WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00014404 Gene Name  F56H6.15
Sequence Name  ? F56H6.15 Organism  Caenorhabditis elegans
Automated Description  Is affected by prg-1; sftb-1; and etr-1 based on RNA-seq studies. Is affected by glycine based on RNA-seq studies. Biotype  SO:0001268
Genetic Position  Length (nt)  ? 187
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00014404

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F56H6.15 F56H6.15 187   I: 12288221-12288407
 

Other

0 CDSs

2 RNAi Result

WormBase ID
WBRNAi00003829
WBRNAi00032989

9 Allele

Public Name
gk962706
gk963849
gk962859
gk964175
gk963095
gk964202
gk964201
WBVar01287125
gk675095

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00014404 12288221 12288407 -1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

0 Downstream Intergenic Region

5 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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
  Transcripts of noncoding genes that showed significantly increased 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_enriched_noncoding-RNA
  Transcripts that showed significantly increased expression in strain CER276 sftb1(cer39[Q552P, R643C,K718E]) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2 WBPaper00058725:sftb-1(cer39)_upregulated
  Protein coding genes with decreased expression in prg-1(wm161) comparing to in N2. Cuffdiff and DEGseq were used to calculate the differential expression of protein-coding genes with and without the prg-1 mutation, and authors selected genes which had more than two-fold difference in expression (P < 0.05, q < 0.01 of Storey) from DEGseq outcomes. The intersection of genes which authors selected from DEGseq outcomes and genes which had more than two-fold difference in expression (P < 0.05) from Cuffdiff outcomes was defined as differentially expressed genes. WBPaper00045316:prg-1_downregulated_L4
  Transcripts that showed significantly increased 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_upregulated

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00014404 12288221 12288407 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
187

1 Sequence Ontology Term