miR-29b and miR-223 targets downregulated after optic nerve crush

From: Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration

Ensembl ID Gene mRNA changea miRNA Context + scoreb No. binding sites
ENSDART00000087565 eva1a 0.61 miR-29b −0.46 1 (8mer)
eva-1 homolog a (miR-223) c (−0.09) 1 (7mer-1A)
ENSDART00000050945 layna 0.45 miR-29b −0.50 1 (8mer)
Layilin a (miR-223) c (−0.16; −0.17) 2 (7mer-1A)
ENSDART00000064163 nefmb 0.28 miR-29b −0.41 1 (8mer)
Neurofilament, medium polypeptide, b
ENSDART00000018351 ina (zgc:65851) 0.50 miR-29b −0.41; −0.05 2 (8mer; 7mer-1A)
Internexin neuronal intermediate filament alpha (miR-223) c (−0.02; >0.03; >0.01) 3 (8mer; 7mer-m8; 7mer-1A)
ENSDART00000021556 si:ch211-51a6.2 0.57 miR-29b −0.33 1 (7mer-m8)
Homolog of prss12 miR-223 −0.32; −0.07 2 (7mer-m8; 7mer-1A)
ENSDART00000126365 smoc1 0.41 miR-223 −0.39; > − 0.02 2 (8mer; 7mer-m8)
SPARC related modular calcium binding 1
ENSDART00000124670 lrrn3 0.65 miR-223 −0.32 1 (8mer)
Leucine rich repeat neuronal protein 3-like
ENSDART00000081039 d sb:cb252 52.9 miR-223 −0.31 1 (7mer-m8)
Homolog of es1-like
  1. aFold change represents microarray expression. All genes had an adjusted p-value ≤0.05
  2. bSee Methods for summary of Targetscan Fish context + score
  3. cPredicted binding sites of miR-223 in genes with a context scores less stringent then our cut-off (i.e., ≤ − 0.30)
  4. dMicroarray results revealed sb:cb252 was the most upregulated gene on microarray, yet it was also one of the top predicted miR-223 target genes by Targetscan Fish; we chose to included it in subsequent experiments to determine if it was a valid miR-223 target
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BMC Genomics

ISSN: 1471-2164

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