WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00189953 Gene Name  R155.5
Sequence Name  ? R155.5 Organism  Caenorhabditis elegans
Automated Description  Enriched in male based on RNA-seq studies. Is affected by several genes including csr-1; hsp-6; and hsf-1 based on RNA-seq studies. Is affected by multi-walled carbon nanotube; Doxycycline; and paraquat based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 463
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00189953

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:R155.5.1 R155.5.1 332   III: 1970071-1970533
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:R155.5 R155.5 210   III: 1970118-1970191

0 RNAi Result

10 Allele

Public Name
gk962532
gk964281
gk781291
WBVar00044028
WBVar01836993
WBVar02102255
WBVar01793258
gk167792
WBVar01708340
WBVar01708339

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00189953 1970071 1970533 -1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

0 Downstream Intergenic Region

33 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage. EdgeR, fold change > 2, FDR < 0.001. WBPaper00056290:hsp-6(mg585)_downregulated
  Transcripts that showed significantly decreased 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_downregulated
  Transcripts that showed signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. FDR < 0.05, fold change > 2 WBPaper00067368:pabp-2(RNAi)_upregulated_N2
  Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. Log2 Fold change > 2 or <-1, p-value < 0.05. WBPaper00053599:female_vs_male_downregulated
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_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 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
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 decreased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2. DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. WBPaper00049545:jmjd-3.1(+)_downregulated
  siRNAs that showed significantly lower expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine). DESeq2 v1.13.8, fold change > 2, FDR < 0.01. WBPaper00056161:male_enriched_siRNA
Bacteria infection: Bacillus thuringiensis mRNAs that showed significantly increased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. Cuffdiff, ajusted p-value < 0.01. WBPaper00046497:B.thuringiensis_0.5mix_upregulated_12h
  mRNAs that showed increased expression in csr-1(RNAi) animales comparing to in control RNAi animals. Set 1 transcripts were defined as P-value < 0.05 and fold change > 1.9. DESeq was used. Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution. An adjusted P-value was calculated using the Benjamini-Hochberg method for multiple testing correction. WBPaper00046805:csr-1(RNAi)_upregulated_Set1
  Transcripts that showed significantly increased expression in uthIs235 [sur-5p-hsf-1-unc-54 3'UTR + myo-2p-tdTomato-unc-54 3' UTR] comparing to in N2. DESeq2 FDR < 0.05, fold change > 2. WBPaper00067474:HSF-1(OverExpress)_upregulated
Bacteria infection: Staphylococcus aureus Transcripts that showed significantly increased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals colonized by microbiota but not infected by pathogen. DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05. WBPaper00067479:Microbiota-Pathogen_vs_Microbiota_upregulated
Bacteria: B.subtilis Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult. edgeR 3.16.5, FDR < 0.05, fold change > 2. WBPaper00059117:B.subtilis_upregulated
  Transcripts that showed significantly increased expression in hlh-26(ok1453) animals exposed to E. faecium for 8 hours, comparing to N2 animals exposed to E. faecium for 8 hours. Fold change > 2. WBPaper00062585:hlh-26(ok1453)_upregulated_E.faecium
  Transcripts that showed significantly increased expression in skn-1gf(lax188) comparing to in N2 animals at L4 stage fed with OP50 and exposed to PA14 for 4 hours. DESeq2, FDR < 0.05, fold change > 2. WBPaper00067255:skn-1(lax188)_upregulated_PA
  Transcripts that showed significantly decreased 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)_downregulated
  Transcripts enriched in male him-5(e1490 animals, comparing to in N2 hermaphrodite animals from L3 larva to young adult stages. DESeq FDR < 0.01. WBPaper00050231:male_enriched
Bacteria infection: Staphylococcus epidermidis Transcripts that showed significantly increased expression in mab-5(e1239) animals exposed to S. epidermidis for 24 hours since L4 larva stage, comparing to uninfected mab-5(e1239) animals. DESeq2, (FDR)-adjusted P-value < 0.05 and fold change >= 2. WBPaper00066587:S.epidermidis_upregulated_mab-5(e1239)
  Transcripts that showed significantly increased expression in skn-1(lax188);daf-2(e1370) comparing to in skn-1(lax188) animals DESeq2, fold change > 2, FDR < 0.05. WBPaper00067765:daf-2(e1370)_upregulated_skn-1(lax188)
  Transcripts that showed significantly increased expression in CB4856 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. edgeR (version 3.24.3), fold change > 4, FDR < 0.01. WBPaper00062456:doxycycline_upregulated_CB4856_transcript
  Transcripts that showed significantly increased expression in N2 comparing to in skn-1 gain of function allele lax188 animals DESeq2, fold change > 2, FDR < 0.05. WBPaper00067765:skn-1(lax188)_downregulated_N2
  Transcripts that showed significantly increased expression in N2 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. edgeR (version 3.24.3), fold change > 4, FDR < 0.01. WBPaper00062456:doxycycline_upregulated_N2_transcript
  Transcripts that showed significantly decreased expression in shk-1(yum1003) comparing to in N2 animals. DESeq2 v1.36.0, fold change > 2, FDR < 0.05. WBPaper00067803:shk-1(yum1003)_downregulated
  Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis. To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. WBPaper00045521:Spermatogenic
Bacteria infection: Vibrio cholerae A1552, 8 hours at L4 larva stage. Transcripts that showed significantly increased 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_upregulated_shk-1(yum1003)
Bacteria diet: Chryseobacterium sp. CHNTR56 MYb120 Transcripts that showed significantly increased expression after animals were fed by Chryseobacterium sp. CHNTR56 MYb120, comparing to animals fed by OP50. edgeR FDR <= 0.05, fold change >= 4. WBPaper00061424:Diet_MYb120_upregulated
  Genes that showed increased 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)_upregulated
Bacteria diet: Comamonas sp. 12022 MYb131 Transcripts that showed significantly increased expression after animals were fed by Comamonas sp. 12022 MYb131, comparing to animals fed by OP50. edgeR FDR <= 0.05, fold change >= 4. WBPaper00061424:Diet_MYb131_upregulated

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1155631 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr1017635 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00189953 1970071 1970533 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
463

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_1970534..1971181   648 III: 1970534-1971181 Caenorhabditis elegans