WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00021567 Gene Name  Y45G12C.4
Sequence Name  ? Y45G12C.4 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including etr-1; rsr-2; and ash-2 based on tiling array; RNA-seq; and microarray studies. Is affected by aldicarb and fluvastatin based on microarray and RNA-seq studies. Is predicted to encode a protein with the following domains: Uncharacterised oxidoreductase Dhs-27; Protein kinase-like domain superfamily; Oxidoreductase and Kinase-like Enzymes; Uncharacterized oxidoreductase dhs-27; and CHK kinase-like. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1912
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00021567

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:Y45G12C.4.1 Y45G12C.4.1 1257   V: 2546239-2548150
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:Y45G12C.4 Y45G12C.4 1257   V: 2546239-2546379

3 RNAi Result

WormBase ID
WBRNAi00048608
WBRNAi00015769
WBRNAi00020625

9 Allele

Public Name
gk963301
gk963591
gk963553
gk964259
gk963850
gk963027
gk962689
gk962688
gk963769

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00021567 2546239 2548150 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_chrV_2548151..2548568   418 V: 2548151-2548568 Caenorhabditis elegans

36 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts of coding genes that showed significantly decreased 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_depleted_coding-RNA
adult vs dauer larva Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. N.A. WBPaper00050488:adult_vs_dauer_regulated_N2_20C
  mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. WBPaper00045420:fertilization_downregulated_transcript
20C vs 25C Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage. N.A. WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult
  Transcripts that showed significantly increased expression in emb-4(hc60) comparing to in N2. DESeq2 WBPaper00052884:emb-4(hc60)_upregulated
  Transcripts depleted in RIS neurons comparing to in all cells. edgeR 3.24.3, FDR < 0.01 WBPaper00058969:RIS_depleted
20C vs 25C Transcripts that showed differential expression in 20C vs 25C in mir-34(gk437) animals at adult stage. N.A. WBPaper00050488:20C_vs_25C_regulated_mir-34(gk437)_adult
20C vs 25C Transcripts that showed differential expression in 20C vs 25C in N2 animals at adult stage. N.A. WBPaper00050488:20C_vs_25C_regulated_N2_adult
  Transcripts that showed differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C. N.A. WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C
  Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 20C. EdgeR, FDR < 0.05, fold change < 0.5. WBPaper00055971:nhl-2(ok818)_20C_upregulated
  Genes that showed increased expression in bar-1(ga80) animal comparing to in N2. All statistical analyses were performed using the statistical programming language R (version 2.13.1 x 64). A linear model was used to determine the effect and significance of the genotype on the expression levels (probe intensity + genotype + error). Using permutations of the original data in the same linear model, authors determined thresholds adjusted for multiple testing (FDR 0.05: -log10(p) > 2; FDR 0.01: -log10(p) > 3). To correct for the developmental difference between bar-1(ga80) and N2 authors used the developmental gene expression data from Snoek et al. (2014) together with the gene expression data generated for this study (bar-1(ga80) vs. N2) in one linear model (probe intensity, sample age + genotype + error). The intensities were corrected for batch effect and for sample age authors used an age of 44 hours for the bar-1(ga80) samples (as estimated), and 48 hours for the N2 samples. WBPaper00045257:bar-1(ga80)_upregulated
Bacteria infection: Photorhabdus luminescens Genes with increased expression after 24 hours of infection by P.lumniescens Fold changes shown are pathogen vs OP50. For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. WBPaper00038438:P.lumniescens_24hr_upregulated_TilingArray
  Transcripts that showed differential expression in dauer N2 vs dauer mir-34(gk437) animals at 20C. N.A. WBPaper00050488:N2_vs_mir-34(gk437)_regulated_dauer_20C
  Transcripts that showed significantly decreased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage. DESeq, FDR < 0.05 WBPaper00055626:pry-1(mu38)_downregulated
  Proteins expressed in intestine cytoplasm, according to tissue specific APX enzyme expression using spp-5 promoter driven NES(cytoplasm)-GFP-APX, followed with mass spectrometry. Fold change > 2. WBPaper00051245:intestine_cytoplasm_expressed
  Transcripts that showed significantly decreased expression in ash-2(RNAi) comparing to in wild type animals injected with vector. Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed. WBPaper00066232:ash-2(RNAi)_downregulated_WT
  Transcripts that showed significantly increased expression in eat-2(ad1113) comparing to in N2. DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs. WBPaper00065746:eat-2(ad1113)_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. Transcripts that showed significantly increased expression in N2 animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. DESeq2, fold change > 2. WBPaper00061081:E.faecalis_upregulated_N2
  Transcripts that showed differential expression in dauer N2 vs dauer mir-34(OverExpression) animals at 20C. N.A. WBPaper00050488:N2_vs_mir-34(OverExpression)_regulated_dauer_20C
  Proteins specifically expressed in cytoplasm, according to tissue specific APX enzyme expression driven NES(cytoplasm)-GFP-APX, followed with mass spectrometry. Fold change > 2. WBPaper00051245:cytoplasm_specific
  Transcripts that showed significantly increased expression in skpo-1(ok1640) animals comparing to in N2 when fed by OP50. DESeq2, fold change > 2. WBPaper00061081:skpo-1(ok1640)_upregulated_OP50
  Genes with more than 1.4 fold decrease of expression after exposing to 16mg/l aldicarb Data filtering based on a cut-off of 1.4 fold change in expression revealed 8,282 aldicarb responsive genes (4,960 up-regulated, 3,322 down-regulated). Statistical analysis of this set of fold change filtered genes using T-test with Benjamini and Hochberg false discovery correction identified 380 significant up-regulated genes and 282 significant down-regulated genes. WBPaper00038061:aldicarb_downregulated
  Transcripts that showed significantly decreased expression in lin-22(ot267) comparing to in N2 at L3 larva. Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1). WBPaper00053295:lin-22(ot267)_downregulated
  Genes that showed significantly decreased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control. Fold change > 1.2 or < 0.8. WBPaper00042477:rsr-2(RNAi)_downregulated_TilingArray
  Transcripts that showed differential expression in adult N2 vs adult mir-34(OverExpression) animals at 25C. N.A. WBPaper00050488:N2_vs_mir-34(OverExpression)_regulated_adult_25C
  Transcripts that showed significantly decreased expression in dlk-1(km12) animals exposed to fluvastatin sodium for 9 hours at L4 larva stage, comparing to dlk-1(km12) animals grown without fluvastatin exposure. DESeq2 FDR < 0.05 WBPaper00059604:fluvastatin_downregulated_dlk-1(km12)
  Transcripts that showed significantly decreased expression in N2 animals exposed to fluvastatin sodium for 9 hours at L4 larva stage, comparing to N2 animals grown without fluvastatin exposure. DESeq2 FDR < 0.05 WBPaper00059604:fluvastatin_downregulated_N2
  Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 20C. N.A. WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_20C
  Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 25C. N.A. WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_25C
  Transcripts that showed differential expression in adult mir-34(OverExpression) vs adult N2 animals at 20C. N.A. WBPaper00050488:mir-34(OverExpression)_vs_N2_regulated_adult_20C

1 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1160095 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00021567 2546239 2548150 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1912

1 Sequence Ontology Term