WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00006101 Gene Name  str-35
Sequence Name  ? T08H10.2 Organism  Caenorhabditis elegans
Automated Description  Is affected by clk-1 and sir-2.1 based on microarray studies. Is predicted to encode a protein with the following domains: 7TM GPCR, serpentine receptor class r (Str) and Serpentine type 7TM GPCR chemoreceptor Str. Biotype  SO:0001217
Genetic Position  V :-5.25236 ±0.029499 Length (nt)  ? 2154
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00006101

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T08H10.2.1 T08H10.2.1 1029   V: 4474843-4476996
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:T08H10.2 T08H10.2 1029   V: 4474843-4475201

2 RNAi Result

WormBase ID
WBRNAi00018474
WBRNAi00018477

23 Allele

Public Name
gk963301
gk963591
gk963553
gk964259
gk964351
gk963850
gk392442
gk887833
WBVar01650457
WBVar02124233
WBVar02122026
WBVar02121040
WBVar02121041
WBVar02122652
WBVar01677816
WBVar01677815
WBVar01677817
WBVar02004922
WBVar00585291
ttTi24504
WBVar01819389
gk232991
gk232992

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00006101 4474843 4476996 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_chrV_4476997..4477560   564 V: 4476997-4477560 Caenorhabditis elegans

8 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. N.A. WBPaper00026929:sir-2.1_overexpression_regulated
  Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. WBPaper00045774:clk-1_downregulated
  Genome-wide analysis of developmental and sex-regulated gene expression profile. self-organizing map cgc4489_group_9
  Genes that showed significantly changed expression during aging (ANOVA, p < 0.0001) ANOVA, p < 0.0001. WBPaper00032062:age_regulated_genes
Bacteria infection: Burkholderia pseudomallei BpR15 Genes that showed decreased expression in adult animals after 12 hour exposure to B. pseudomallei R15 vs. exposure to OP50 After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives. WBPaper00044091:Bpseudomallei_repressed_12h
  hermaphrodite soma-enriched Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. [cgc6390]:herm_soma-enriched
Bacteria infection: Burkholderia pseudomallei BpR15 Genes that showed decreased expression in adult animals after 4 hour exposure to B. pseudomallei R15 vs. exposure to OP50 After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives. WBPaper00044091:Bpseudomallei_repressed_4h
Bacteria infection: Burkholderia pseudomallei BpR15 Genes that showed decreased expression in adult animals after 8 hour exposure to B. pseudomallei R15 vs. exposure to OP50 After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives. WBPaper00044091:Bpseudomallei_repressed_8h

1 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2035198 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00006101 4474843 4476996 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
2154

1 Sequence Ontology Term