WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00005329 Gene Name  srh-110
Sequence Name  ? F08E10.4 Organism  Caenorhabditis elegans
Automated Description  Enriched in ASHL based on single-cell RNA-seq studies. Is affected by several genes including rrf-2; rrf-3; and mrps-5 based on microarray studies. Is affected by resveratrol and Sirolimus based on microarray studies. Biotype  SO:0000336
Genetic Position  V :12.9093 ±0.000242 Length (nt)  ? 1054
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00005329

Genomics

0 Transcripts

 

Other

0 CDSs

0 RNAi Result

120 Allele

Public Name
gk963271
gk963489
gk963304
gk963637
WBVar02123303
gk964050
gk963587
gk963588
WBVar02124497
WBVar02124059
WBVar02124270
WBVar02122864
WBVar02121796
WBVar02123142
WBVar02124430
WBVar02122255
gk962704
WBVar02122328
gk962630
WBVar02121298
WBVar02122699
WBVar02121656
WBVar02124636
WBVar02123716
gk962558
WBVar02124375
WBVar02079469
WBVar01692738
WBVar00091136
WBVar00091251

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00005329 17478333 17479386 -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_17478084..17478332   249 V: 17478084-17478332 Caenorhabditis elegans

9 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
  Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. N.A. WBPaper00026929:Resveratrol_regulated_daf-16
  Genes from eat-2(ad465) animals with significantly increased expression after 72 hours of treatment on growth media with 10uM rapamycin in 2% DMSO. Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes. WBPaper00048989:eat-2(ad465)_rapamycin_upregulated
  Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:daf-2(e1370)_downregulated
  Transcripts that showed significantly decreased expression in mrps-5(RNAi) comparing to in control animals. Fold change > 4, p-value < 0.01 WBPaper00056330:mrps-5(RNAi)_downregulated
  Coexpression clique No. 211, srj-42-srw-113, on the genome-wide coexpression clique map for the nematode GPL200 platform. All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. WBPaper00061527:srj-42-srw-113
  Genes predicted to be downregulated more than 2.0 fold in rrf-2(ok210) mutant worms as compared to wild-type animals (t-test P-value < 0.05). A t-test (5% confidence) was applied to the triplicate sample data for each transcript in each mutant to identify genes significantly elevated or decreased compared with the wild type. WBPaper00027111:rrf-2(ok210)_downregulated
  Genes predicted to be downregulated more than 2.0 fold in rrf-3(pk1426) mutant worms as compared to wild-type animals (t-test P-value < 0.05). A t-test (5% confidence) was applied to the triplicate sample data for each transcript in each mutant to identify genes significantly elevated or decreased compared with the wild type. WBPaper00027111:rrf-3(pk1426)_downregulated
  Single-cell RNA-Seq cell group 47_1 expressed in neuron. scVI 0.6.0 WBPaper00065841:47_1

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00005329 17478333 17479386 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1054

1 Sequence Ontology Term