WormMine: Gene WBGene00050891

• WormBase Gene ID: WBGene00050891
• Gene Name: C08E8.9
• Sequence Name: C08E8.9
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in ASEL; ASER; PLM; and neurons based on RNA-seq and single-cell RNA-seq studies. Is affected by several genes including etr-1; hpl-2; and ogt-1 based on tiling array and RNA-seq studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 180

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00050891

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C08E8.9.1	C08E8.9.1	180	V: 18364858-18365037

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C08E8.9	C08E8.9	180	V: 18364858-18365037

0 RNAi Result

10 Allele

• gk963271
• gk963489
• gk963304
• gk963809
• gk963637
• gk962704
• gk963970
• gk963971
• WBVar01596898
• ttTi1725

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00050891
• Start: 18364858
• End: 18365037
• Strand: 1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_18365038..18367138
• Length (nt): 2101
• Chromosome Location: V: 18365038-18367138
• Organism: Caenorhabditis elegans

10 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
	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 that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in PLM neuron cells comparing to in whole animal, according to dissected single neuron RNASeq analysis.	Fold change >= 4.	WBPaper00050344:PLM-neuron_enriched
	Transcripts down regulated in hpl-2(tm1489) L3 larva comparing to N2 in tiling array analysis.	Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction.	WBPaper00040560:hpl-2_L3_upregulated
	Transcripts that showed significantly increased expression in ASER neuron cells comparing to in whole animal, according to dissected single neuron RNASeq analysis.	Fold change >= 4.	WBPaper00050344:ASER-neuron_enriched
	Single-cell RNA-Seq cell group 35_4 expressed in neuron.	scVI 0.6.0	WBPaper00065841:35_4
	Transcripts enriched in ASER according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASER_enriched
	Transcripts enriched in ASEL according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASEL_enriched

2 Expression Patterns

• Primary Identifier: Expr2000610
• Pattern: 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).

• Primary Identifier: Expr1144176
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00050891
• Start: 18364858
• End: 18365037
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 180

1 Sequence Ontology Term