WormMine: Gene WBGene00001188

• WormBase Gene ID: WBGene00001188
• Gene Name: egl-20
• Sequence Name: W08D2.1
• Organism: Caenorhabditis elegans
• Automated Description: Enables receptor tyrosine kinase binding activity. Involved in several processes, including left/right axis specification; neuron migration; and regulation of locomotion. Located in extracellular space. Expressed in several structures, including body wall muscle cell from C lineage; intestinal muscle; neuroblasts; rectal epithelial cell; and somatic nervous system. Is an ortholog of human WNT16 (Wnt family member 16).
• Biotype: SO:0001217
• Genetic Position: IV :4.42274 ±0.000639
• Length (nt): 3176

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001188

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W08D2.1.3	W08D2.1.3	1925	IV: 9812357-9815532
Transcript:W08D2.1.1	W08D2.1.1	1873	IV: 9812418-9815526
Transcript:W08D2.1.2	W08D2.1.2	1950	IV: 9812420-9815526

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W08D2.1	W08D2.1	1182	IV: 9813183-9813278

24 RNAi Result

• WBRNAi00009266
• WBRNAi00089852
• WBRNAi00101394
• WBRNAi00054972
• WBRNAi00097716
• WBRNAi00091575
• WBRNAi00027854
• WBRNAi00101702
• WBRNAi00065340
• WBRNAi00098910
• WBRNAi00070194
• WBRNAi00101560
• WBRNAi00101562
• WBRNAi00101561
• WBRNAi00101342
• WBRNAi00024206
• WBRNAi00101445
• WBRNAi00089925
• WBRNAi00090085
• WBRNAi00090243
• WBRNAi00101486
• WBRNAi00101691
• WBRNAi00101686
• WBRNAi00101696

65 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963883
• gk963884
• gk964226
• gk964227
• WBVar02058532
• hu105
• hu120
• n585
• gk672556
• gk209641
• gk681681
• gk209642
• lq42
• gk769169
• gk209639
• lq74
• gk639374
• gk209640
• ju105
• gk887265
• gk636278
• gk833458
• gk626087
• WBVar01730483
• gk393728
• gk911850

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001188
• Start: 9812357
• End: 9815532
• 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_chrIV_9810734..9812356
• Length (nt): 1623
• Chromosome Location: IV: 9810734-9812356
• Organism: Caenorhabditis elegans

143 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_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
	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:bodywall-muscle_L1-larva_expressed
	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 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
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	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 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 that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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
	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 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
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:PVD-OLL-neurons_L3-L4-larva_expressed
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	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 npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated

19 Expression Patterns

• Primary Identifier: Expr1030760
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr989
• Remark: See also WBPaper00045644.
• Pattern: At hatching and during the time of Q cell migration, egl-20::gfp was expressed exclusively within a group of epidermal and muscle cells located in the posterior of the animal near the anus. These cells are equi-distant from either Q cell at hatching and are symmetrically distributed on the left and right sides of the animal. Both the level and the distribution of EGL-20::GFP are similar on the left and right sides of the animal.

• Primary Identifier: Expr7985
• Remark: Picture: Figure 2, Figure S2.
• Pattern: Expression of egl-20 was observed in late embryos and continued throughout larval development. As previously reported, egl-20 was expressed in a group of epidermal and muscle cells in the posterior of the animal near the anus. Expression of egl-20 persisted in these cells throughout larval life. During the L4 stage, expression of egl-20 was observed in the P6.p descendants.

• Primary Identifier: Expr3846
• Pattern: Larvae containing this transgene express GFP in a group of epidermal and muscle cells in the posterior near the anus. In embryos bearing this transgene, GFP fluorescence could not be detected the time when the HSNs migrate. muIs49 embryos were stained with an anti-GFP antiserum and these embryos expressed GFP in several cells of the developing tail beginning just before the comma stage and continuing throughout embryogenesis and larval development. To reveal the relationship between migrating HSNs and EGL-20-expressing cells, embryos carrying both muIs49 and muIs13 (Pegl-5::lacZ) transgenes were stained with antisera against GFP and LacZ. The Hox gene egl-5 is expressed in HSNs and a few cells in the tail. It was observed that the HSNs migrated away from the EGL-20 source.

• Primary Identifier: Expr3848
• Remark: No detailed description on expression patterns in adult stage.
• Pattern: The integrated array muIs49 contained a genomic egl-20 fragment with GFP fused in frame to sequences encoding the C terminus of EGL-20; larvae containing this transgene express GFP in a group of epidermal and muscle cells in the posterior near the anus. In embryos bearing this transgene, GFP fluorescence could not be detected the time when the HSNs migrate. muIs49 embryos were stained with an anti-GFP antiserum and these embryos expressed GFP in several cells of the developing tail beginning just before the comma stage and continuing throughout embryogenesis and larval development.

