WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003308 Gene Name  mir-80
Sequence Name  ? K01F9.3 Brief Description  mir-80 encodes a microRNA, a small non-protein coding RNA and is conserved in C. briggsae; based on RNA sequence the mir-80 family also includes C. elegans miR-81 and miR-82 and human miR-143; mir-80 is strongly expressed at all developmental stages 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-80 is unknown.
Organism  Caenorhabditis elegans Automated Description  Involved in regulation of gene expression. Expressed in excretory cell; hypodermis; pharynx; somatic nervous system; and tail neurons. Used to study Parkinson's disease.
Biotype  SO:0001265 Genetic Position  :±
Length (nt)  ? 98
Paste the following link
Quick Links:
SummaryGenomicsOther
 
Quick Links:
SummaryGenomicsOther
 
Lists
This Gene isn't in any lists. Upload a list.

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003308

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:K01F9.3b K01F9.3b 23   III: 8865285-8865307
Transcript:K01F9.3a K01F9.3a 22   III: 8865328-8865349
 

Other

0 CDSs

0 RNAi Result

12 Allele

Public Name
gk964518
gk963887
WBVar02123912
WBVar02123385
WBVar02123386
WBVar02124475
WBVar02122460
WBVar02121004
nDf53
WBVar02122944
WBVar02121875
gk180957

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003308 8865270 8865367 -1

3 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  

0 Downstream Intergenic Region

34 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. DESeq2 version 1.22.2, p < 0.05 WBPaper00064716:paraquat_downregulated
  Transcripts depleted in purified oocyte P bodies comparing to in the whole animal. DESeq2, FDR < 0.05, fold change > 2. WBPaper00065975:P-body_vs_WholeAnimal_depleted
  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
Hypoxia: 0.5% oxygen 2 hours. Transcripts that showed significantly increased expression after hypoxia in an egl-9 / hif-1 independent manner. DESeq2 p-value <0.05, expression of hypoxia vs. normxia >= 2, expression in egl09(sa307) vs N2 < 2, expression of egl-9(sa307); hif-1(ia04) vs N2 <= 2. WBPaper00055344:hypoxia_regulated_HIF-1_independent
Bacteria diet: Clostridium butyricum MIYAIRI 588 (CBM 588) Transcripts that showed significantly increased expression after fed with probiotic bacteria Clostridium butyricum MIYAIRI 588 (CBM 588) for five days, comparing to control groups that were fed with OP50. DESeq 1.30.0, log2 fold change > 2, p-value < 0.05 WBPaper00055944:C.butyricum_vs_OP50_upregulated
  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
  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
  miRNA that showed increased 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_upregulated
Fasting for 48 hours, from 3 days post L4 to 5 days post L4. MicroRNAs that showed significantly decreased expression after 48 hours of fasting p < 0.0002, Fishers exact test. WBPaper00051247:fasting_downregulated
  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
  MicroRNAs that showed significantly decreased expression in alg-2(ok304), comparing to in N2. DESeq2, Fold change > 1.5. WBPaper00051404:alg-2(ok304)_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
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 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
  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
  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
  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 increased expression in drsh-1(ok369) comparing to in N2. Fold change > 1.5. WBPaper00055896:drsh-1(ok369)_upregulated
  miRNAs in F2 generation up regulated by exposure to 20uM and 20mM nicotine during F0 generation. Statistical analysis was based on t-test for independent samples via SPSS to compare each of the nicotine treatments with control (i.e. low vs. control and high vs. control). Welch test correction was performed to account for unequal variance in each of the compared groups (control and treatment). In addition, to increase the statistical stringency, miRNAs differential expression was deemed significant only if it fulfilled two criteria: p value , 0.05 and expression changed by at least 50% relative to control. WBPaper00049006:nicotine_upregulated_F2

5 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr11257 The mir-80::mCherry reporter exhibit a broad cellular expression pattern, somewhat similar to the published extra-chromosomal array line (vulva, hypodermis, body wall muscle, head neurons, tail neurons, excretory cell, dorsal/ventral nerve cord, and weaker expression in intestine [anterior or posterior] and pharynx). The pattern is distinctive in exhibiting highest expression in the two most anterior gut cells and in posterior gut under high food conditions. Interestingly, mir-80 does not appear expressed in the ASI neurons in any lines.  
    Expr8413 Expressed from late embryos to adulthood. Expressed in excretory cells, uterus, vulva, dnc, distal tip cells, posterior intestine, amphid neurons, head and body wall muscle.  
    Expr2498 Intense signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults.  
    Expr10928    
Expression data on embryo and adult stages were not shown in the paper. --wjc.   Expr1671 Expressed in L1, L2, L3, L4.  

1 GO Annotation

Annotation Extension Qualifier
  involved_in

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00003308 8865270 8865367 -1

1 Ontology Annotations

Annotation Extension Qualifier
  involved_in

0 Regulates Expr Cluster

1 Sequence

Length
98

1 Sequence Ontology Term