WormMine

WS296

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003328 Gene Name  mir-235
Sequence Name  ? T09B4.12 Brief Description  mir-235 encodes a microRNA, a small non-protein coding RNA and may have a potential ortholog in C. briggsae; based on RNA sequence identity miR-235 belongs to the miR-25 family of microRNAs that also includes the human microRNAs miR-92-1, miR-92-2, miR-25-1, miR-25-2 and miR-32; miR-235 is weakly 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-235 is unknown.
Organism  Caenorhabditis elegans Automated Description  Expressed in AMsoL; AMsoR; and hypodermis.
Biotype  SO:0001265 Genetic Position  I :0.84296 ±0.010005
Length (nt)  ? 97
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003328

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T09B4.12b T09B4.12b 22   I: 6162306-6162327
Transcript:T09B4.12a T09B4.12a 23   I: 6162347-6162369
 

Other

0 CDSs

0 RNAi Result

8 Allele

Public Name
gk962858
gk962706
gk963902
gk964505
gk448621
gk112486
n4504
WBVar02122995

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003328 6162291 6162387 -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_chrI_6161666..6162290   625 I: 6161666-6162290 Caenorhabditis elegans

36 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 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
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
  Transcripts that showed significantly decreased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066485:ogt-1(ok1474)_downregulated_neuron
  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
  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
  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
  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
  Transcripts that showed significantly decreased expression in VC1743[mett-10(ok2204)] comparing to in N2 when animals grow on peptone-rich (NA22) plates. DESeq2, p-value < 0.05, fold change > 2. WBPaper00061357:mett-10(ok2204)_downregulated_NA22
  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
  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
  Micro RNAs that showed significantly increased 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_upregulated_neuron
  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 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 decreased 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_downregulated_adult
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
  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)
  microRNA that showed significantly increased expression in CT20 zaIs5 [alg-1p-GFP-alg-1; rol-6(su1006)] comparing to in control animals of PE255 feIs5 [sur-luciferase-GFP; rol-6(su1006)]. fold change > 2. WBPaper00066713:alg-1(overexpression)_upregulated
  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
  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
  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
Fasting for 48 hours, from 3 days post L4 to 5 days post L4. MicroRNAs that showed significantly increased expression after 48 hours of fasting p < 0.0002, Fishers exact test. WBPaper00051247:fasting_upregulated
  microRNA that showed significantly increased expression in glp-1(e2144) comparing to in N2 animals. fold change > 2. WBPaper00066713:glp-1(e2144)_upregulated
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

4 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr11010 Pmir-235::gfp is apparently expressed in the entire hypodermis from late embryogenesis to adult. In addition to the hypodermis, its expression was also seen in glia-like socket cells surrounding amphid neurons during L1 diapause (AmsoL/R). By northern blotting it was observed that the level of mature miR-235 progressively increased during the period of L1 diapause.  
    Expr8419 Expressed from late embryos to adulthood. Expression detected in hypodermis,especially at L1-L2. Also detected in vulva, rectum and some amphid neurons.  
    Expr10948    
    Expr2473 Faint 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 		Start End Strand
WBGene00003328 6162291 6162387 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
97

1 Sequence Ontology Term