WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00195034 Gene Name  F40G9.20
Sequence Name  ? F40G9.20 Organism  Caenorhabditis elegans
Automated Description  Enriched in Q cell based on RNA-seq studies. Is affected by several genes including hsf-1; osm-3; and srbc-48 based on RNA-seq studies. Is affected by Cadmium Chloride based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  :± Length (nt)  ? 20
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00195034

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F40G9.20 F40G9.20 20   III: 178876-178895
 

Other

0 CDSs

0 RNAi Result

5 Allele

Public Name
gk962532
gk964281
WBVar02122373
WBVar02124464
WBVar02121155

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00195034 178876 178895 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_178896..179541   646 III: 178896-179541 Caenorhabditis elegans

33 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
Heat shock: 35C for 1 hour. Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour. The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977)
  Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa. DESeq2, FDR <0.05, fold change > 2. WBPaper00059664:srbc-48(ac23)_upregulated
  Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
  Transcripts that showed significantly increased expression in osm-3(p802) exposed to PA14, comparing to in osm-3(p802) animals exposed to PA14. fold change > 2, FDR < 0.05 WBPaper00066858:osm-3(p802)_upregulated_PA14
Bacteria ibfection: Pseudomonas aeruginosa PA14 Transcripts that showed significantly decreased expression in N2 animals exposed to PA14, comparing to in N2 animals grown on OP50. fold change > 2, FDR < 0.05 WBPaper00066858:PA14_downregulated_N2
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. Transcripts that showed significantly increased expression in whole animal at lin-15(n765ts); oyIs95 animals shifted from 20C to 25C for 16 hours at L4 larva stage, comparing to animals shifted from 20C to 15C for 16 hours at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00065158:25C_vs_15C_upregulated_WholeAnimal
  Transcripts that showed significantly increased expression in xpf-1(tm2842) comparing to in N2 animals. DESeq2 1.14.1, fold change > 2, FDR < 0.01. WBPaper00062497:xpf-1(tm2842)_upregulated
  Transcripts that showed significantly decreased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. Fold change > 2, FDR < 0.01. WBPaper00065993:glp-1(e2141)_downregulated
  Transcripts that showed significantly decreased expression in hda-2(ok1479) comparing to in N2 animals. DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. WBPaper00062159:hda-2(ok1479)_downregulated
  Transcripts enriched in Q cell. DESeq2 (version 2.11.40.7) FDR < 0.05, fold change > 2. WBPaper00066652:Q-cell_enriched
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
  Transcripts that showed significantly increased expression after treated with 300uM CdCl2 from L1 to late L3 larva stage, in N2 animals injected with empty RNAi vector. DESeq2, v1.12.0, fold change > 2, FDR < 0.05 WBPaper00057068:Cadmium_upregulated
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. Transcripts that showed significantly increased expression in AFD neurons at lin-15(n765ts); oyIs95 animals shifted from 20C to 25C for 16 hours at L4 larva stage, comparing to animals shifted from 20C to 15C for 16 hours at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00065158:25C_vs_15C_upregulated_AFD
  Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 4 genes increased expression transiently during dauer commitment. Benjamini Hochberg corrected q-value < 0.01. WBPaper00053388:dauer_regulated_Cluster4
  Transcripts that showed significantly decreased expression in daf-1(m40);daf-3(mgDf90) comparing to in daf-1(m40) at 1-day post L4 adult hermaphrodite animals. CuffDiff fold change >= 2, q < 0.05. WBPaper00059421:daf-3(mgDf90)_downregulated
  Transcripts that showed significantly increased expression in lpd-3(ok2138) comparing to in N2 animals. DESeq2, fold change > 4, FDR < 0.05. WBPaper00064661:lpd-3(ok2138)_upregulated
  Transcripts that showed significantly increased expression in lin-53(RNAi) embryos comparing to control animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067044:lin-53(RNAi)_upregulated
  Transcripts the showed altered expression after auxin induced sacy-1 depletion (24 hours of 2mM auxin treatment at 20C starting from young adult hermaphrodite stage). DESeq2 WBPaper00059334:sacy-1(depletion)_regulated
  Transcripts that showed significantly decreased expression in hsf-1(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:hsf-1(RNAi)_downregulated_WT
  Transcripts that showed significantly decreased expression in mab-5(e1751) without infection comparing to in N2 animals without infection. DESeq2, (FDR)-adjusted P-value < 0.05 and fold change >= 2. WBPaper00066587:mab-5(e1751)_downregulated_uninfected
  Transcripts that showed significantly increased expression in shk-1(yum1003) comparing to in N2 animals. DESeq2 v1.36.0, fold change > 2, FDR < 0.05. WBPaper00067803:shk-1(yum1003)_upregulated
  Transcripts that showed significantly increased expression in animals overexpressing fmo-4. fold change > 2, p-value < 0.05 WBPaper00067820:fmo-4(overexpression)_upregulated
Bacteria infection: Vibrio cholerae A1552, 8 hours at L4 larva stage. Transcripts that showed significantly decreased expression in shk-1(yum1003) animals infected by bacteria strain Vibrio cholerae A1552. DESeq2 v1.36.0, fold change > 2, FDR < 0.05. WBPaper00067803:V.cholerae_downregulated_shk-1(yum1003)
  Transcripts that showed significantly decreased expression in daf-1(m40);daf-3(mgDf90) comparing to in N2 at 1-day post L4 adult hermaphrodite animals. CuffDiff fold change >= 2, q < 0.05. WBPaper00059421:daf-1(m40);daf-3(mgDf90)_downregulated
  Transcripts that showed significantly increased expression in ZD101 tir-1(qd4) comparing to in N2 animals. DESeq2, fold change > 2, FDR < 0.01. WBPaper00067704:tir-1(qd4)_upregulated
Bacteria diet: heat-killed E. coli. Transcripts that showed significantly increased expression in L1 animals exposed to heat-killed bacteria for 4 hours, comparing to animals exposed to no food. DESeq2, fold change > 2, FDR < 0.05. WBPaper00064403:Heat-killed-E.Coli_upregulated
  Transcripts that showed significantly decreased expression in adr-1(tm668) comparing to in N2. DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. WBPaper00055226:adr-1(tm668)_downregulated
  Transcripts that showed significantly decreased expression in tdc-1(n3419);odIs77 comparing to in odIs77 control animals. EdgeR, FDR<0.01 WBPaper00060921:tdc-1(n3419)_downregulated
  Transcripts that showed significantly increased expression in uaf-1(n4588) comparing to in N2 at embryo stage. DEGSeq 1.18.0, p < 0.05, fold change > 2. WBPaper00055364:uaf-1(n4588)_upregulated
Growth temperature Transcripts that are significantly upregulated at 25C compared to both 15C and 20C, with no statistical difference between 15C and 20C, in worms feeding E. coli OP50. DESeq2 and EdgeR, adjusted p-value < 0.05. WBPaper00053814:25C_upregulated_OP50

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00195034 178876 178895 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
20

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIII_177816..178875   1060 III: 177816-178875 Caenorhabditis elegans