WormMine: Gene WBGene00000168

• WormBase Gene ID: WBGene00000168
• Gene Name: apx-1
• Sequence Name: K08D9.3
• Brief Description: apx-1 encodes one of ten C. elegans DSL (Delta, Serrate, LAG-2) proteins, integral transmembrane and secreted proteins that function as signaling ligands for the Notch family receptors GLP-1 and LIN-12; in the 4-cell embryo, maternally supplied APX-1 functions as a GLP-1 ligand for an inductive interaction that specifies the fate of the ABp blastomere; later in embryogenesis, APX-1 is required for formation of the LIN-12-dependent, invariant asymmetrical twist that occurs as part of normal gut morphogenesis; during larval development, APX-1 is required redundantly with DSL-1 and LAG-2 for the LIN-12-mediated lateral signal that spatially patterns the primary and secondary vulval cell lineages; in the early embryo, APX-1 is first detected at the anterior edge of the P1 blastomere, with later expression visible in P2 at sites of contact with ABp, and in the cytoplasm of the EMS and P3 blastomeres; expression in the vulval precursor cells (VPCs) is detected in the primary VPC, P6.p, and its descendants; embryonic APX-1 expression is dependent upon PIE-1 activity, while later vulval expression is mediated by the Ras signaling pathway and the SUR-2 transcriptional cofactor.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable Notch binding activity. Involved in several processes, including lateral inhibition; regulation of germ cell proliferation; and regulation of vulval development. Predicted to be located in cytoplasm; nucleus; and plasma membrane. Expressed in several structures, including P6.paa; P6.pap; P6.ppa; non-striated muscle; and vulva. Human ortholog(s) of this gene implicated in spondylocostal dysostosis 1. Is an ortholog of human DLL3 (delta like canonical Notch ligand 3).
• Biotype: SO:0001217
• Genetic Position: V :-12.5303 ±0.036189
• Length (nt): 13026

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000168

Genomics

6 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:K08D9.3f.1	K08D9.3f.1	2347	V: 3210196-3223221
MRNA	Transcript:K08D9.3a.1	K08D9.3a.1	2346	V: 3210200-3223218
NcPrimaryTranscript	Transcript:K08D9.3b	K08D9.3b	1683	V: 3211680-3222449
NcPrimaryTranscript	Transcript:K08D9.3c	K08D9.3c	1272	V: 3212091-3222449
NcPrimaryTranscript	Transcript:K08D9.3d	K08D9.3d	1026	V: 3215251-3222449
MRNA	Transcript:K08D9.3e.1	K08D9.3e.1	642	V: 3218970-3222449

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K08D9.3f	K08D9.3f	1542	V: 3210229-3210505
CDS:K08D9.3a	K08D9.3a	1548	V: 3210229-3210505
CDS:K08D9.3e	K08D9.3e	642	V: 3218970-3219261

40 RNAi Result

• WBRNAi00106566
• WBRNAi00081739
• WBRNAi00081741
• WBRNAi00081731
• WBRNAi00081733
• WBRNAi00081729
• WBRNAi00050277
• WBRNAi00081070
• WBRNAi00081067
• WBRNAi00027585
• WBRNAi00063586
• WBRNAi00063591
• WBRNAi00063594
• WBRNAi00063595
• WBRNAi00063598
• WBRNAi00080995
• WBRNAi00080994
• WBRNAi00081011
• WBRNAi00081012
• WBRNAi00081027
• WBRNAi00081031
• WBRNAi00081033
• WBRNAi00081032
• WBRNAi00081037
• WBRNAi00081038
• WBRNAi00081041
• WBRNAi00081042
• WBRNAi00081045
• WBRNAi00081047
• WBRNAi00081046

387 Allele

• otn10144
• otn10145
• gk963301
• otn8871
• gk963591
• gk963553
• gk964259
• gk964351
• gk963850
• gk963027
• gk962689
• gk962688
• WBVar01586332
• WBVar01586331
• WBVar01586334
• WBVar01586333
• WBVar01586336
• WBVar01586335
• WBVar01586338
• WBVar01586337
• WBVar01586339
• WBVar01586341
• WBVar01586340
• WBVar01586343
• WBVar01586342
• WBVar01586345
• WBVar01586344
• WBVar01586347
• WBVar01586346
• WBVar01586349

