WormMine: Gene WBGene00001177

• WormBase Gene ID: WBGene00001177
• Gene Name: egl-8
• Sequence Name: B0348.4
• Brief Description: egl-8 encodes a phospholipase C beta; egl-8 activity is required for pharyngeal pumping, defecation, activity levels, and innate immunity; egl-8 is genetically downstream of egl-30 with respect to aldicarb-induced paralysis, and is expressed in most or all neurons, with the strongest staining in the head and tail ganglia, and in the intestine.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable phosphatidylinositol phospholipase C activity. Involved in several processes, including G protein-coupled dopamine receptor signaling pathway; positive regulation of acetylcholine secretion, neurotransmission; and taxis. Located in plasma membrane. Expressed in intestine; nervous system; non-striated muscle; and vas deferens. Used to study nicotine dependence. Is an ortholog of human PLCB4 (phospholipase C beta 4).
• Biotype: SO:0001217
• Genetic Position: V :-20.0209 ±0.010072
• Length (nt): 22887

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001177

Genomics

25 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:B0348.4h.1	B0348.4h.1	4693	V: 20818-43696
Transcript:B0348.4c.1	B0348.4c.1	2249	V: 20819-30723
Transcript:B0348.4q.1	B0348.4q.1	4874	V: 20819-43680
Transcript:B0348.4l.1	B0348.4l.1	4503	V: 20819-43687
Transcript:B0348.4j.1	B0348.4j.1	4750	V: 20819-43691
Transcript:B0348.4m.1	B0348.4m.1	4471	V: 20819-43691
Transcript:B0348.4i.1	B0348.4i.1	4655	V: 20819-43695
Transcript:B0348.4g.1	B0348.4g.1	4907	V: 20819-43704
Transcript:B0348.4k.1	B0348.4k.1	4717	V: 20821-43696
Transcript:B0348.4o.1	B0348.4o.1	5122	V: 20823-43689
Transcript:B0348.4v.1	B0348.4v.1	4541	V: 20825-43572
Transcript:B0348.4f.1	B0348.4f.1	4928	V: 20825-43695
Transcript:B0348.4b.1	B0348.4b.1	5005	V: 20825-43697
Transcript:B0348.4a.1	B0348.4a.1	4973	V: 20825-43701
Transcript:B0348.4s.1	B0348.4s.1	4664	V: 20837-43563
Transcript:B0348.4u.1	B0348.4u.1	4546	V: 20844-43695
Transcript:B0348.4n.1	B0348.4n.1	4590	V: 20872-43170
Transcript:B0348.4p.1	B0348.4p.1	4212	V: 21007-43170
Transcript:B0348.4r.1	B0348.4r.1	4137	V: 21007-43170
Transcript:B0348.4t.1	B0348.4t.1	3894	V: 21007-43170
Transcript:B0348.4w.1	B0348.4w.1	3921	V: 21007-43170
Transcript:B0348.4x.1	B0348.4x.1	3714	V: 21007-43170
Transcript:B0348.4y.1	B0348.4y.1	3678	V: 21007-43170
Transcript:B0348.4e.1	B0348.4e.1	5016	V: 21007-43683
Transcript:B0348.4d.1	B0348.4d.1	5056	V: 21007-43687

Other

25 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:B0348.4b	B0348.4b	4296	V: 21007-21090
CDS:B0348.4f	B0348.4f	4221	V: 21007-21090
CDS:B0348.4h	B0348.4h	3978	V: 21007-21090
CDS:B0348.4j	B0348.4j	4041	V: 21007-21090
CDS:B0348.4k	B0348.4k	4005	V: 21007-21090
CDS:B0348.4m	B0348.4m	3762	V: 21007-21090
CDS:B0348.4n	B0348.4n	4455	V: 21007-21090
CDS:B0348.4u	B0348.4u	3858	V: 21007-21090
CDS:B0348.4v	B0348.4v	3957	V: 21007-21090
CDS:B0348.4r	B0348.4r	4137	V: 21007-21090
CDS:B0348.4t	B0348.4t	3894	V: 21007-21090
CDS:B0348.4x	B0348.4x	3714	V: 21007-21090
CDS:B0348.4e	B0348.4e	4503	V: 21007-21090
CDS:B0348.4d	B0348.4d	4539	V: 21007-21090
CDS:B0348.4a	B0348.4a	4260	V: 21007-21090
CDS:B0348.4c	B0348.4c	1779	V: 21007-21090
CDS:B0348.4g	B0348.4g	4185	V: 21007-21090
CDS:B0348.4i	B0348.4i	3942	V: 21007-21090
CDS:B0348.4l	B0348.4l	3798	V: 21007-21090
CDS:B0348.4o	B0348.4o	4419	V: 21007-21090
CDS:B0348.4p	B0348.4p	4212	V: 21007-21090
CDS:B0348.4q	B0348.4q	4176	V: 21007-21090
CDS:B0348.4s	B0348.4s	4101	V: 21007-21090
CDS:B0348.4w	B0348.4w	3921	V: 21007-21090
CDS:B0348.4y	B0348.4y	3678	V: 21007-21090

