WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00196933 Gene Name  F43D9.8
Sequence Name  ? F43D9.8 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including hmg-3; pmt-2; and ogt-1 based on RNA-seq and microarray studies. Is affected by paraquat based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  :± Length (nt)  ? 147
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Lists
This Gene is in one list:
metrics_list_union (10192)

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00196933

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F43D9.8 F43D9.8 147   III: 10506679-10506825
 

Other

0 CDSs

0 RNAi Result

8 Allele

Public Name
gk964518
gk963887
gk963675
gk963676
gk963083
gk383294
tm3624
WBVar01657161

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00196933 10506679 10506825 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_chrIII_10506826..10507057   232 III: 10506826-10507057 Caenorhabditis elegans

17 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 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 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 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
Starvation for 8 hours at mid-L4 larva stage. Transcripts that showed significantly increased expression in efk-1(ok3609) animals starved for 8 hours on unseeded plate at mid-L4 larva stage. Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR. Fold change > 2, FDR < 0.05. WBPaper00067829:starvation_upregulated_efk-1(ok3609)
Starvation for 8 hours at mid-L4 larva stage. Transcripts that showed significantly increased expression in N2 animals starved for 8 hours on unseeded plate at mid-L4 larva stage. Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR. Fold change > 2, FDR < 0.05. WBPaper00067829:starvation_upregulated_N2
Starvation for 8 hours at mid-L4 larva stage. Transcripts that showed significantly increased expression in zip-2(tm4248) animals starved for 8 hours on unseeded plate at mid-L4 larva stage. Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR. Fold change > 2, FDR < 0.05. WBPaper00067829:starvation_upregulated_zip-2(tm4248)
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. Transcripts that showed significantly decreased expression in AFD neurons comparing to in whole animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00065158:AFD_depleted
  Transcripts that showed significantly increased expression in pmt-2(RNAi) animals comparing to control animals iinjected with empty vector. Fold-change > 1.5, ANOVA P values < 0.05. WBPaper00055482:pmt-2(RNAi)_upregulated
  Transcripts that showed significantly increased 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_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
Starvation for 8 hours at mid-L4 larva stage. Transcripts that showed significantly increased expression in cep-1(gk138) animals starved for 8 hours on unseeded plate at mid-L4 larva stage. Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR. Fold change > 2, FDR < 0.05. WBPaper00067829:starvation_upregulated_cep-1(gk138)
  Transcripts that showed significantly decreased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066485:ogt-1(ok1474)_downregulated_neuron
  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 were enriched in oogenic fog-2(q71) gonads comparing to in spermatogenic fem-3(q96gf), according to RNAseq analysis. To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. WBPaper00045521:Oogenic
  Transcripts that showed significantly decreased expression in sams-3(RNAi) comparing to N2 animals injected with empty vector. Deseq FDR < 0.01, fold change > 2. WBPaper00065005:sams-3(RNAi)_downregulated
  ncRNAs with significantly decreased expression in cep-1(gk138) than in N2 after UV irradiation, according to RNAseq. ncRNAs with more than 2 fold difference in expression are considered differentially expressed WBPaper00045380:cep-1(gk138)_downregulated_UV

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00196933 10506679 10506825 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
147

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

0 Upstream Intergenic Region