WormMine: Gene WBGene00001186

• WormBase Gene ID: WBGene00001186
• Gene Name: egl-18
• Sequence Name: F55A8.1
• Brief Description: egl-18 encodes a member of the GATA-family of transcription factors that affects cell migration, cell fate specification; expressed in the head, in hypodermal seam cells, VC neurons, and vulval precursor cells.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cell fate specification; membrane fusion; and nematode larval development. Located in nucleus. Expressed in several structures, including ABprpppppaa; body wall muscle cell from MS lineage; nervous system; seam cell; and vulva.
• Biotype: SO:0001217
• Genetic Position: IV :-13.3499 ±0.410094
• Length (nt): 15519

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001186

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F55A8.1a.2	F55A8.1a.2	1669	IV: 1902322-1917840
Transcript:F55A8.1b.1	F55A8.1b.1	1644	IV: 1913446-1917838
Transcript:F55A8.1a.1	F55A8.1a.1	1624	IV: 1913454-1917835

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F55A8.1a	F55A8.1a	1131	IV: 1913472-1913597
CDS:F55A8.1b	F55A8.1b	1140	IV: 1913472-1913597

97 RNAi Result

• WBRNAi00077981
• WBRNAi00077761
• WBRNAi00089855
• WBRNAi00067050
• WBRNAi00067802
• WBRNAi00067801
• WBRNAi00067856
• WBRNAi00064626
• WBRNAi00064708
• WBRNAi00064798
• WBRNAi00048442
• WBRNAi00025661
• WBRNAi00074439
• WBRNAi00074438
• WBRNAi00074440
• WBRNAi00077982
• WBRNAi00072533
• WBRNAi00074442
• WBRNAi00074444
• WBRNAi00068349
• WBRNAi00068351
• WBRNAi00068350
• WBRNAi00064824
• WBRNAi00068847
• WBRNAi00068849
• WBRNAi00068848
• WBRNAi00101989
• WBRNAi00101988
• WBRNAi00101990
• WBRNAi00077986

384 Allele

• gk963722
• WBVar00569317
• WBVar00569319
• WBVar00569320
• WBVar00569321
• WBVar00569322
• WBVar00569328
• WBVar00569332
• WBVar00569333
• gk963025
• gk963102
• gk195077
• gk195078
• gk452219
• WBVar01996814
• gk964255
• gk963103
• WBVar02019937
• gk586937
• gk864465
• gk530675
• WBVar01823462
• WBVar01921380
• WBVar02067801
• WBVar02067800
• WBVar02067799
• WBVar02067798
• WBVar02067797
• WBVar02067796
• gk195062

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001186
• Start: 1902322
• End: 1917840
• 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_1917841..1917976
• Length (nt): 136
• Chromosome Location: IV: 1917841-1917976
• Organism: Caenorhabditis elegans

202 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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 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
	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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	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 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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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
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
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
	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
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster3
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:A-class-motor-neurons_L2-larva_expressed
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	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:dopaminergic-neurons_L3-L4-larva_expressed

16 Expression Patterns

• Primary Identifier: Expr1030758
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13829
• Pattern: egl-18 is expressed in the HSN at L4 coinciding with the onset of differentiation. egl-18 is also expressed in other neurons, including the NSM serotonergic neuron, but not in the ADF serotonergic neuron. egl-18 is expressed embryonically and its expression is maintained in HSN after differentiation.

• Primary Identifier: Expr7314
• Pattern: Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/11/elt-5sma3gfp-transcriptional-fusion.html

• Primary Identifier: Expr7583
• Remark: Clone: pUL#JRH/AA1
• Pattern: Expression is strong in early to late embryos, in a restricted yet extensive pattern in earlier stages. Seam cells express postembryonically through to adult. Also some nerve cells show expression in head, nerve cord and tail, and around the vulva.

• Primary Identifier: Expr11007
• Pattern: egl-18 is asymmetrically expressed in larval seam division daughters with stronger expression in the posterior seam-fated cells in which the Wnt pathway is activated. All ten seam cells in newly hatched L1 larvae showed strong egl-18 expression. After their first division, egl-18::mCherry expression was asymmetric between the daughters, with stronger expression in the posterior daughters that maintain the seam cell fate. Expression in the anterior daughter faded after division, before the hypodermal daughters moved out of the seam cell line. During the L2 stage, several seam cells undergo a symmetric expansion division, generating two seam daughters and increasing the seam cell number from 10 to 16 (Sulston and Horvitz, 1977). In the early L2, strong symmetric expression of egl-18::mCherry was seen in both seam-fated daughters of these divisions. When these seam-fated daughters underwent their subsequent L2 and L3 stage asymmetric divisions, reporter expression faded in their anterior, hypodermal-fated daughters as observed in the L1 stage. In the adult, differentiated seam cells continue to show strong expression of the egl-18::mCherry reporter as described previously (Budovskaya et al., 2008).

