WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00249816 Gene Name  F42G8.18
Sequence Name  ? F42G8.18 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including swsn-1; nuo-6; and isp-1 based on RNA-seq and microarray studies. Is affected by paraquat; adsorbable organic bromine compound; and nitrotriazolone based on microarray studies. Biotype  SO:0000336
Genetic Position  Length (nt)  ? 333
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00249816

Genomics

0 Transcripts

 

Other

0 CDSs

0 RNAi Result

9 Allele

Public Name
gk964278
gk964500
gk963722
gk963417
gk963416
tm10795
gk653266
gk909773
gk449087

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00249816 8121908 8122240 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_chrIV_8122241..8122648   408 IV: 8122241-8122648 Caenorhabditis elegans

12 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Genes with expression altered >= 3-fold in dpy-10(e128) mutants. Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). WBPaper00035873:dpy-10_regulated
  Genes with expression altered >= 3-fold in dpy-9(e12) mutants. Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). WBPaper00035873:dpy-9_regulated
  Transcripts with significantly decreased expression after treatment with 0.1mM paraquat vs. control Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. WBPaper00045263:0.1mM-paraquat_downregulated
  Transcripts with significantly decreased expression in isp-1(qm150) vs. N2, and in isp-1(qm150)ced-4(n1162) vs. ced-4(n1162). Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. WBPaper00045263:isp-1(qm150)_downregulated
  Transcripts with significantly decreased expression in nuo-6(qm200) vs. N2, and in nuo-6(qm200);ced-4(n1162) vs. ced-4(n1162). Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. WBPaper00045263:nuo-6(qm200)_downregulated
  Transcripts with significantly decreased expression under all of these conditions Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. WBPaper00045263:ProLongevity-mtROS_downregulated
  Genes that showed significantly decreased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in M. aeruginosa batch culture. Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5. WBPaper00046853:AOBr_M.aeruginosa-batch-culture_downregulated
Bacteria diet: Comamonas sp. DA1877 Genes upregulated on Comamonas DA1877 relative to E. coli OP50, Gravid adult stage Moderated T statistics in Limma was used to calculate significance. Significance was determined using an adjusted p value. Changes in gene expression that were 2-fold (p < 0.001) or greater were considered significantly changed. WBPaper00042258:DA1877_upregulated_GravidAdult
  Transcripts that showed significantly decreased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms. DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) WBPaper00060764:swsn-1(os22ts)_downregulated
  Genes up regulated in aak-2 over expression line uthIs202[Paak-2c To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. WBPaper00038172:aak-2overexpression_up_regulated
  Transcripts that showed significantly altered expression after 24 hour exposure to nitrotriazolone (NTO). Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%. WBPaper00055899:nitrotriazolone_regulated
  Genes downregulated in hcf-1(-), upregulated in sir-2.1(O/E) and no change in daf-2(-). To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. WBPaper00040184:hcf-1down_sir-2.1up_daf-2nc

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00249816 8121908 8122240 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
333

1 Sequence Ontology Term