WormMine: Gene WBGene00003286

• WormBase Gene ID: WBGene00003286
• Gene Name: mir-58.1
• Sequence Name: Y67D8A.4
• Brief Description: mir-58.1 encodes a microRNA, a small non-protein coding RNA and is conserved in C. briggsae; mir-58.1 is expressed constitutively throughout development in normal worms and in glp-4(bn2) adults; many of the known microRNAs are involved in post-transcriptional regulation of genes.
• Organism: Caenorhabditis elegans
• Automated Description: Expressed in several structures, including excretory cell; hypodermis; intestine; pharynx; and spermatheca.
• Biotype: SO:0001265
• Genetic Position: IV :-5.44068 ±0.089176
• Length (nt): 97

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003286

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y67D8A.4a	Y67D8A.4a	23	IV: 3233269-3233291
Transcript:Y67D8A.4b	Y67D8A.4b	22	IV: 3233314-3233335

Other

0 CDSs

0 RNAi Result

9 Allele

• gk963722
• gk962726
• gk963907
• tm11340
• tm11092
• gk476571
• tm11350
• n4640
• gk322956

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003286
• Start: 3233254
• End: 3233350
• Strand: 1

2 Data Sets

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

0 Downstream Intergenic Region

30 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	Transcripts that showed significantly increased expression in animals after 24 hour exposure to 100ug per ml silica nanoparticles (SiNPs).	The random variance model (RVM)t-test was applied toidentify differentially expressed mRNAs and miRNAsbetween the SiNPs-treated group and the control group. P-value <0.05 and fold change (FC) >1.5 were considered as the threshold screening between the SiNP-treated groupand the control group.	WBPaper00060100:SiNP_upregulated_mRNA
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage.	Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00065158:AFD_enriched
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure.	Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours.	DESeq2, FDR < 0.05	WBPaper00056868:P.aeruginosa_upregulated_smallRNA
	Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12	Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01.	WBPaper00040221:DAF-12_target_ALF4
	Transcripts of noncoding genes that showed significantly increased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_enriched_noncoding-RNA
	Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2	DESeq2	WBPaper00057162:meg-3_meg-4_upregulated_sRNA
	Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in intestine.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_upregulated_intestine
	Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in coelomocyte.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_upregulated_coelomocyte
	miRNAs that showed increased expression in 1 day post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.	A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.	WBPaper00046156:eat-2(ad1116)_Day1_upregulated
	Micro RNAs that showed significantly decreased expression in hrpk-1(tm5522) comparing to in N2 at L4 larva stage.	DESeq, fold change > 2, p-value <= 0.05.	WBPaper00058673:hrpk-1(tm5522)_downregulated_miRNA_L4
	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
	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
Heat Shock: 35C 4 hours at L4 larva stage.	Micro RNAs that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_miRNA
	miRNAs with age dependent abundance in wild type animals.	Details available in Supplementary material of the paper. Diff Exp, is the approximate ratio of expression comparing Young to Old animals (11 day difference in age). The raw p-value is for the null hypothesis that the Diff exp Ratio = 1 (based on robust inference - see supplemental information) and the associated 95% CI of the ratio.	WBPaper00042527:age_dependent_miRNA
	Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in body wall muscle.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_upregulated_BodyWallMuscle
	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
Bacteria infection: Pseudomonas aeruginosa PA14	miRNAs up regulated by Pseudomonas aeruginosa infection.	N.A.	WBPaper00046303:P.aeruginosa_upregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_upregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated_miRNA
	Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in neuron.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_downregulated_neuron
	Micro RNAs that showed significantly increased expression in drsh-1(ok369) comparing to in N2.	Fold change > 1.5.	WBPaper00055896:drsh-1(ok369)_upregulated
Temperature Shift: 35 centigrade for 4 hours.	miRNAs down regulated after 4 hours of exposure to 35C.	miRNAs with > 1.9 fold change in expression were considered differentially expressed.	WBPaper00046567:HeatStress_downregulated
	miRNAs that showed significantly increased expression in glh-1(gk100) at 26 centigrade, comparing to in N2 animals at 26 centigrade.	DESeq2 q-value < 0.05.	WBPaper00049990:glh-1(gk100)_26C_vs_N2_26C_upregulated
	Micro RNAs that showed significantly increased expression in animals after 24 hour exposure to 100ug per ml silica nanoparticles (SiNPs).	The random variance model (RVM)t-test was applied toidentify differentially expressed mRNAs and miRNAsbetween the SiNPs-treated group and the control group. P-value <0.05 and fold change (FC) >1.5 were considered as the threshold screening between the SiNP-treated groupand the control group.	WBPaper00060100:SiNP_upregulated_miRNA
	miRNAs that showed significantly increased expression in glp-4(bn2) at 26 centigrade, comparing to in N2 animals at 26 centigrade.	DESeq2 q-value < 0.05.	WBPaper00049990:glp-4(bn2)_26C_vs_N2_26C_upregulated
	miRNA that showed decreased expression after 20mM nicotine treatment	Statistical analysis was based on t-test for independent samples via SPSS. The results were further narrowed based on two criteria. Only the genes whose expression changed with a P < 0.05 and a fold change > 0.5, when compared to control, were considered as differentially expressed. Fold change was calculated as 2**(DeltaCt(treatment)-DeltaCt(control))-1. DeltaCt = Ct(miRNA)-Ct(aveMRNA).	WBPaper00042480:20mM_nicotine_downregulated
	miRNAs that showed significantly increased expression after 48 hour treatment in 10uM sanguinarine.	Fold change > 2.	WBPaper00055663:sanguinarine_upregulated

5 Expression Patterns

• Primary Identifier: Expr12847
• Pattern: Excretory canal, excretory cell soma, pharynx, intestine, hypodermis, spermatheca, absent in nervous system and in seam cells; expressed at all stages, adults have the highest expression.

• Primary Identifier: Expr8461
• Remark: Picture: N.A.
• Pattern: No expression detected.

• Primary Identifier: Expr12855
• Pattern: Nervous system.

• Primary Identifier: Expr10927

• Primary Identifier: Expr2488
• Pattern: Intense signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003286
• Start: 3233254
• End: 3233350
• Strand: 1

0 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Proteins identified by MudPIT in miR-58(wt) miRNA pulldown.	Fold change > 4 enriched in miRNA pulldowns over the scrambled control,	WBPaper00064080:miR-58_miRNA_interacting

1 Sequence

• Length: 97

1 Sequence Ontology Term