WormMine: Gene WBGene00001185

• WormBase Gene ID: WBGene00001185
• Gene Name: egl-17
• Sequence Name: F38G1.2
• Brief Description: egl-17 encodes a fibroblast growth factor (FGF)-like protein; egl-17 activity is required for proper migration of the sex myoblasts, the cells that give rise to the egg-laying muscles, from the posterior region of the mid-body to a more central position in the animal, flanking the center of the gonad; egl-17 is expressed in the primary and secondary vulval cell lineages and in cells in the male tail.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable growth factor activity; type 1 fibroblast growth factor receptor binding activity; and type 2 fibroblast growth factor receptor binding activity. Involved in regulation of cell migration and regulation of egg-laying behavior. Located in extracellular space. Expressed in several structures, including M4 neuron; P5.p; P7.p; male-specific anatomical entity; and vulval cell. Human ortholog(s) of this gene implicated in several diseases, including germ cell cancer (multiple); hypogonadotropic hypogonadism (multiple); and prostate disease (multiple). Is an ortholog of human FGF18 (fibroblast growth factor 18) and FGF8 (fibroblast growth factor 8).
• Biotype: SO:0001217
• Genetic Position: X :-19.7025 ±0.016129
• Length (nt): 2634

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001185

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F38G1.2.1	F38G1.2.1	870	X: 489685-492318
Transcript:F38G1.2.2	F38G1.2.2	787	X: 489774-492278

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F38G1.2	F38G1.2	651	X: 489794-489846

6 RNAi Result

• WBRNAi00089856
• WBRNAi00046734
• WBRNAi00027850
• WBRNAi00090304
• WBRNAi00089986
• WBRNAi00090145

56 Allele

• gk963652
• gk963725
• WBVar01600306
• WBVar00074312
• WBVar00074311
• WBVar01979012
• gk770673
• gk725680
• gk448427
• gk574607
• gk531902
• gk437757
• gk593555
• gk435323
• gk830523
• gk784972
• gk931790
• gk509175
• gk642444
• gk347557
• gk402649
• gk458311
• gk493314
• gk319274
• ay6
• ay8
• ay59
• n1450
• n1452
• n1451

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001185
• Start: 489685
• End: 492318
• 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_492319..493227
• Length (nt): 909
• Chromosome Location: X: 492319-493227
• Organism: Caenorhabditis elegans

78 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
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
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_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 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
	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
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:oscillating_dev_expression
	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:dopaminergic-neurons_L3-L4-larva_expressed
	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 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 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
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult
	Genes that showed significantly decreased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_downregulated
	Genes upregulated in dcr-1(-/-) adult animals by at least 1.5 fold and P < 0.01, as determined by a multisample t-test and the Benjamini and Hochberg false discovery rate correction.	Statistical t-test: P < 0.05 for rde-4(-/-) and rde-1(-/-) analyses; P < 0.01 for dcr-1(-/-) analysis with a threshold of 1.5-fold misregulation.	WBPaper00029437:dcr-1_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:daf-2(e1370)_upregulated_neuron
	Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:daf-16(mu86)_upregulated_neuron
heat-shock hlh-1	Genes enriched in HLH-1 heat shock dataset.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:hlh_1_enriched
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly decreased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_downregulated
	Transcripts that showed significantly decreased expression in eat-2(ad465);dve-1(RNAi) animals comparing to eat-2(ad465) animals injected with empty vector.	fold change > 2, FDR < 0.01	WBPaper00067391:dve-1(RNAi)_downregulated_eat-2(ad465)
	Transcripts that showed significantly increased expression in sur-5p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:sur-5p-jmjd-1.2(+)_upregulated
	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:intestine_L1-larva_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:pharyngeal-muscle_L1-larva_expressed
	Significantly upregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:cyc-1(RNAi)_upregulated

22 Expression Patterns

• Primary Identifier: Marker11
• Remark: Picture: Figure 7A', 7B'. Reporter gene fusion type not specified.
• Pattern: Expressed in primary fate VPC.

• Primary Identifier: Marker16
• Remark: Picture: N.A. Reporter gene fusion type not specified.
• Pattern: Expressed in primary fate VPC.

• Primary Identifier: Expr7978
• Remark: Picture: Fig. 1B. Reporter gene fusion type not specified.
• Pattern: The arIs92 [egl-17p::cfp-lacZ] reporter is initially expressed in a graded fashion, highest in P6.p and lower in P5.p and P7.p. The expression in P5.p and P7.p disappears, and CFP-LacZ remains detectable only in P6.p and its descendants .

• Primary Identifier: Expr1150610
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1434
• Reporter Gene: [egl-17::GFP] translational fusion. Contains 3.9 kb of 5'UTR, the full-length EGL-17 sequence and 3'UTR.
• Pattern: GFP expression in ayIs4[egl-17::GFP] hermaphrodites is first observed in two large unidentified cells in the head at the 3-fold stage of embryogenesis. After hatching, expression in these cells fades and is then observed in the M4 pharyngeal neuron where it remains throughout postembryonic development. Weak GFP expression can occasionally be observed in the ventral hypodermis in late first stage larvae (L1). This weak expression disappears by the L1 lethargus and was not characterized further. Strong GFP expression is observed in the VPCs and their descendants in two phases starting in late L2 and persisting through adulthood. During early vulval development (late L2-L3), expression is observed in P6.p and its descendants, fading in the early L4. In the mid L4, GFP expression is seen in the N and T descendants of P5.p and P7.p where it remains throughout adulthood.

