WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00284848 Gene Name  M02E1.4
Sequence Name  ? M02E1.4 Organism  Caenorhabditis elegans
Automated Description  Enriched in CP neuron and nerve ring neurons based on single-cell RNA-seq studies. Is affected by several genes including unc-25; inx-14; and tmc-1 based on RNA-seq studies. Is affected by leptomycin B based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  X:± Length (nt)  ? 1485
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00284848

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:M02E1.4.1 M02E1.4.1 487   X: 313274-314758
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:M02E1.4 M02E1.4 354   X: 313276-313346

0 RNAi Result

25 Allele

Public Name
gk963652
gk963725
WBVar01757038
WBVar00074210
gk522528
gk874962
gk553507
gk885113
gk522527
gk838426
gk678768
gk714975
gk467320
gk511362
gk432935
gk554410
gk707924
gk451602
gk950387
WBVar01617926
gk959727
WBVar01907821
gk268778
gk268779
WBVar02048361

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00284848 313274 314758 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_chrX_314759..322522   7764 X: 314759-322522 Caenorhabditis elegans

24 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
Bacteria: E.faecalis strain OG1RF Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. WBPaper00059754:E.faecalis_OG1RF_upregulated
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
  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 animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
  Transcripts that showed significantly decreased expression in strain GC1459 containing daf-18(ok480) comparing to control strain GC1171. edgeR, p-value < 0.05, fold change > 2. WBPaper00061699:daf-18(ok480)_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 day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_glp-1(e2141)
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. Transcripts that showed significantly increased expression in skpo-1(ok1640) animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. DESeq2, fold change > 2. WBPaper00061081:E.faecalis_upregulated_skpo-1(ok1640)
Acidic Environment: PH 4.33 vs. PH 6.33. Transcripts that showed significantly increased expression after 3 hours of exposure to acidic environment (PH 4.33), comparing to control animals exposed to PH 6.33 environment. DESeq2 (1.16.1). The Benjamini and Hochberg's approach was used to adjust the resulting P-values to control the false discovery rate. Corrected value of P < 0.05 and fold change > 2 were set as the threshold for significantly differential expression. WBPaper00060434:pH4.33_vs_pH6.33_uprgulated
  Transcripts that showed significantly increased expression in animals exposed to Leptomycin B for 3 hours at 2C. p < 0.01, logFC > 1 or p < 0.01, logFC < -1. WBPaper00066610:Leptomycin-B_upregulated_2C_3h
Fungi: Myzocytiopsis humicola extract Transcripts that showed significantly decreased expression in N2 L4 larva animals after 4 hours of exposure to oomycete Myzocytiopsis humicola extract. Differentially expressed genes as determined by Kallisto and Sleuth (pval < 0.01, qval < 0.1, fold change > 2). WBPaper00065995:M.humicola-extract_downregulated_N2
  Transcripts that showed significantly decreased expression in tmc-1(rg1003) comparing to in N2. DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs. WBPaper00065746:tmc-1(rg1003)_downregulated
  Transcripts that showed significantly decreased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_downregulated_neural
  Single-cell RNA-Seq cell group 32_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:32_0
  Single-cell RNA-Seq cell group 76_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:76_0
heat-killed OP50 Transcripts that showed significantly increased expression in N2 L1 animals fed with heat-killed OP50 for 4 hours comparing to those animals fed with OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067214:Heat-Killed-OP50_upregulated
  Single-cell RNA-Seq cell group 115_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:115_0
  Transcripts that showed significantly increased expression in vit-5(RNAi) comparing to in N2 animals injected with empty vector. DESeq R package (1.18.0), P < 0.05 and fold change > 2 WBPaper00064939:vit-5(RNAi)_upregulated
  Transcripts that showed significantly decreased expression in eat-2(ad1113) comparing to in N2. DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs. WBPaper00065746:eat-2(ad1113)_downregulated
Bacteria: C.neoformans strain H99 Transcripts that showed significantly increased expression after infection by C. neoformans H99. Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. WBPaper00059754:C.neoformans_H99_upregulated
  Transcripts that showed signicantly decreased expression in unc-25(e156) comparing to in N2 animals. DESeq R package (1.18.0), fold change > 2, FDR < 0.05. WBPaper00065734:unc-25(e156)_downregulated
Fungi: Myzocytiopsis humicola extract Transcripts that showed significantly decreased expression in old-1(ok1273) L4 larva animals after 4 hours of exposure to oomycete Myzocytiopsis humicola extract. Differentially expressed genes as determined by Kallisto and Sleuth (pval < 0.01, qval < 0.1, fold change > 2). WBPaper00065995:M.humicola-extract_downregulated_old-1(ok1273)

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00284848 313274 314758 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1485

1 Sequence Ontology Term