WormMine: Gene WBGene00001184

• WormBase Gene ID: WBGene00001184
• Gene Name: egl-15
• Sequence Name: F58A3.2
• Brief Description: egl-15 encodes the sole C. elegans fibroblast growth factor receptor and is orthologous to the vertebrate FGFRs (FGFR1-4); egl-15 is required for several processes including fluid homeostasis and sex myoblast (SM) migration, which is essential for proper development of the egg-laying system; phosphorylation of the SAX-7 L1CAM is dependent upon EGL-15 activity and inhibits colocalization of SAX-7 with the ankyrin UNC-44; EGL-15 activators include the FGF-like signaling molecules EGL-17 and LET-756; EGL-15 negative regulators include CLR-1, a receptor protein-tyrosine phosphatase.
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein kinase activity. Involved in several processes, including egg-laying behavior; muscle cell cellular homeostasis; and nematode larval development. Predicted to be located in plasma membrane. Predicted to be part of receptor complex. Expressed in head neurons; hypodermis; intestine; male sex myoblast; and vulval muscle. Used to study bone disease. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; bone disease (multiple); carcinoma (multiple); and hematologic cancer (multiple). Is an ortholog of human FGFR2 (fibroblast growth factor receptor 2).
• Biotype: SO:0001217
• Genetic Position: X :2.85574 ±0.003057
• Length (nt): 7022

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001184

Genomics

13 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F58A3.2h.1	F58A3.2h.1	3775	X: 11016400-11023421
Transcript:F58A3.2g.1	F58A3.2g.1	3650	X: 11016400-11023421
Transcript:F58A3.2f.1	F58A3.2f.1	3850	X: 11016401-11023421
Transcript:F58A3.2p.1	F58A3.2p.1	3594	X: 11016408-11023404
Transcript:F58A3.2a.6	F58A3.2a.6	3380	X: 11016410-11023046
Transcript:F58A3.2a.5	F58A3.2a.5	3590	X: 11016410-11023192
Transcript:F58A3.2a.4	F58A3.2a.4	3958	X: 11016410-11023310
Transcript:F58A3.2a.3	F58A3.2a.3	3659	X: 11016410-11023386
Transcript:F58A3.2a.2	F58A3.2a.2	4669	X: 11016410-11023408
Transcript:F58A3.2a.1	F58A3.2a.1	3895	X: 11016410-11023421
Transcript:F58A3.2b.1	F58A3.2b.1	2967	X: 11016441-11021893
Transcript:F58A3.2l.1	F58A3.2l.1	3120	X: 11016441-11022161
Transcript:F58A3.2n.1	F58A3.2n.1	2985	X: 11016441-11022401

Other

8 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F58A3.2f	F58A3.2f	3276	X: 11016441-11016528
CDS:F58A3.2b	F58A3.2b	2967	X: 11016441-11016528
CDS:F58A3.2a	F58A3.2a	3123	X: 11016441-11016528
CDS:F58A3.2g	F58A3.2g	3141	X: 11016441-11016528
CDS:F58A3.2h	F58A3.2h	3462	X: 11016441-11016528
CDS:F58A3.2l	F58A3.2l	3120	X: 11016441-11016528
CDS:F58A3.2n	F58A3.2n	2985	X: 11016441-11016528
CDS:F58A3.2p	F58A3.2p	3306	X: 11016441-11016528

31 RNAi Result

• WBRNAi00107695
• WBRNAi00048920
• WBRNAi00089857
• WBRNAi00066999
• WBRNAi00067492
• WBRNAi00067649
• WBRNAi00067987
• WBRNAi00068076
• WBRNAi00001784
• WBRNAi00008891
• WBRNAi00025741
• WBRNAi00064754
• WBRNAi00071728
• WBRNAi00087720
• WBRNAi00071633
• WBRNAi00071632
• WBRNAi00111665
• WBRNAi00060149
• WBRNAi00060148
• WBRNAi00060150
• WBRNAi00060151
• WBRNAi00066756
• WBRNAi00086089
• WBRNAi00101902
• WBRNAi00086083
• WBRNAi00086098
• WBRNAi00086097
• WBRNAi00086138
• WBRNAi00089909
• WBRNAi00090069

123 Allele

• gk964260
• gk964029
• gk962707
• gk964028
• gk963810
• WBVar01928258
• WBVar01690222
• WBVar01690224
• WBVar01690223
• WBVar01820524
• n2182
• n2184
• n2189
• n2202
• n2205
• n2203
• n2210
• n2206
• n2217
• ok2314
• gk953869
• gk293250
• gk293249
• gk293248
• gk293247
• gk293246
• gk293245
• gk293244
• gk293258
• n1454

