WormMine

WS297

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219206 Gene Name  W05H12.4
Sequence Name  ? W05H12.4 Organism  Caenorhabditis elegans
Automated Description  Enriched in ABaraapapp; ABaraapppp; intestine; and neurons based on single-cell RNA-seq; RNA-seq; and microarray studies. Is affected by several genes including sin-3; sir-2.1; and egl-43 based on RNA-seq and microarray studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1255
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219206

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:W05H12.4.1 W05H12.4.1 1205   I: 13411660-13412914
Transcript:W05H12.4.2 W05H12.4.2 1146   I: 13411664-13412914
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:W05H12.4 W05H12.4 294   I: 13411900-13411959

7 RNAi Result

WormBase ID
WBRNAi00054839
WBRNAi00019628
WBRNAi00022464
WBRNAi00026497
WBRNAi00026499
WBRNAi00036309
WBRNAi00026498

25 Allele

Public Name
gk963849
gk964175
gk963138
WBVar02066595
gk127058
gk127059
gk127060
gk127061
gk127062
WBVar02120584
WBVar02122905
WBVar02121358
WBVar01352212
WBVar01704961
WBVar01352201
WBVar00542112
WBVar01890582
gk740554
WBVar01850630
WBVar01557075
gk732852
WBVar00160830
gk890469
gk458092
gk630940

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219206 13411660 13412914 1

2 Data Sets

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

0 Downstream Intergenic Region

26 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_upregulated_neural
  Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. DESEQ2, fold change > 2 and FDR < 0.01. WBPaper00062103:neuron_enriched
  Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:body-muscle_expressed
  Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:intestine_expressed
  Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:sin-3(tm1276)_upregulated
  Transcripts that showed signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. FDR < 0.05, fold change > 2 WBPaper00067368:pabp-2(RNAi)_upregulated_N2
  Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. DESeq2, fold change > 2, adjusted p-value < 0.01 WBPaper00058598:sin-3(tm1276)_downregulated
  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
  Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage. DESeq2, FDR < 0.05 WBPaper00058691:cfp-1(tm6369)_upregulated
  Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage. DESeq2, FDR < 0.05, fold change > 2. WBPaper00066978:daf-2(e1370)_upregulated_neuron
  Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage. DESeq2, FDR < 0.05, fold change > 2. WBPaper00066978:daf-16(mu86)_upregulated_neuron
  Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. DESeq2, FDR < 0.05, fold change > 2. WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
  Genes enriched in intestine. To identify genes that are significantly enriched by mRNA tagging, we first normalized the total amount of Cy3 and Cy5 signal to each other in each hybridization. We measured the ratio of the signals from the co-immunoprecipitated mRNA (Cy5) to total RNA in the cell extract (Cy3), and calculated the percentile rank for each gene relative to all genes in each hybridization. The mean percentile rank was determined from eight repeats of the mRNA-tagging experiment. Student's t-test was used to determine which genes showed a mean enrichment significantly greater than the median enrichment for all genes (P<0.001). WBPaper00026980:intestine_enriched
  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)
Feeding for 4 hours after L1 arrest. Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 N2 animals, comparing to animals continue to starve. DESeq2, FDR < 0.05, fold change > 2. WBPaper00067518:food_downregulated_N2
  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 increased expression in let-767(RNAi) L4 animals comparing to animals fed with empty vector. log2 fold change > 1.5 or < -1.5, p-value < 0.05 WBPaper00066679:let-767(RNAi)_upregulated
  Transcripts that interact with both BAZ-2 and SET-6 in Chip-Seq analysis. N.A. WBPaper00059356:BAZ-2_SET-6_interacting
  Transcripts that showed significantly increased expression in N2 day 10 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day10_vs_Day1_upregulated_Illumina
  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
  Genome-wide analysis of developmental and sex-regulated gene expression profile. self-organizing map cgc4489_group_5
  Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis. N.A. WBPaper00059471:EGL-43_interacting
  Top 300 transcripts enriched in ABaraapapp, ABaraapppp according to single cell RNAseq. Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. WBPaper00061340:Neuroblast_M2_M3
  Transcripts that showed significantly increased expression in bet-1(RNAi) animals comparing to in N2. DESeq2, p-value < 0.05 and fold change > 2. WBPaper00064735:bet-1(RNAi)_vs_N2_upregulated
  Transcripts that showed significantly increased expression in bet-1(uth41) animals comparing to in N2. DESeq2, p-value < 0.05 and fold change > 2. WBPaper00064735:bet-1(uth41)_vs_N2_upregulated
  Transcripts that showed significantly increased expression in bet-1B overexpression animals comparing to in N2. DESeq2, p-value < 0.05 and fold change > 2. WBPaper00064735:bet-1B(OE)_vs_N2_upregulated

4 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2025034 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).  
    Expr1158382 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2006809 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).  
    Expr1040517 Tiling arrays expression graphs  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00219206 13411660 13412914 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1255

1 Sequence Ontology Term