WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00045162 Gene Name  F25H2.15
Sequence Name  ? F25H2.15 Organism  Caenorhabditis elegans
Automated Description  Enriched in germ line and sensory neurons based on RNA-seq studies. Is affected by several genes including etr-1; rsr-2; and prg-1 based on RNA-seq studies. Is affected by multi-walled carbon nanotube and bisphenol A based on RNA-seq studies. Biotype  SO:0001267
Genetic Position  :± Length (nt)  ? 178
Paste the following link
Quick Links:
SummaryGenomicsOther
 
Quick Links:
SummaryGenomicsOther
 
Lists
This Gene isn't in any lists. Upload a list.

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00045162

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F25H2.15 F25H2.15 178   I: 10565266-10565443
 

Other

0 CDSs

1 RNAi Result

WormBase ID
WBRNAi00003867

7 Allele

Public Name
gk962858
gk962706
gk963902
gk963849
gk847567
gk120921
gk532599

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00045162 10565266 10565443 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_chrI_10565444..10566349   906 I: 10565444-10566349 Caenorhabditis elegans

29 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes. DESeq2, FDR < 0.05, fold change > 2. WBPaper00065975:P-body_vs_oocyte_depleted
  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 hpl-2(tm1489) comparing to in N2 animals. DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. WBPaper00054493:hpl-2(tm1489)_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
Bacteria: B.thuringiensis Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. Cuffdiff WBPaper00060358:B.thuringiensis_pathogen_regulated_N2
  Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. WBPaper00060014:set-2(tm1630)_upregulated
  Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage. DESeq2, fold change > 2 WBPaper00058725:sftb-1(cer6)_upregulated
  Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector. Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples. WBPaper00051039:germline_enriched
  Transcripts that showed significantly increased expression in ints-1(RNAi) animals comparing to control RNAi animals, at late L3 larva stage. DESeq2, v1.12.0, fold change > 2, FDR < 0.05 WBPaper00057068:ints-4(RNAi)_upregulated
  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 interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing. DESeq2, fold change > 2,, p-value < 0.01 WBPaper00055334:DLC-1_interacting
  Transcripts that showed significantly increased expression in ints-4(RNAi) animals treated with 300uM CdCl2 from L1 to late L3 larva stage, comparing to control RNAi animals with the same Cadmium treatment. DESeq2, v1.12.0, fold change > 2, FDR < 0.05 WBPaper00057068:ints-4(RNAi)_upregulated_Cadmium
  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
  Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. WBPaper00049377:MWCNT_downregulated
  Transcripts that showed significantly decreased expression after 24 hours of induction of human beta Amyloid at young adult stage A 2-fold change in expression level and a false discovery rate analog of p < 0.05. WBPaper00064130:Beta-Amyloid_24h_downregulated_mRNA
  Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. Fold change > 2, p-value < 0.05. WBPaper00060661:sensory-neuron_enriched
  Targets of endo-siRNA that showed significantly increased expression in BFF40[meg-3(tm4259);meg-4(ax2026);mex-5::gfp::h2b::tbb-2] comparing to in SX1263[Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)] dissected gonad isolated from 1-day old adult hermaphrodites. DESeq2, fold change > 2, FDR < 0.01 WBPaper00057140:meg-3(tm4259)_meg-4(ax2026)_upregulated
  Transcripts that showed significantly increased expression after exposure to 500uM BPA (Bisphenol A), comparing to 0.1% ethanol control group. Cuffdiff was used to compare the aligned reads between the BPA- or BPS-treated group and the control ethanol group to identify genes and gene transcripts that were differentially expressed. Multiple hypothesis testing was corrected using the q value method to estimate false discovery rate (FDR). Genes and transcripts showing differential expression or alternative splicing at P < 0.05 were selected. WBPaper00049954:BPA_upregulated
  Transcripts of noncoding genes that showed significantly increased expression in muscle. DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. WBPaper00062325:muscle_enriched_noncoding-RNA
  Transcripts that showed significantly increased expression in strain CER276 sftb1(cer39[Q552P, R643C,K718E]) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2 WBPaper00058725:sftb-1(cer39)_upregulated
  Protein coding genes with decreased expression in prg-1(wm161) comparing to in N2. Cuffdiff and DEGseq were used to calculate the differential expression of protein-coding genes with and without the prg-1 mutation, and authors selected genes which had more than two-fold difference in expression (P < 0.05, q < 0.01 of Storey) from DEGseq outcomes. The intersection of genes which authors selected from DEGseq outcomes and genes which had more than two-fold difference in expression (P < 0.05) from Cuffdiff outcomes was defined as differentially expressed genes. WBPaper00045316:prg-1_downregulated_L4
  Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2 DESeq2 WBPaper00057162:meg-3_meg-4_upregulated_sRNA
male mating Transcripts that showed significantly increased expression in sterile glp-1(e2144) animals after exposed to males during day 2 to day 7 adult stage. DESeq2 v.1.10.1, fold change > 2, FDR < 0.05. WBPaper00065315:mating_upregulated_Day2-7
  Protein coding genes with decreased expression in prg-1(wm161) comparing to in N2. Cuffdiff and DEGseq were used to calculate the differential expression of protein-coding genes with and without the prg-1 mutation, and authors selected genes which had more than two-fold difference in expression (P < 0.05, q < 0.01 of Storey) from DEGseq outcomes. The intersection of genes which authors selected from DEGseq outcomes and genes which had more than two-fold difference in expression (P < 0.05) from Cuffdiff outcomes was defined as differentially expressed genes. WBPaper00045316:prg-1_downregulated_L2
  Transcripts that showed significantly decreased expression in etr-1(lq61) comparing to in N2 animals at L1 larva stage. DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. WBPaper00062325:etr-1(lq61)_downregulated
  Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control, according to RNAseq analysis. This analysis uses Cufflinks-Cuffdiff to quantify and identify transcripts with a significant level of expression between different conditions. WBPaper00042477:rsr-2(RNAi)_upregulated_RNAseq
Transgenerational starvation Transcripts that showed significantly altered expression in starved F4 animals of P0 animals that went through early life starvation at L1 stage, and three fed generations, comparing to in starved animals with ancestors that were not starved. DESeq2 WBPaper00065199:Transgeneration-starvation_regulated_starved
  ncRNAs with significantly increased 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)_upregulated_UV
Bacteria: P. aeruginosa infected parents. Transcripts that showed significantly decreased expression in embryos from parents fed with P. aeruginosa PA14. DESeq2, Fold Change > 2 or < 0.5. WBPaper00059566:P.aeruginosa_downregulated

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00045162 10565266 10565443 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
178

1 Sequence Ontology Term