• Primary Identifier: Expr1633
• Pattern: First, pKK52 expression begins at the 28-cell stage in all four granddaughters and 16 great-great granddaughters of the MS and AB founder cells, respectively; this expression continues in many, possibly all, of their descendants until around the time of hatching. Second, expression becomes more pronounced in seam cells about 1 hour after their birth. This seam expression remains strong throughout embryonic and larval development, but becomes slightly reduced in adults. Third, robust expression is also seen in several cells in the head region, at least some of which are cells in the nervous system (neurons and/or support cells), beginning at approximately the comma stage and continuing through adulthood. For simplicity, this component of the expression pattern was referred as nervous system expression, although the precise identity of these cells were not determined.

• Primary Identifier: Expr1635
• Remark: Authors was unable to obtain consistent and reliable staining of early embryos, larvae and adults, and therefore have not confirmed the reporter expression pattern at these stages. See Expr1633 for Reporter_gene expression pattern.
• Pattern: Anti-ELT-5 staining is readily detected in the nuclei of seam cells during mid- to late-embryogenesis. At these stages, many unidentified cells in the head region also stained, consistent with the pattern seen for the GFP reporters. This staining is eliminated in elt-5(RNAi) embryos.
• Subcellular Localization: nuclei

• Primary Identifier: Expr11067
• Pattern: An egl-18::gfp translational fusion is expressed in the nuclei of the main body epidermal syncytium hyp7, but appears to be excluded from the tail tip cells hyp8-11.

• Primary Identifier: Expr2277
• Remark: Similar vulval expression was observed when GFP was fused to the start codon of either egl-18 or elt-6 in a reporter containing ~8 kb of contiguous genomic sequence that includes this ~800 bp region, suggesting that the ~800 bp region is likely to be a vulval enhancer for both genes. As the expression levels and patterns of pKK63 showed substantial variability, even among chromosomal integrants of the transgene, the characterization of the spatial and temporal pattern of egl-18/elt-6::GFP expression is based on the composite pattern that emerged from examination of many animals. egl-18 = elt-5
• Pattern: The reporter construct (pKK63) is sufficient to drive GFP expression in the VPCs and their descendants as well as in the six VC motoneurons that innervate vulval muscles, which are likely to be co-regulated with vulval cells. When expression of egl-18::GFP is first detected in VPCs around the mid-L2 stage, all six VPCs are equally likely to express GFP. However, beginning at around the late-L2/early-L3 stage, until the VPCs divide in the mid-L3 stage, the expression in P5.p-P7.p is generally higher than in the other VPCs, and P6.p often shows the strongest expression. Expression persists in the descendants of P5.p-P7.p through the L4 stage, and P6.p descendants typically show stronger expression than descendants of P5.p and P7.p. This pattern is similar to that of lin-39 expression in the developing vulva.

• Primary Identifier: Expr2011209
• 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: Expr2856
• Remark: Reporter gene fusion type not specified.
• Pattern: Strong GFP expression was seen in all 12 P cells (six of which are precursors of VPCs) in the embryos and L1-stage larvae. Weaker and more variable expression was observed in VPCs at the L2 larval stage. Expression was more readily detected in VPCs and their descendants at the L3 stage. Expression persisted in vulval cells (P5.pP7.p descendants) through the L4 stage becoming weaker in adulthood. Expression faded in the descendants of P3.p, P4.p, and P8.p, presumably in part because they fused with the surrounding syncytium.

• Primary Identifier: Expr1020536
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1152228
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2029445
• 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: Expr13571
• Pattern: In WT animals, egl-18 is enriched in the posterior daughter cell following the L2 asymmetric division of H2, and also enriched in the posterior daughter cells following the subsequent V1-V4 asymmetric division.

• Primary Identifier: Expr11833
• Remark: Sequence feature
• Pattern: A 650-bp region between 1.5 and 0.9 kb upstream of egl-18a, when fused with pes-10 basal promoter, was sufficient for moderate levels of GFP expression in the developing vulva. Additional analyses revealed that the downstream half (350 bp) of the 650-bp region was sufficient for vulval expression. Neither half of the 350-bp region (pYB16 and pYB19) resulted in vulval expression above the background, which suggests that both halves of the f350-bp region are important for vulval expression. The removal of this f350-bp regulatory element in nT1 animals is likely to result in substantially reduced vulval expression of the egl-18 and elt-6 GATA factors.

20 GO Annotation

24 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001186
• Start: 1902322
• End: 1917840
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 15519

1 Sequence Ontology Term