WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003321 Gene Name  mir-228
Sequence Name  ? T12E12.7 Brief Description  mir-228 encodes a microRNA, a small non-protein coding RNA and appears to be conserved in C. briggsae; based on RNA sequence identity, miR-228 belongs to the miR-124 family of microRNAs along with miR-124 and human miR-124a-1, miR-124a-2, miR-124-a-3 and human miR-183; Drosophila miR-268 also appears to be homologous to miR-228; miR-228 is strongly expressed at all stages of development in normal worms and in glp-4(bn2) mutant worms; many of the known microRNAs are involved in post-transcriptional regulation of genes; the precise function of miR-228 is unknown.
Organism  Caenorhabditis elegans Automated Description  Expressed in germ line; neuronal sheath cell; and seam cell.
Biotype  SO:0001265 Genetic Position  IV :1.84542 ±0.00491
Length (nt)  ? 98
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003321

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T12E12.7a T12E12.7a 23   IV: 5562040-5562062
Transcript:T12E12.7b T12E12.7b 22   IV: 5562082-5562103
 

Other

0 CDSs

1 RNAi Result

WormBase ID
WBRNAi00018643

8 Allele

Public Name
gk964500
gk963722
gk963417
gk963150
gk963375
gk963416
gk832205
n4382

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003321 5562025 5562122 1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIV_5562123..5562139   17 IV: 5562123-5562139 Caenorhabditis elegans

25 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  miRNA with decreased 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_downregulated_adult
  Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. DESEQ2, fold change > 2 and FDR < 0.01. WBPaper00062103:neuron_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
  MicroRNAs that showed significantly altered expression in hsf-1(+);+HS vs hsf-1(RNAi);+HS. Worms remained on RNAi plates until the L4 larval-stage before being heat shocked by submerging plates in a 33C water bath for 30 minutes. The Benjamini-Hochberg correction for multiple testing was then used to determine significantly altered miRNAs between each treatment condition. Micro RNAs with q-value < 0.05 was considered differentially expressed. WBPaper00052959:hsf-1(RNAi)_regulated_miRNA_HS-dependent
  miRNA with increased 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_upregulated_adult
  Micro RNAs that showed significantly increased 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)_upregulated_miRNA_L4
  micro RNAs that exhibit changes in expression during adulthood (p-value < = 0.05). Authors searched for targets with seed matches of perfect Watson-Crick base-pair complementarity to positions two-eight of the miRNAs (counting from the 5' end). In order to consider these seed matches as potential target sites, authors required a minimal cut-off for binding specificity of the remainder of the miRNA to the target. Recent evidence suggests that this is not required for function in humans, but 3' binding does occur in studies of C. elegans. Authors used the scoring algorithm from Robins et al. (2005). The binding cut-off is determined by creating a second-order Markov model of the background for the 3' UTRs. The cut off was p-value < = 0.05. WBPaper00028344:adult_expr_change
  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 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
  miRNA with increased 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_upregulated_embryo
  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
  MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals. Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. WBPaper00053318:Aging_downregulated_miRNA_N2
  miRNAs that showed significantly decreased expression after 48 hour treatment in 10uM sanguinarine. Fold change > 2. WBPaper00055663:sanguinarine_downregulated
  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
  miRNA with increased 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_upregulated_L3
  MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite. Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. WBPaper00053318:mir-71(n4115)_upregulated_miRNA
  miRNA with increased expression in N2 L1 larva comparing to in N2 embryo. 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_L1_vs_embryo_upregulated_adult
  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
  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 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_downregulated_BodyWallMuscle
  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
  miRNAs that showed increased expression in 8 days 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)_Day8_upregulated

7 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
Picture: Figure 4B.   Expr7878 miR-228 expression is indicated in inner/outer labial, cephalic, and amphid sensilla, the posterior deirid, and in phasmid sensilla of the young adult worm. Additionally, expression is observed in seam cells. Based on morphology of GFP-positive cells in sensilla, expression is provisionally identified in sheath and/or socket cells rather than ciliated neurons.  
    Expr8414 Expressed from mid embryo continuing through adulthood. Expressed in amphids, excretory cells, seam cells, vulva, body neurons, rectum and posterior intestine.  
    Expr13931 miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.  
    Expr10945    
    Expr2504 Intense signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults.  
    Expr11969 mir-228::GFP expression increases during early adulthood, reaches a peak, and then begins to slowly decrease in mid to late adulthood.  
    Expr2657 Precursor miRNA: Strong expression in L1. Weak expression in L2 and L3. No expression in embryo, L4 and adult. mature miRNA: Strong expression in L1, L2 and L3. Intermediate expression in L4. Weak expression in embryo and adult.  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00003321 5562025 5562122 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
98

1 Sequence Ontology Term