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000168
• Start: 3210196
• End: 3223221
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_3223222..3223611
• Length (nt): 390
• Chromosome Location: V: 3223222-3223611
• Organism: Caenorhabditis elegans

158 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 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
	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:AVE-neuron_L1-larva_expressed
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
	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 in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
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
	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 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 (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:coelomocytes_L2-larva_expressed
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_expressed
	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:glr-1(+)-neurons_L2-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 hira-1(gk835598) comparing to in N2 animals at L4 larva stage.	Differential expression analysis was done with Rversion 2.15.3 using DESeq_1.10.1. Fold change > 2, p-value < 0.01.	WBPaper00059739:hira-1(gk835598)_upregulated_L4
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_downregulated
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 significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated

12 Expression Patterns

• Primary Identifier: Expr2009374
• 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: Expr1030095
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8699
• Remark: Picture: Fig 1B, Fig S1.
• Pattern: apx-1 reporters driven by a 9-kb region upstream of the apx-1 coding sequence (a nuclear-localized Papx-1::NLSlacZ and Papx-1::GFP) show expression in the two proximal-most pairs of sheath cells and the four distal-most cells of the spermatheca. Expressed in somatic gonad, pharynx and vulva.

• Primary Identifier: Expr545
• Remark: See Expression pattern 546 for distribution of APX-1 protein. early embryo(author) = blastula embryo(curator).
• Pattern: Between the newly-fertilized 1-cell stage and the 8-cell stage, apx-1 mRNA is present in all blastomeres at equivalent levels. After the 8-cell stage, apx-1 mRNA rapidly disappears from somatic blastomeres; in 12-cell stage embryos, apx-1 mRNA is visible in the P3 blastomere, but disappears from MS and all other blastomeres. In the 36-cell stage and later embryos, apx-1 mRNA was detected in one to five unidentified nuclei.

• Primary Identifier: Expr1153978
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr10805
• Pattern: Expression of apx-1 was observed in both secondary vulval epithelial cells and vm1 muscle cells during the L4 stage.

• Primary Identifier: Expr12810
• Pattern: apx-1::lacZ is present in cells immediately adjacent to ventral M lineage cells, but not next to dorsal M lineage cells. Further co-localization using the MH27 monoclonal antibody indicated that the apx-1::lacZ expressing cells near the M lineage are hypodermal cells.

• Primary Identifier: Expr2841
• Remark: No detailed description on cellular expression patterns in other life stage or tissue.
• Pattern: In the early L3 stage, as assessed by the extent of gonad extension, apx-1 is not expressed. Later, when the gonad is more extended and beginning to reflex, apx-1 begins to be expressed in P6.p. Expression continues in P6.p descendants.

• Primary Identifier: Expr2027610
• 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: Expr546
• Remark: early embryo(author) = blastula embryo(curator).
• Pattern: APX-1 protein is detected first in the late 2-cell stage at the anterior periphery of P1. It is found in and EMS at the 4-cell stage. Later, it is seen faintly in P3.
• Subcellular Localization: APX-1 was mainly plasma membrane-associated, but punctate patterns below the membrane and in the cytoplasm. APX-1 is seen in the membrane where P1 contacts AB.p, and the punctate structures are present where P1 contacts AB.a and AB.p. In early 4-cell stage embryos, APX-1 staining is seen where P2 contacts AB.p and in punctate structures in P2 and in the cytoplasm of EMS.APX-1 is not detected in AB.a or AB.p. At the 12-cell stage, APX-1 is detected faintly in P3 cytoplasm only. Later, APX-1 appears in a few unidentified cells.

• Primary Identifier: Expr1011137
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr13496
• Pattern: Both 1st fate markers lag-2p::yfp and apx-1p::yfp were expressed as L2d larvae molt into dauer. The expression of 1st fate markers was extinguished in the VPCs of dauer larvae whereas the VPC identity markers were maintained.

29 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000168
• Start: 3210196
• End: 3223221
• Strand: 1

29 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 13026

1 Sequence Ontology Term