• Primary Identifier: Expr7882
• Remark: Picture: Figure S3.
• Pattern: Expressed in the B, F, K, and U hypodermal cells, also anal depressor muscle.

• Primary Identifier: Expr9343
• Pattern: egl-20 was mostly localized to the posterior half of L1 larvae, in a pattern that was already present at the comma stage of embryonic development. egl-20 was expressed in the rectal epithelial cells K, F, U and B, in the anal depressor muscle and in P11/12, which is in agreement with previous reporter studies (Whangbo and Kenyon, 1999). However, it was found that in L1 larvae, egl-20 was also expressed in the posterior ventral body wall muscle quadrants VL23 and VR24 and the rectal epithelial cell Y.

• Primary Identifier: Expr11176
• Pattern: Expression of egl-20 is high throughout the entire life span of the worm and increases during aging. As in development, egl-20 expression was observed only in the posterior of the animal. The egl-20/Wnt is expressed in the anal depressor muscle and in the postembryonic rectal epithelial cells (B, F, K, and U) during aging. These cells also express egl- 20/Wnt during larval development (Gleason et al. 2006). However, the authors did not observe any expression in hypodermal or muscle cells, as previously reported.

• Primary Identifier: Expr14755
• Pattern: In early larvae, this reporter was expressed in a cluster of posterior cells including rectal epithelial cells, the overlying dorsal and ventral body wall muscles, the stomatointestinal muscles, the anal depressor muscle, and P11/12, along with weak expression in several head neurons, which is largely consistent with smFISH data on egl-20 transcript localization (Harterink et al., 2011a) and previous transgenes (Whangbo and Kenyon, 1999). This reporter also labeled several posterior neurons and their projections along the ventral nerve cord that terminated in the nerve ring. Tagged Wnt protein clearly localized near reporter-labeled axons in the head.

• Primary Identifier: Expr14756
• Pattern: We first observed tagged Wnt/EGL-20 fluorescence in posterior cells in comma-stage embryos along with isolated punctae in more anterior regions and found that tagged Wnt spread from the posterior to the mid-body region of the embryo within 60 min . In early larvae, tagged Wnt/EGL-20 formed an anteroposterior gradient along approximately the posterior half of the worm with low levels of protein detectable along the entire body axis. Tagged Wnt localized most conspicuously to posterior cells near its source along with longitudinal body wall muscles, epithelial seam cells, neuroblasts, and ventral midline cells.

• Primary Identifier: Expr11634
• Pattern: Pegl-20::mCherry is mainly expressed in the tail during the embryonic and adult stages.

• Primary Identifier: Expr13837
• Pattern: The egl-20p::mCherry reporter showed the co-localization of the signal with the ventral nerve cord in the posterior region of C. elegans.

• Primary Identifier: Expr13838
• Pattern: The EGL-20::mCherry fusion protein formed aggregates along or co-localized with the ventral and dorsal nerve cord, indicating a potential function for Wnt/EGL-20 in neurons.

• Primary Identifier: Expr2011212
• 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: Expr1023425
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1158507
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr3930
• Remark: No GO_term assigned.
• Subcellular Localization: Immunostaining of animals expressing a functional EGL-20::proteinA fusion under the control of the egl-20 promoter revealed that EGL-20 forms an anteroposterior gradient. The gradient is mainly visible at early stages. EGL-20 shows a punctate staining.

• Primary Identifier: Expr2029448
• 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: Expr15698
• Pattern: Using transcriptional reporters of the five Wnt ligands [cis-regulatory elements of the Wnt ligands placed upstream of a nuclear GFP (Gleason et al., 2006)], we observed that three Wnt ligands (CWN-1, CWN-2 and MOM-2) are expressed in the embryo at the time of the terminal division of the SMDD/AIY mother cell. We could not detect expression of the two remaining Wnt ligands (LIN-44 and EGL-20) at that time but start seeing expression at later stages, during elongation, in the posterior end of the embryo. Interestingly, at the time of the terminal division of the SMDD/AIY mother cell, cwn-1, cwn-2 and mom-2 are transcribed at a higher level in the posterior region of the embryo than in the anterior region. These observations are consistent with an analysis of the transcription pattern of Wnt ligands by fluorescent in situ hybridization (Harterink et al., 2011). cwn-1, cwn-2 and mom-2 are transcribed in several tissues: cwn-1 (posterior muscle), cwn-2 ( posterior neuronal progenitors, posterior epidermis, intestine and posterior muscle) and mom-2 (posterior epidermis and muscle). Their zygotic expression starts during gastrulation and remains during embryonic elongation.

62 GO Annotation

3 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001188
• Start: 9812357
• End: 9815532
• Strand: -1

62 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3176

1 Sequence Ontology Term