WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003292 Gene Name  mir-64
Sequence Name  ? Y48G9A.13 Brief Description  mir-64 encodes a microRNA (miRNA), a small noncoding RNA that is likely involved in post-transcriptional regulation of gene expression; miR-64 is expressed at high levels during all developmental stages and in glp-4 mutant hermaphrodites lacking a germline; miR-64 is also detected in him-8 mutants, starved L1 larvae, and dauer larvae; miR-64 does not appear to have orthologs in other species, and the targets of miR-64 are not yet known; miR-64 is part of a miRNA gene cluster that also contains mir-65 and mir-66.
Organism  Caenorhabditis elegans Automated Description  Is affected by several genes including prg-1; mrps-5; and glh-1 based on RNA-seq studies. Is affected by multi-walled carbon nanotube based on RNA-seq studies. Used to study Parkinson's disease.
Biotype  SO:0001265 Genetic Position  :±
Length (nt)  ? 110
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003292

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:Y48G9A.13a Y48G9A.13a 23   III: 2172869-2172891
Transcript:Y48G9A.13b Y48G9A.13b 21   III: 2172915-2172935
 

Other

0 CDSs

0 RNAi Result

11 Allele

Public Name
gk962532
gk964281
nDf63
WBVar01708535
WBVar01770935
tm3711
gk960867
tm8356
tm11420
nc40
nDf52

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003292 2172848 2172957 1

2 Data Sets

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

0 Downstream Intergenic Region

29 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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
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 mrps-5(RNAi) animals comparing to animals injected with empty vector. Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA
  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
  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
  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
  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_L2
  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 increased expression in alg-5(ram2), comparing to in N2. DESeq2, Fold change > 1.5. WBPaper00051404:alg-5(ram2)_upregulated_miRNA
  miRNA with decreased expression in prg-1(wm161) L4 larva comparing to in prg-1(wm161) 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_prg-1_L4_vs_L3_downregulated_adult
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
  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
Bacteria infection: Pseudomonas aeruginosa PA14 miRNAs up regulated by Pseudomonas aeruginosa infection. N.A. WBPaper00046303:P.aeruginosa_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 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 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
  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

1 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2491 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 		Start End Strand
WBGene00003292 2172848 2172957 1

0 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly decreased expression in mir- 229,64,65,66(nDf63) III comparing to in N2 animals. DESeq2 v1.30.1, fold change > 2, FDR < 0.05. WBPaper00064999:miR-229-64-65-66_downregulated
  Transcripts that showed significantly increased expression in mir- 229,64,65,66(nDf63) III comparing to in N2 animals. DESeq2 v1.30.1, fold change > 2, FDR < 0.05. WBPaper00064999:miR-229-64-65-66_upregulated

1 Sequence

Length
110

1 Sequence Ontology Term