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001184
• Start: 11016400
• End: 11023421
• 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_chrX_11023422..11028439
• Length (nt): 5018
• Chromosome Location: X: 11023422-11028439
• Organism: Caenorhabditis elegans

192 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
	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
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	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
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 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
	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 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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_aging
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	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
starvation 12 hours	Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals.	EdgeR, FDR < 0.05, fold change >= 2.	WBPaper00067259:starvation_upregulated_intestine
	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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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
	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 sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	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
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_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:dopaminergic-neurons_L3-L4-larva_expressed

13 Expression Patterns

• Primary Identifier: Expr1030757
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8096
• Remark: Anatomy_term: migrating sex myoblast. Picture: Figure 1, S1.
• Pattern: EGL-15(5B) is primarily expressed in the hypodermis, EGL-15(5A) is primarily expressed in the M lineage. Moreover, expression analysis of these isoforms across development revealed that 5A is present in the M lineage at all stages

• Primary Identifier: Expr2119
• Remark: Clone = pUL#L428A Other strain-- UL904 Strain = UL903 Updated sequence connections
• Pattern: Expression is first seen in a few cells in embryos just after comma stage. In older embryos and young larvae expression is seen in hypodermal and intestinal cells throughout the worm. In L4 larvae and adult worms expression is seen in the vm1 and vm2 vulval muscles.

• Primary Identifier: Expr2943
• Remark: A similar pattern of EGL-15 expression has been observed for many other arrays containing transgenic egl-15 constructs. The expression in the hypodermis is very similar to that observed in Pe15*2::GFP animals, in which expression was observed in the major hypodermis but was excluded from the seam cells. A similar expression pattern can be observed in rescued egl-15(null) animals expressing an egl-15 transgene driven by a hypodermal promoter (Prol-6 and Pdpy-7). Hypodermal expression of EGL-15 is also reported in animals expressing Pegl-15::lacZ, consistent with the antibody staining in this paper. Endogenous EGL-15 was not detected in wild-type animals, probably due to the low-level expression of the endogenous receptor. Therefore, a strain overexpressing a chromosomally integrated egl-15(+) array (ayIs29) was generated , and immunofluorescence staining was performed on this strain using affinity-purified anti-EGL-15 antibodies.
• Pattern: EGL-15 expression was observed in hypodermal cells as well as the sex myoblasts, the type I vulval muscles and some unidentified neurons in the head . The staining is specific to EGL-15, since no signal is observed with secondary antibody alone. Hypodermal expression is obvious throughout all four larval stages, with stronger expression in the early larval stages.

• Primary Identifier: Expr2950
• Remark: Lineage expression: expressed in sex myoblast and descendents in later larva stages.
• Pattern: egl-15::gfp expression in larval stage animals is observed in the hypodermis but not in axons. Expression can also be observed in the sex myoblasts and their descendents during later larval stages.
• Subcellular Localization: egl-15 localizes to the membrane of hypodermal cells.

• Primary Identifier: Expr15862
• Pattern: EGL-15 could be detected at vulval muscles of adult hermaphrodites expressing wild type egl-15.

• Primary Identifier: Expr2011207
• 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: Expr1802
• Remark: Reporter gene fusion type not specified.
• Pattern: A stably integrated egl-15::gfp transgene is expressed in the four Type 1 vulval muscles (vm1s): one in each of the four egg-laying muscle quadrants.

• Primary Identifier: Expr1152659
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1018058
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr3461
• Pattern: In N2 animals, EGL-15 was first detectable in L2, increased in L3, and then diminished in L4.

• Primary Identifier: Chronogram1358
• Remark: Original chronogram file: chronogram.2602.xml
• Reporter Gene: [F58A3.2:gfp] transcriptional fusion.

• Primary Identifier: Expr2029443
• 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).

56 GO Annotation

18 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001184
• Start: 11016400
• End: 11023421
• Strand: 1

56 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 7022

1 Sequence Ontology Term

• Name: gene

33 Strains

• WBStrain00026633
• WBStrain00026784
• WBStrain00027098
• WBStrain00027092
• WBStrain00027059
• WBStrain00027056
• WBStrain00027065
• WBStrain00027062
• WBStrain00027063
• WBStrain00027066
• WBStrain00027067
• WBStrain00027219
• WBStrain00027220
• WBStrain00027119
• WBStrain00027152
• WBStrain00028762
• WBStrain00028763
• WBStrain00028768
• WBStrain00028770
• WBStrain00028775
• WBStrain00028774
• WBStrain00029368
• WBStrain00029367
• WBStrain00029366
• WBStrain00030543
• WBStrain00030708
• WBStrain00036868
• WBStrain00046993
• WBStrain00005621
• WBStrain00005619

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_11014527..11016399
• Length (nt): 1873
• Chromosome Location: X: 11014527-11016399
• Organism: Caenorhabditis elegans