WormMine: Gene WBGene00000435

• WormBase Gene ID: WBGene00000435
• Gene Name: ceh-10
• Sequence Name: W03A3.1
• Brief Description: ceh-10 encodes a member of the Paired-like class of homeodomain proteins; the CEH-10 homeodomain is closely related to the homeodomains of two vertebrate retina proteins (Chx10 from mice and Vsx-1 from goldfish); ceh-10 is required for CAN cell fate specification and migration, complete loss of ceh-10 function results in failure of CAN cell migration and loss of expression of CEH-23 and CEH-10 itself in the CAN and AIY interneurons; CEH-10, along with TTX-3 and CEH-23, constitutes a regulatory cascade of transcription factors that controls all sub-type specific features of the AIY interneurons.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including egg-laying behavior; generation of neurons; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Expressed in ABalapppaa; CAN; head neurons; seam cell; and somatic nervous system. Human ortholog(s) of this gene implicated in eye disease (multiple). Is an ortholog of human VSX2 (visual system homeobox 2).
• Biotype: SO:0001217
• Genetic Position: III :-1.44616 ±0.00013
• Length (nt): 2069

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000435

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W03A3.1.1	W03A3.1.1	1127	III: 5799047-5801115

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W03A3.1	W03A3.1	1035	III: 5799073-5799177

7 RNAi Result

• WBRNAi00054638
• WBRNAi00019528
• WBRNAi00005463
• WBRNAi00027655
• WBRNAi00075607
• WBRNAi00084769
• WBRNAi00084771

48 Allele

• gk964518
• gk175426
• gk175427
• gk175428
• gk175429
• gk964338
• gk964339
• WBVar01263925
• WBVar01263927
• WBVar01263928
• tm777
• WBVar01656711
• h15899
• gk581271
• ct78
• gk784636
• vba1
• gk408995
• vba28
• gk719044
• gk682635
• gk839424
• gm71
• gm58
• WBVar01893462
• gm100
• tm1338
• tm2171
• gm120
• WBVar00056735

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000435
• Start: 5799047
• End: 5801115
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

103 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
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 increased expression in wdr-5(ok1417) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:wdr-5(ok1417)_upregulated
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly increased 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_upregulated
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
Bacteria infection: Photorhabdus luminescens	Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection.	MAANOVA and BRB-Array-Tools.	WBPaper00030985:Photorhabdus_luminescens_downregulated
	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
	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 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
	Transcripts that showed significantly increased expression in wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage.	fold change > 2	WBPaper00058711:wdr-5(ok1417)_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
	Transcripts that showed significantly increased expression in pie-1(ne4443[PIE-1-Degron-GFP])	DESeq2. Differentially expressed genes were defined as twofold change and adjusted p-value less than 0.05.	WBPaper00061478:pie-1(ne4433)_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
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C.	Transcripts that showed significantly decreased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 24 hours at 25C.	DESeq R package (1.18.0), FDR < 0.05 and fold change > 2.	WBPaper00062184:PA14_downregulated
	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 dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_upregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated
Starvation	Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl)	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:starvation_regulated_LowSalt
	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
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Transcripts that showed significantly increased expression in animals fed with JM103 bacteria producing Cry5B, comparing to control animals fed with JM103.	ANOVA, p-value < 0.05.	WBPaper00056167:Cry5B_upregulated
	Strictly embryonic class (SE): genes that are the subset of embryonic genes that are not also classified as maternal.	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_SE

13 Expression Patterns

• Primary Identifier: Expr2009858
• 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: Marker63
• Remark: Picture: N.A. Reporter gene fusion type not specified.
• Pattern: RID cell fate marker

• Primary Identifier: Expr1030246
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7696
• Remark: Clone: pUL#JRH4B11
• Pattern: Expression is first seen in comma stage embryos in posterior regions; in seam cells from late embryo to L1; L1 to adult in dorsal and ventral nerve cords as well as other cells in the nerve ring including a process to the tip of the head.

• Primary Identifier: Expr1584
• Pattern: The large majority of ceh-10 mRNA is found in the embryo and likewise the majority of ceh-10 directed reporter gene expression is also found within the embryo. The earliest point at which ceh-10/lacZ expression can be detected is in a single nucleus at the extreme anterior pole of the embryo, at mid-proliferation stage when the embryo has approximately 350 cells. In late proliferation stage embryos, two nuclei and then four nuclei, all at the embryo anterior, express the transgene. As the embryo begins morphogenesis, six nuclei, all at the very anterior pole, stain for beta-galactosidase activity. By the 1.5-fold stage, the embryo has eight staining nuclei, six at the anterior and two additional cells just ventral to the posterior bulb of the pharynx. By the time the embryo has completed morphogenesis, up to twelve staining nuclei can be detected. ceh-10/lacZ expression in L1 larvae is somewhat variable, in that staining in a particular cell is not always seen in every larva; the likely reason is that the level of ceh-10 mRNA declines after hatching and beta-galactosidase staining in L1 larvae presumably results from enzyme perdurance. Most ceh-10/lacZ staining occurs in the region around the nerve ring, which is dense with the nuclei and processes of neurons. The expressing anterior nuclei were identified as: AIYL/R (interneurons), CEPDL/R (mechanosensory neurons), RID (motor neuron), ALA (lateral neuron), RMED (nerve ring motor neuron), AINL/R (interneurons) and AVJL/R (ventral neurons). ceh-10 is also expressed in the CAN cells (the excretory Canal Associated Neuron).

• Primary Identifier: Expr15660
• Reporter Gene: personal communication (Vincent Bertrand)

• Primary Identifier: Expr10639
• Pattern: By 6 h postfertilization (hpf), Ceh-10::GFP expression appeared in precursor cell ABalapppaa (bean stage of embryonic development), and subsequently in the daughter cells ALA (ABalapppaaa) and RMED (ABalapppaap). GFP expression was also subsequently observed in the canal-associated neurons, CANR (ABalappappa) and CANL (ABalapaaapa). The observed pattern of ceh-10p:GFP expression in these neuronal cells, and their subsequent migration through the onset of early twitching (~7:10:00 hpf, twofold stage), was reproducible across all 12 inspected embryos.

• Primary Identifier: Expr9696
• Remark: Picture: Figure 2B.
• Pattern: After cleavage of the SMDD/AIY mother, ceh-10 starts to be expressed in AIY, but not in SMDD. Finally, during embryonic elongation, the expression of ceh-10 increases in AIY, and the AIY motif starts to be activated in AIY.

• Primary Identifier: Expr1020972
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2028098
• 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: Expr1386
• Remark: Expression in other life stages is not described in the paper.
• Pattern: A 1.25kb and a 1.85 kb transcript can be detected in poly A+ RNA from wild type embryos, both decrease substantially in RNA isolated from larval stages.

• Primary Identifier: Expr1170034
• Pattern: Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191

• Primary Identifier: Expr1158187
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

21 GO Annotation

39 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000435
• Start: 5799047
• End: 5801115
• Strand: 1

21 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2069

1 Sequence Ontology Term