66 RNAi Result

• WBRNAi00095471
• WBRNAi00061092
• WBRNAi00089835
• WBRNAi00038958
• WBRNAi00038959
• WBRNAi00061095
• WBRNAi00064662
• WBRNAi00078898
• WBRNAi00080607
• WBRNAi00095155
• WBRNAi00095164
• WBRNAi00024384
• WBRNAi00008298
• WBRNAi00008299
• WBRNAi00095153
• WBRNAi00060282
• WBRNAi00060283
• WBRNAi00060284
• WBRNAi00060285
• WBRNAi00060287
• WBRNAi00060288
• WBRNAi00060289
• WBRNAi00060286
• WBRNAi00060290
• WBRNAi00063869
• WBRNAi00063876
• WBRNAi00061094
• WBRNAi00061093
• WBRNAi00095178
• WBRNAi00095180

439 Allele

• gk963889
• WBVar02122967
• gk962853
• sa47
• sa32
• WBVar00242818
• WBVar00242819
• WBVar00242817
• WBVar00242820
• WBVar01970379
• WBVar01970378
• WBVar01970377
• WBVar01970376
• WBVar01970382
• WBVar01970381
• WBVar01970380
• WBVar01970385
• WBVar01970384
• WBVar01970383
• tm774
• WBVar01609519
• WBVar01609517
• WBVar01609518
• WBVar01609520
• gk429197
• WBVar01772439
• WBVar01516452
• WBVar01772440
• WBVar02022821
• WBVar02022822

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001177
• Start: 20818
• End: 43704
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_43705..45309
• Length (nt): 1605
• Chromosome Location: V: 43705-45309
• Organism: Caenorhabditis elegans

162 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:all-neurons_L1-larva_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	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 glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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 GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	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

8 Expression Patterns

• Primary Identifier: Expr1030753
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1199
• Remark: The absence of this staining in egl-8 (md1971) and egl-8 (n488) demonstrates its specificity. The lines of EGL-8 staining colocalize with the staining of MH27, a monoclonal antibody that stains epithelial and intestinal adherens junctions. MH27 staining also extended part of the way around each of the loops of EGL-8 staining, which may represent sites where the ends of the intestinal cells join together.
• Pattern: In wild-type worms, EGL-8 staining primarily in the nervous system and the intestine. EGL-8 staining observed in most or all neurons, although the amount of staining varied between individual neurons. In general, neurons in the head and tail ganglia showed stronger staining than the motor neurons of the ventral cord. In the head ganglia, one pair of amphid neurons showed especially strong staining. Staining was not detected in the sublateral processes or in the dorsal cord. EGL-8's intestinal staining was restricted to two lines of staining running down the long axis of the body and to pairs of loop-like structures at regular intervals. The strongest staining was in the posterior region of the intestine. Confocal microscopy determined that the two lines of staining are on the luminal (apical) side of the intestinal cells.
• Subcellular Localization: Within neurons, EGL-8 stained in both cell somas and in processes.

• Primary Identifier: Expr1201
• Pattern: Expressed in the ventral cord motor neurons, as well as in many other neurons. In addition, the egl-8 PLC GFP construct was also expressed in the posterior region of the intestine.

• Primary Identifier: Expr12670
• Pattern: egl-8 is expressed in the vas deferens, spicule protractor muscles, diagonal muscles and a male-specific neuron that is probably CP8 or CP9 and is also widely expressed in the nervous system, as expected from previous work (Lackner et al., 1999; Miller et al., 1999).

• Primary Identifier: Expr2011230
• 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: Expr1023374
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029466
• 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: Expr1143135
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

38 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001177
• Start: 20818
• End: 43704
• Strand: 1

38 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 22887

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00022014
• WBStrain00022776
• WBStrain00026788
• WBStrain00031721
• WBStrain00033391
• WBStrain00004701

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_13370..20817
• Length (nt): 7448
• Chromosome Location: V: 13370-20817
• Organism: Caenorhabditis elegans