• Primary Identifier: Expr630
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: egl-17 expression is observed in several cells of the B lineage and the Y.p progeny Y.p(l/r)aa during L3 lethargus. The cells from B lineage appear to be in two of the socket cells, one on each side (likely _(l/r)d), B.paa and B.pppa). At the end of L4 lethargus, expression is observed in a cluster of socket cells per spicule. Shortly after male reaches adulthood, expression is maintained only in B.paa cells.

• Primary Identifier: Expr2011208
• 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: Expr11284
• Remark: Feature : "egl-17.distal"
• Pattern: The distal enhancer activity was observed in P6.p and its descendants from the two-cell stage and increased with time. Distal enhancer activity persisted into much later stages than the proximal enhancer did.

• Primary Identifier: Expr12425
• Pattern: At the time when the CANs are migrating (1.5 fold embryo), GFP was detected in only two hyp5 hypodermal cells at the anterior tip of the embryo.

• Primary Identifier: Marker105
• Pattern: Marker for primary fate VPC.

• Primary Identifier: Expr2354
• Remark: Compelete expression pattern in vulva is described. No detail on expression pattern in other life stages or tissues. Reporter gene fusion type not specified.
• Pattern: egl-17::gfp is expressed in the P6.p lineage during the L3 stage before the last round of division, however, this expression usually fades by the L4 stage. During the L4 stage and the adult, egl-17::gfp is expressed in vulC and vulD cells.

• Primary Identifier: Expr11283
• Remark: Feature : "egl-17.vulDC"
• Pattern: A 64-bp fragment, located between 366 and 303 bp upstream of the egl-17 ATG, was sufficient to activate reporter expression in vulD and vulC cells from mid-L4 through adulthood, termed the vulDC enhancer.

• Primary Identifier: Expr11285
• Remark: Feature : "egl-17.proximal"
• Pattern: The proximal enhancer activated reporter gene expression in P6.p from the one-cell stage, and drastically decreased in the four-cell stage. Distal enhancer activity persisted into much later stages than the proximal enhancer did.

• Primary Identifier: Expr11838
• Reporter Gene: put in construct WBsfxxx::(del)pes-10
• Pattern: mk125-132 (4331-4474) is sufficient to drive strong expression in vulC and vulD.

• Primary Identifier: Chronogram547
• Remark: Original chronogram file: chronogram.1565.xml
• Reporter Gene: [F38G1.2:gfp] transcriptional fusion.

• Primary Identifier: Expr11839
• Reporter Gene: put in construct WBsfxxx::(del)pes-10
• Pattern: mk84-148 contains two regions that together confer strong expression in VulE and VulF.

• Primary Identifier: Chronogram1060
• Remark: Original chronogram file: chronogram.2126.xml
• Reporter Gene: [F38G1.2:gfp] transcriptional fusion.

• Primary Identifier: Expr1814
• Remark: Reporter gene fusion type not specified.
• Pattern: ayIs9 expresses GFP in a subset of cells within the somatic gonad. These GFP cells are the dorsal uterine (DU) cells based on their positions and division patterns. Furthermore, GFP expression was abolished in all animals in which the DUs were ablated (n=10), but could always be observed in control animals in which the DUs were left intact (n=25). Based on these results, EGL-17 appears to be expressed in the somatic gonad by the DU cells.

• Primary Identifier: Expr12298

• Primary Identifier: Chronogram1357
• Remark: Original chronogram file: chronogram.2601.xml
• Reporter Gene: [F38G1.2:gfp] transcriptional fusion.

• Primary Identifier: Expr1028125
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029444
• 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).

16 GO Annotation

84 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001185
• Start: 489685
• End: 492318
• Strand: 1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2634

1 Sequence Ontology Term

• Name: gene

28 Strains

• WBStrain00022912
• WBStrain00023045
• WBStrain00023046
• WBStrain00026853
• WBStrain00026868
• WBStrain00027040
• WBStrain00027058
• WBStrain00028766
• WBStrain00028767
• WBStrain00028764
• WBStrain00028760
• WBStrain00028771
• WBStrain00030934
• WBStrain00030957
• WBStrain00030964
• WBStrain00030925
• WBStrain00030869
• WBStrain00030865
• WBStrain00030877
• WBStrain00030875
• WBStrain00030729
• WBStrain00030730
• WBStrain00030732
• WBStrain00051157
• WBStrain00007653
• WBStrain00007652
• WBStrain00007582
• WBStrain00004296

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_488445..489684
• Length (nt): 1240
• Chromosome Location: X: 488445-489684
• Organism: Caenorhabditis elegans