WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00271643 Gene Name  W07G1.25
Sequence Name  ? W07G1.25 Organism  Caenorhabditis elegans
Automated Description  Enriched in dorsal uterine cell; intestinal cell; and intestine based on single-cell RNA-seq studies. Is affected by several genes including cyd-1; stt-3; and etr-1 based on RNA-seq studies. Is affected by four chemicals including glycine; Cadmium Chloride; and Camptothecin based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  :± Length (nt)  ? 323
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00271643

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:W07G1.25 W07G1.25 323   II: 13945325-13945647
 

Other

0 CDSs

0 RNAi Result

25 Allele

Public Name
gk963801
gk963053
gk962684
WBVar02122794
WBVar02123754
WBVar02123372
WBVar02123669
gk489109
gk772888
gk831375
WBVar01606303
WBVar02075198
WBVar02121739
WBVar02123500
WBVar02122928
WBVar02120657
WBVar02120818
WBVar02123575
WBVar02122112
WBVar02120963
WBVar02121860
WBVar01318665
WBVar00011813
WBVar00231855
WBVar01895621

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00271643 13945325 13945647 -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_chrII_13944477..13945324   848 II: 13944477-13945324 Caenorhabditis elegans

39 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 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_upregulated_mRNA
  Transcripts that showed significantly increased expression in exos-8(RNAi) animals. fold change > 2, FDR < 0.05 WBPaper00068292:exos-8(RNAi)_upregulated
  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 endu-2(tm4977) comparing to in N2 animals at young adult stage. 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:endu-2(tm4977)_upregulated
  Single-cell RNA-Seq cell group 3_4 expressed in intestine. scVI 0.6.0 WBPaper00065841:3_4
  Transcripts that showed significantly decreased expression after animals grew in 500 uM glycine from hatch till 1-day post L4 adult, comparing to untreated animals. Differential expression was assessed using a nempirical Bayes moderated t-test within limmas linear model framework including the precision weights estimated by voom.Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Curator applied threshold: fold change > 2, adjusted p-value < 0.01. WBPaper00056330:glycine_downregulated
  Transcripts that showed significantly increased expression in DLS357 [ceh-60(ok1485)] comparing to in N2 at day 1 adults. DESeq2, fold change > 2, FDR < 0.01. WBPaper00056550:ceh-60(ok1485)_upregulated_AdultDay1
  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
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 decreased 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_downregulated_glp-1(e2141)
  Transcripts that showed significantly decreased 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_downregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly decreased 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_downregulated_fem-3(q20)
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS, comparing to control animals exposed to OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:HYS_vs_OP50_upregulated
  Transcripts that showed significantly increased expression in gonad cyd-1(RNAi) animals in daf-2(e1370) at late L4 stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067493:gonad-cyd-1(RNAi)_upregulated_daf-2(e1370)
  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
  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
  Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP), comparing to in N2 animals. edgeR p-value < 0.01 and fold change > 4. WBPaper00061613:human-amyloid-beta_upregulated
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)
  Transcripts that showed significantly increased expression in pals-22(jy3) comparing to in N2 animals. limma-voom, fold change > 2, FDR < 0.05 WBPaper00064532:pals-22(jy3)_upregulated
  Transcripts that showed significantly increased expression in N2 animals exposed to 30 uM CdCl2 for five days starting from L4. edgeR, fold change > 2, p < 0.05. WBPaper00066204:CdCl2_upregulated_mRNA
  Transcripts that showed significantly increased expression in N2 day 15 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day15_vs_Day1_upregulated_Illumina
  Transcripts that showed significantly increased expression in animals exposed to Camptothecin for 3 hours at 2C. p < 0.01, logFC > 1 or p < 0.01, logFC < -1. WBPaper00066610:Camptothecin_upregulated_2C_3h
  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
Diet: supplemented with milk fat-containing protein powder from L1 to day 2 adult stage. Transcripts that showed significantly decreased expression in N2 animals fed with OP50 supplemented with milk fat-containing protein powder from L1 to day 2 adult stage. Differential expression analysis between two conditions (three biological replicates per condition) was performed using DESeq2. Genes with p-value < 0.05 and Fold Change > 2 found by DESeq2 were assigned as differentially expressed. WBPaper00067530:Milk-protein_downregulated
  Transcripts that showed significantly increased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals. edgeR p-value < 0.01 and fold change > 4. WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_upregulated
  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
  Transcripts that showed significantly increased 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)_upregulated_WT
  Transcripts that showed significantly increased expression in hsf-1(RNAi) comparing to in ash-2 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)_upregulated_ash-2
  Transcripts that showed significantly increased expression in hsp-4(RNAi) comparing to N2 animals with control vector. edgeR (v3.19, Bioconductor), p < 0.05, log2FC > 1.5 or < -1.5 WBPaper00068266:hsp-4(RNAi)_upregulated_N2

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00271643 13945325 13945647 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
323

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_chrII_13945648..13946945   1298 II: 13945648-13946945 Caenorhabditis elegans