WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003330 Gene Name  mir-237
Sequence Name  ? F22F1.4 Brief Description  mir-237 encodes a microRNA, a small non-protein coding RNA and appears to be conserved in C. briggsae; mir-237 shares strong sequence homology with the C. elegans lin-4 heterochronic gene that is essential for the L1 to L2 larval stage transition; mir-237 thus belongs to the lin-4 family of microRNAs which also includes human miR-125b-1 and miR-125b-2; miR-237 RNA expression is detected at the beginning of the L3 larval stage and continues to be expressed into the adult stage; miR-237 is also strongly expressed in glp-4(bn2) mutant worms; gfp expression studies indicate that miR-237 is expressed in the Z1 and Z4 precursor cells of the somatic gonad at the L1 stage, in the vulval precursor cells, anchor cell, a subset of uterine cells the distal tip cells of the gonad, neurons in the head and tail region and in seam cells in the L3 larval stage; based on expression patterns and the abnormalities in the gonad and vulva caused by mir-237 overexpression, mir-237 appears to promote normal vulva and gonad morphogenesis.
Organism  Caenorhabditis elegans Automated Description  Expressed in gonad; seam cell; somatic gonad precursor; and vulval precursor cell.
Biotype  SO:0001265 Genetic Position  X :-0.481454 ±0.017613
Length (nt)  ? 99
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003330

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F22F1.4a F22F1.4a 23   X: 8154099-8154121
Transcript:F22F1.4b F22F1.4b 22   X: 8154136-8154157
 

Other

0 CDSs

0 RNAi Result

8 Allele

Public Name
gk964260
gk962707
gk964193
gk964194
gk963896
gk963732
tm2238
n4296

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003330 8154084 8154182 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_chrX_8154183..8154444   262 X: 8154183-8154444 Caenorhabditis elegans

34 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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
  Micro RNAs that showed significantly decreased 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_downregulated_intestine
  Micro RNAs that showed significantly decreased 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_downregulated_coelomocyte
  Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in hypodermis. 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_hypodermis
  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
  miRNAs that showed significantly increased expression in pry-1(mu38) comparing to in N2. Fold change > 2, FDR < 0.05 WBPaper00057033:pry-1(mu38)_upregulated
  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
  miRNA with increased 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_upregulated_adult
  miRNA with decreased 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_downregulated_adult
  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_adult
  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_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
  MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood mir-71(n4115) 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_mir-71(n4115)
  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
  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) L1 larva comparing to in prg-1(wm161) 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_prg-1_L1_vs_embryo_upregulated_adult
  miRNA with increased expression in prg-1(wm161) L3 larva comparing to in prg-1(wm161) 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_prg-1_L3_vs_L2_upregulated_adult
  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_adult
  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
  Micro RNAs that showed significantly increased expression in hrpk-1(zen17) comparing to in N2 at embryo stage. DESeq, fold change > 2, p-value <= 0.05. WBPaper00058673:hrpk-1(zen17)_upregulated_miRNA_embryo
  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
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
  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
  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

6 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr8421 Expressed from L1 to adulthood. Expressed in distal tip cells from L1 to adults. Also expressed in hypodermis, starting at L2 and strong at L4 and adults. In vulva, expression is seeing from L2 till adulthood. Also expressed in head neurons and seam cells.  
    Expr12249 mir-237, was not expressed in the seam cells until eL3, which mirrored the up-regulation of this gene at this stage by northern blot. mir-237, was detected two stages earlier at L1 in the somatic gonad progenitor cells, Z1 and Z4. This result differs from our northern blot data, which showed that miR-237 RNA was first detected at L2 (Expr3739). We believe that the mir-237::gfp expression at the L1 stage is accurate, and since mir-237 is only expressed in the Z1 and Z4 cells at this stage, miR-237 RNA is below the levels of detection by northern blot analysis. Once the Z1 and Z4 somatic gonad derivatives expand at L2, miR-237 RNA can be seen by northern blot. By the L3 stage, and persisting into the adult, mir-237 was expressed in the developing gonad, including the anchor cell, a subset of unidentified uterine cells, and the distal tip cells. The up-regulation of mir-237 expression in animals carrying the mir-237::gfp construct at the L3 stage in a variety of tissues, such as the gonad and the hypodermis, mirrors the increased miR-237 RNA levels observed at L3 by northern blot analysis. In addition, mir- 237 and mir- 84, were both expressed in the anchor cell and in the VPCs except P6.p at the mL3 stage. It is interesting to note that expression of mir-237, mir-84, and mir-48 was absent in the P6.p cell during the mid- to late L3 stage, and expression of mir-237 and mir-84 but not mir-48 was present in the anchor cell.  
    Expr10888    
    Expr13380 In WT animals, miR-48, miR-241, and miR-237 miRNAs were expressed at very low levels during the L1, when LIN-14 is normally expressed, and increased in abundance 20- to 30-fold by the L3 when LIN-14 is down-regulated.  
    Expr3739 miR-237 was detected at low levels during L2, was upregulated at early L3, and peaked during the L4 stage.  
    Expr2524 No signal detected in embryos, L1 and L2 larva. Intense signals detected in L3, L4 larva, adults, and glp-4(bn2) adults.  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00003330 8154084 8154182 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
99

1 Sequence Ontology Term