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

Fuller-Carter, Paula I.; Carter, Kim W.; Anderson, Denise; Harvey, Alan R.; Giles, Keith M.; Rodger, Jennifer

doi:10.1186/s12864-015-1772-1

Table 2 Top downregulated genes 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 symbol	Gene name	Fold change	Adjusted p-value	GO process or function^a
ENSDART00000055936	isl2b	islet2b	0.18	0.000315	DNA-dependent transcription
ENSDART00000137322	kcnip3	Kv channel interacting protein 3, calsenilin	0.29	0.000151	Potassium channel activity; neuronal apoptotic processes
ENSDART00000051693	irx4a	Iroquois homeobox protein 4a	0.15	0.002945	DNA-dependent transcription
ENSDART00000082745	emb	Embigin	0.26	0.001049	Cell adhesion; integral to membrane functioning
ENSDART00000090267	scn4ba	Sodium channel, voltage-gated, type IV, beta a	0.28	0.000848	Voltage-gated sodium channel activity
ENSDART00000052338	irx4b	Iroquois homeobox protein 4b	0.24	0.001560	DNA-dependent transcription
ENSDART00000052802	calb2b	Calbindin 2b, (calretinin)	0.26	0.001408	Calcium ion binding; neuronal excitability
ENSDART00000027398	kcna2	Potassium voltage-gated channel, Shaker-related subfamily, member 2	0.33	0.000641	Potassium ion transport; synaptic transmission
ENSDART00000067514	rbpms2a	RNA binding protein with multiple splicing 2a	0.36	0.000558	Nucleotide binding
	Unknown	Unknown	0.44	0.000407
ENSDART00000018351	zgc:65851	Paralog of internexin neuronal intermediate filament protein, alpha	0.28	0.001732	Neurofilament cytoskeleton organization
ENSDART00000134832	rbpms2b	RNA binding protein with multiple splicing 2b	0.42	0.000690	Nucleic acid binding
ENSDART00000114765	kcnd1	Potassium voltage-gated channel, Shal-related subfamily, member 1	0.42	0.000917	Potassium ion transport; synaptic transmission
ENSDART00000113796	cacnb3b	Calcium channel, voltage-dependent, beta 3b	0.42	0.001316	Calcium ion transmembrane transport
ENSDART00000064012	ca4a	Carbonic anhydrase IV a	0.52	0.000690	Carbonate dehydratase activity; zinc ion binding
ENSDART00000113081	gpr158	G-protein coupled receptor 158	0.51	0.000947	G-protein coupled receptor activity
ENSDART00000124112	pou4f2	POU domain, class 4, transcription factor 2	0.30	0.006744	DNA-dependent transcription
ENSDART00000031167	tfap2d	Transcription factor AP-2 delta	0.43	0.001926	DNA-dependent transcription
ENSDART00000031091	vsnl1a	Visinin-like 1a	0.45	0.001678	Calcium ion binding
ENSDART00000077838	ryr3	Ryanodine receptor 3	0.51	0.001445	Calcium ion transmembrane transport
ENSDART00000098599	si:ch211-151 h10.2	Uncharacterised protein	0.44	0.002573
ENSDART00000127084	LOC100537452	Uncharacterized protein	0.45	0.002423
ENSDART00000084303	kcnq3	Potassium voltage-gated channel, KQT-like subfamily, member 3	0.45	0.002495	Potassium ion transport; synaptic transmission
ENSDART00000055281	kcnc3b	Potassium voltage-gated channel, Shaw-related subfamily, member 3b	0.53	0.001560	Potassium ion transport; synaptic transmission
ENSDART00000126365	smoc1	SPARC related modular calcium binding 1	0.41	0.004141	Extracellular matrix; calcium ion binding
ENSDART00000090092	ank1	Ankyrin 1, erythrocytic	0.43	0.003530	Cytoskeletal adaptor activity
ENSDART00000023562	syt2	Synaptotagmin 2	0.50	0.002264	Calcium ion binding; synaptic transmission
ENSDART00000105932	si:dkeyp-110e4.11	Uncharacterised protein	0.43	0.004012

Ranked by combined –log₁₀ p-value and ≥1.5 absolute fold change
^aGO terms determined by ZFIN and Uniprot databases

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ISSN: 1471-2164

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