WormMine: Gene WBGene00023456

• WormBase Gene ID: WBGene00023456
• Gene Name: mir-360
• Sequence Name: Y23B4A.3
• Brief Description: mir-360 encodes a microRNA, a small non-protein coding RNA and seems to be conserved in C. briggsae; many of the known microRNAs are involved in post-transcriptional regulation of genes; the precise function of miR-360 is unknown.
• Organism: Caenorhabditis elegans
• Automated Description: Is affected by several genes including prg-1; alg-1; and alg-2 based on RNA-seq studies. Is affected by multi-walled carbon nanotube and graphene oxide based on RNA-seq studies.
• Biotype: SO:0001265
• Genetic Position: X :-4.07224 ±0.013376
• Length (nt): 110

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00023456

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y23B4A.3a	Y23B4A.3a	21	X: 5919174-5919194
Transcript:Y23B4A.3b	Y23B4A.3b	21	X: 5919213-5919233

Other

0 CDSs

0 RNAi Result

5 Allele

• gk964260
• gk926097
• gk964356
• n4635
• WBVar01815658

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00023456
• Start: 5919149
• End: 5919258
• Strand: 1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_5919259..5919396
• Length (nt): 138
• Chromosome Location: X: 5919259-5919396
• Organism: Caenorhabditis elegans

16 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	miRNAs that showed increased expression after exposure to graphene oxide (GO)	The dysregulated expression of miRNAs in GO-exposed nematodes was analyzed by DESeq (an R package, a powerful tool to estimate the variance and test for differential expression). The data were extracted as up- or down-regulated miRNAs according to a cutoff of 2 fold change, and were presented in the scatter diagram after normalization.	WBPaper00045209:graphene-oxide_upregulated
	miRNA with decreased expression in N2 1-day post L4 adult hermaphrodite comparing to in N2 L4 larva.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_N2_adult_vs_L4_downregulated_adult
	MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(ram2)_downregulated_miRNA
	MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_downregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-2(ok304)_upregulated_miRNA
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_embryo
	MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L1
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L3
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L4
	miRNA with increased expression in N2 L4 larva comparing to in N2 L3 larva.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_N2_L4_vs_L3_upregulated_adult
Fungus: C. albicans	miRNAs that showed significantly increased expression after 4 hours of infection by fungus C.albicans at 25 C, comparing to control animals infected with heat killed C.albicans.	Fold change > 2.	WBPaper00050386:C.albicans_4h_upregulated
	miRNA with decreased expression in N2 L2 larva comparing to in N2 L1 larva.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_N2_L2_vs_L1_downregulated_adult
	MicroRNAs that showed significantly increased expression in alg-5(ram2), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(ram2)_upregulated_miRNA
	MicroRNAs that showed significantly decreased expression after animals were exposed to 1 mg per liter multi-walled carbon nanotubes (MWCNTs) from L1 larva to young adult.	DESeq, cut-off of 2-fold change.	WBPaper00045019:MWCNT_downregulated
	miRNA with increased expression in N2 L3 larva comparing to in N2 L2 larva.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_N2_L3_vs_L2_upregulated_adult

1 Expression Patterns

• Primary Identifier: Expr8449
• Pattern: Expressed from comma stage to adults. Expression seen in marginal cells of pharynx.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00023456
• Start: 5919149
• End: 5919258
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 110

1 Sequence Ontology Term