WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00196684 Gene Name  F59D8.3
Sequence Name  ? F59D8.3 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including npr-8; emr-1; and hmg-3 based on RNA-seq and microarray studies. Is affected by ethanol and fluvastatin based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  :± Length (nt)  ? 176
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00196684

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F59D8.3 F59D8.3 176   X: 3563816-3563991
 

Other

0 CDSs

0 RNAi Result

11 Allele

Public Name
gk963725
gk964260
gk962556
gk276116
gk764652
gk963502
gk505685
gk348695
WBVar02123553
WBVar02121347
WBVar02122052

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00196684 3563816 3563991 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_3563992..3567354   3363 X: 3563992-3567354 Caenorhabditis elegans

34 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
  Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
  Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day5_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day7_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 10 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day10_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 15 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day15_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in day 9 adult hermaphrodites comparing to in day 3 adult animals. DESeq2 v.1.16.1, fold change > 3, FDR < 0.05 WBPaper00067623:Day9_vs_Day3_downregulated
  Transcripts that showed significantly decreased expression in day 17 adult hermaphrodites comparing to in day 3 adult animals. DESeq2 v.1.16.1, fold change > 3, FDR < 0.05 WBPaper00067623:Day17_vs_Day3_downregulated
  Transcripts that showed significantly decreased expression in day 17 adult hermaphrodites comparing to in day 9 adult animals. DESeq2 v.1.16.1, fold change > 3, FDR < 0.05 WBPaper00067623:Day17_vs_Day9_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 that showed significantly decreased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals. CuffDiff, fold change > 2. WBPaper00065096:npr-8(ok1439)_downregulated_Day10_20C
  Transcripts that showed significantly increased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage. DESeq 2, fold change > 4, adjusted p-value < 0.05. WBPaper00055013:hmg-3(bar24)_upregulated
  Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. WBPaper00045521:Gender_Neutral
  Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_glp-1(e2141)
  Transcripts that showed significantly decreased expression in hsp-4(RNAi) comparing to N2 animals with control vector. edgeR (v3.19, Bioconductor), p < 0.05, log2FC > 1.5 or < -1.5 WBPaper00068266:hsp-4(RNAi)_downregulated_N2
  Genes that showed decreased mRNA expression in emr-1(RNAi);lem-2(tm1582) comparing to N2. Library siggenes in R was applied to select the differentially expressed loci using the false discovery rate-based SAM method. Genes presenting a delta value > 4 were considered to be significantly altered. WBPaper00044786:emr-1(RNAi);lem-2(tm1582)_downregulated
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS, comparing to control animals exposed to OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:HYS_vs_OP50_upregulated
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly decreased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to HYS. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:FUR_vs_HYS_downregulated
  Transcripts that showed significantly increased 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_upregulated_N2
  Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:daf-2(e1370)_downregulated
  Transcripts that showed significantly decreased expression in lbp-3 overexpression transgenic lines comparing to wild type control animals. DESeq2 fold change > 2, FDR < 0.05. WBPaper00064156:lbp-3(overexpress)_downregulated
  ncRNAs with significantly decreased expression in cep-1(gk138) than in N2 under normal conditions, according to RNAseq. ncRNAs with more than 2 fold difference in expression are considered differentially expressed WBPaper00045380:cep-1(gk138)_downregulated_normal
  Genes that are significantly down regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2. DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1. WBPaper00046012:tdp-1(ok803)_downregulated
  Genes that showed decreased mRNA expression in emr-1(gk119) comparing to N2. Library siggenes in R was applied to select the differentially expressed loci using the false discovery rate-based SAM method. Genes presenting a delta value > 4 were considered to be significantly altered. WBPaper00044786:emr-1(gk119)_downregulated
  Genes that are upregulated by 0.2M ethanol treatment. Differences in gene expression levels between the two groups of worms were analyzed with Cufflinks 1.0.3, using a cutoff of twofold difference and FDR corrected p < 0.05. WBPaper00041954:ethanol_upregulated
  Coexpression clique No. 202, 172183_at-176110_at, on the genome-wide coexpression clique map for the nematode GPL200 platform. All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. WBPaper00061527:172183_at-176110_at
  Transcripts that showed significantly decreased expression in mafr-1(tm6082) (gain of function) animals comparing to in N2. Student's t-test. Fold Change > = 2. WBPaper00050522:mafr-1(tm6082)_downregulated

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00196684 3563816 3563991 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
176

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

0 Upstream Intergenic Region