WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00044802 Gene Name  ZC262.10
Sequence Name  ? ZC262.10 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including swsn-1; swsn-9; and etr-1 based on RNA-seq and microarray studies. Is affected by methylmercury hydroxide based on RNA-seq studies. Is predicted to encode a protein with the following domains: Tight junction protein, Claudin-like and Tight junction protein, claudin-like. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1128
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00044802

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:ZC262.10.1 ZC262.10.1 528   III: 8345699-8346826
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:ZC262.10 ZC262.10 528   III: 8345699-8345963

0 RNAi Result

21 Allele

Public Name
gk964518
gk963887
WBVar02121414
gk964133
gk962890
WBVar02121003
WBVar02120685
gk963858
gk962809
WBVar02121874
WBVar02123059
WBVar02124407
WBVar02123384
WBVar02121595
WBVar02123228
WBVar02123998
WBVar02124959
WBVar02122943
f122
gk963922
WBVar02122819

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00044802 8345699 8346826 -1

3 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIII_8344337..8345698   1362 III: 8344337-8345698 Caenorhabditis elegans

32 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts of coding genes that showed significantly decreased 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_depleted_coding-RNA
  Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. DESeq2, fold change > 2, p-value < 0.05. WBPaper00061753:csr-1(tor159)_upregulated_25C
  Transcripts that showed significantly increased expression in rsks-1(ok1255) animals after 4 hours of feeding of starvation-induced arrested L1, comparing to N2 animals that went through the same treatment. DESeq2, FDR < 0.05, fold change > 2. WBPaper00067518:rsks-1(ok1255)_upregulated
  Transcripts that showed significantly decreased expression in pals-22(jy3) comparing to in N2 animals. limma-voom, fold change > 2, FDR < 0.05 WBPaper00064532:pals-22(jy3)_downregulated
  Transcripts that showed significantly decreased expression in bcf-1(ylf1) comparing to in N2 adult animals. DESeq2 WBPaper00064933:bcf-1(ylf1)_downregulated_transcript
Bacteria infection: N.ausubeli Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage. FDR < 0.01 WBPaper00065086:JU1400_N.ausubeli_regulated
heat shock: 33C 30min Transcripts that showed significantly decreased expression in hsf-1(RNAi) animals, after heat shock at 33 C for 30min, comparing to in hsf-1(RNAi) animals without heat shock. Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value). WBPaper00049942:HeatShock_downregulated_hsf-1(RNAi)
  Transcripts that showed significantly increased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms. DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) WBPaper00060764:swsn-1(os22ts)_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
  Transcripts that showed significantly increased expression in nhl-2(ok818) comparing to in N2 at 25C. EdgeR, FDR < 0.05, fold change < 0.5. WBPaper00055971:nhl-2(ok818)_25C_downregulated
  Transcripts that showed significantly increased expression in raga-1(ok386) animals after 4 hours of feeding of starvation-induced arrested L1, comparing to N2 animals that went through the same treatment. DESeq2, FDR < 0.05, fold change > 2. WBPaper00067518:raga-1(ok386)_upegulated
  Transcripts that showed significantly decreased expression in flcn-1(ok975) comparing to in N2. Student's t-test. WBPaper00056471:flcn-1(ok975)_downregulated
  Transcripts that showed significantly increased expression in pals-25(icb98) comparing to in N2 animals. limma-voom, fold change > 2, FDR < 0.05 WBPaper00064532:pals-25(icb98)_upregulated
  Transcripts that showed significantly increased expression in sdc-3(ubs20) comparing to in control animals. DESeq2 v.1.34, fold change > 2, FDR < 0.05. WBPaper00067078:sdc-3(ubs20)_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
  Transcripts that showed significantly decreased expression in him-17(me24) comparing to in N2 animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00064769:him-17(me24)_downregulated
postdauer (pheromone) Transcripts that showed significantly decreased expression in ADL neurons FACS-isolated from postdauer (pheromone) one-day old adults of N2 animals, comparing to ADL nuerons isolated from control N2 animals. Data analysis was performed on the CLC Genomics Workbench (Qiagen) with differential expression assessed using EdgeR. WBPaper00067348:Post-dauer_downregulated_N2_ADL
  Transcripts that showed significantly increased 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)_upregulated
  Transcripts that showed significantly increased expression in nhl-2(ok818) comparing to in N2 at 20C. EdgeR, FDR < 0.05, fold change < 0.5. WBPaper00055971:nhl-2(ok818)_20C_downregulated
  Transcripts that showed significantly decreased expression in Day 8 adults comparing to in Day 1 adults in neuron cells. t-test, fold change > 2, p-value < 0.01. WBPaper00062590:Aging_downregulated_neuron
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 significantly decreased expression in nhr-8(hd117) comparing to in N2. Differentially expressed genes were identified using Sleuth (version 0.30.0). WBPaper00062446:nhr-8(hd117)_downregulated
Bacteria infection: N.ferruginous Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ferruginous microsporidia spores for 72 hours at 21C starting from L1 larva stage. FDR < 0.01 WBPaper00065086:JU1400_N.ferruginous_regulated
heat-killed OP50 Transcripts that showed significantly decreased 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_downregulated
postdauer (pheromone) Transcripts that showed significantly decreased expression in ADL neurons FACS-isolated from postdauer (pheromone) one-day old adults of nrde-3(gg66) animals, comparing to ADL nuerons isolated from control nrde-3(gg66) animals. Data analysis was performed on the CLC Genomics Workbench (Qiagen) with differential expression assessed using EdgeR. WBPaper00067348:Post-dauer_downregulated_nrde-3(gg66)_ADL
  Transcripts that showed significantly decreased expression in RA629 swsn-9(ok1354);rdIs49[Cb-unc-119] comparing to in RA577 swsn-9(ok1354); rdIs52 [Pric-19::swsn-9::gfp; Cb-unc-119] (swsn-9 neuronal rescue) animals at young adult worms. DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) WBPaper00060764:swsn-9(ok1354)_downregulated
  Genes with expression level down regulated after treatment with Methylmercury (MeHg) by RNAseq analysis. Differential gene expression analysis was performed using Cuffdiff program of Cufflinks 1.3.0 for 44968 predicted transcripts. Transcripts with false discovery rate-corrected p-values (q-values) of < 0.05 and fold change > 2 (or < 0.5) were defined as differentially expressed. WBPaper00043945:MeHg_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)
Bacteria infection: N.ferruginous Transcripts that showed significantly altered expression in C. elegans wild isolate strain N2 infected by N.ferruginous microsporidia spores for 72 hours at 21C starting from L1 larva stage. FDR < 0.01 WBPaper00065086:N2_N.ferruginous_regulated
  Transcripts that showed significantly decreased expression in dpy-26(ubs4) comparing to in control animals. DESeq2 v.1.34, fold change > 2, FDR < 0.05. WBPaper00067078:dpy-26(ubs4)_downregulated

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1162250 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr1020016 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  

1 GO Annotation

Annotation Extension Qualifier
  located_in

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00044802 8345699 8346826 -1

1 Ontology Annotations

Annotation Extension Qualifier
  located_in

0 Regulates Expr Cluster

1 Sequence

Length
1128

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_8346827..8347187   361 III: 8346827-8347187 Caenorhabditis elegans