WormMine: Gene WBGene00000443

• WormBase Gene ID: WBGene00000443
• Gene Name: ceh-20
• Sequence Name: F31E3.1
• Brief Description: ceh-20 encodes one of three C. elegans homeodomain proteins (CEH-20, CEH-40, and CEH-60) homologous to Extradenticle (Exd/Pbx); together with ceh-40 and unc-62, ceh-20 activity is required for embryonic viability; ceh-20 is also required as a cofactor for LIN-39- and MAB-5- dependent postembryonic mesoderm patterning; in addition, ceh-20 is required for regulating post-embryonic migrations of the Q neuroblast descendants and for regulating vulval development; a CEH-20::GFP fusion protein is expressed in embryos and postembryonically in many cell types including the Q, P, and V cells and their descendants; CEH-20 localizes to the nucleus.
• Organism: Caenorhabditis elegans
• Automated Description: Enables cis-regulatory region sequence-specific DNA binding activity and transcription coactivator binding activity. Contributes to RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including cell differentiation; positive regulation of mesodermal cell fate specification; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Part of RNA polymerase II transcription regulator complex. Expressed in several structures, including P1.p; P2.p; neurons; seam cell; and somatic nervous system. Human ortholog(s) of this gene implicated in congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay; esophagus squamous cell carcinoma; and glaucoma. Is an ortholog of human PBX4 (PBX homeobox 4).
• Biotype: SO:0001217
• Genetic Position: III :-0.852634 ±0.002142
• Length (nt): 1902

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000443

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F31E3.1.1	F31E3.1.1	1279	III: 6979884-6981785

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F31E3.1	F31E3.1	1017	III: 6979887-6979978

30 RNAi Result

• WBRNAi00113294
• WBRNAi00038583
• WBRNAi00002468
• WBRNAi00025340
• WBRNAi00000584
• WBRNAi00008732
• WBRNAi00066002
• WBRNAi00114670
• WBRNAi00071298
• WBRNAi00066006
• WBRNAi00113065
• WBRNAi00086885
• WBRNAi00086888
• WBRNAi00093679
• WBRNAi00116259
• WBRNAi00083966
• WBRNAi00086887
• WBRNAi00086883
• WBRNAi00086884
• WBRNAi00093996
• WBRNAi00093987
• WBRNAi00113171
• WBRNAi00113134
• WBRNAi00046018
• WBRNAi00084136
• WBRNAi00084129
• WBRNAi00084128
• WBRNAi00107115
• WBRNAi00116260
• WBRNAi00116261

47 Allele

• gk964518
• gk963887
• gk964032
• gk964033
• gk410004
• gk601247
• gk461887
• WBVar00240548
• WBVar00244496
• tm431
• WBVar01827679
• gk419747
• gk827870
• gk563490
• gk649168
• ay35
• gk916993
• ay13
• gk761475
• ay37
• gk498545
• snx716
• gk514932
• n2513
• gk360627
• ay9
• WBVar01446399
• ay34
• snx2579
• ay36

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000443
• Start: 6979884
• End: 6981785
• 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_chrIII_6981786..6982080
• Length (nt): 295
• Chromosome Location: III: 6981786-6982080
• Organism: Caenorhabditis elegans

164 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 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 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
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 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 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 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 pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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
	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
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_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 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 xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:Cisplatin_downregulated_WT
	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-1[KKRR] 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(ne4747)_upregulated
	Transcripts that showed significantly increased expression in hda-1[KKRR]-smo-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(ne4748)_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
	Transcripts that showed significantly increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) 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:mep-1(ne4629)_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:glr-1(+)-neurons_L2-larva_expressed
	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:hypodermis_L3-L4-larva_expressed

18 Expression Patterns

• Primary Identifier: Expr4328
• Pattern: Expressed in all VPCs prior to and during vulval induction. After VPC division, CEH-20::GFP accumulation became restricted to the P5.p and P7.p lineages, where it remained apparent until the late L4 larval stage.

• Primary Identifier: Expr2009867
• 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: Expr1030251
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7531
• Remark: Clone: pUL#JRH10F9
• Pattern: Expression observed from early embryo to adult. Early embryo shows general expression which becomes more restricted in mid embryo. Later expression in many (possibly all) nerves including dorsal nerve cord and ventral nerve cord. Also all muscles, hypodermis and vulva. Inconsistent expression in intestine.

• Primary Identifier: Expr15570

• Primary Identifier: Expr3231
• Remark: Lineage expression: V lineage. Transgenic ceh-20(mu290) animals bearing pLY11 were rescued for the QR.pax positioning phenotype, the Muv/Egl, and the Vn.a division phenotype, suggesting that ceh-20::gfp was expressed in cells that require its function for these processes.
• Pattern: ceh-20::gfp expression was detected in QR and QL and their descendants throughout their migrations to the end of L1. V cells and their daughters also expressed ceh-20::gfp. Expression persisted in the descendants of the V cells through the adult stage. At hatching, all P cells expressed ceh-20::gfp. Before the anterior and posterior Pn.p cells fuse, they also expressed ceh-20. In L3 hermaphrodites, expression was maintained in P(3-8).p. ceh-20::gfp expression was identified in several other cell types. These included M, BDU, ALM, HSN, body wall muscle cells, I4, all L1 ventral cord neurons and a few unidentified neurons in the head behind the posterior bulb of the pharynx.
• Subcellular Localization: In all cells expressing ceh-20, the expression was stronger in the nucleus than in the cytoplasm. ceh-20::gfp expression and nuclear localization did not change in the unc-62(mu232) background.

• Primary Identifier: Expr12586
• Pattern: The Hox cofactor ceh-20 in ALM, but not PLM, neurons.

• Primary Identifier: Expr8785
• Remark: Picture: Fig 4.
• Pattern: Transcriptional reporter: Transgenic animals carrying ceh-20p::gfp showed a similar expression pattern to the translational ceh-20::gfp reporter outside of the M lineage, but failed to show expression in the M lineage. Translational reporter: Nuclear GFP signal was detected in a wide array of cells outside of the M lineage, including a subset of embryonic cells, hypodermal cells, gut cells, bodywall muscles, VNC neurons and VPCs. Within the M lineage, CEH-20::GFP was detected in the M cell and throughout the early M lineage. It persisted in the differentiated BWMs as well as in the SMs and all the SM descendants.

• Primary Identifier: Expr11180
• Pattern: Wild type ceh-20 constructs were expressed predominantly in seam nuclei. ceh-20::gfp expression was observed to be higher in anterior daughters of asymmetric seam cell divisions compared with posterior daughters.

• Primary Identifier: Expr13094
• Pattern: Refers to NEXTDB In-situ hybridization pattern in the adult gonad.

• Primary Identifier: Expr11077
• Pattern: ceh-20 reporter gene construct is expressed in the PDE neurons throughout their life. ceh-20 is expressed in a few neurons in the head, mostly in the second pharyngeal bulb area, including the ADE neurons. Coexpression of ast-1, ceh-43, and ceh-20 was detected in at least one nondopaminergic neuron (SDQL).

• Primary Identifier: Expr11089
• Pattern: ceh-20 was expressed in nearly all of the cells, including the T cell. During T cell mitosis, CEH-20 was distributed uniformly. Soon after T cell division (before V6 division), the nuclear level of CEH-20 was equal in the daughter cells, while in the late stage, after V6 division, the nuclear level in T.a was slightly greater and that in T.p was slightly less, resulting in the differential subcellular localization of CEH-20 between the daughter cells (8/33 animals showed the asymmetric localization; i.e., strong nuclear localization in T.a and weak nuclear and cytoplasmic localization in T.p).

• Primary Identifier: Expr2028107
• 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: Expr1012944
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1149914
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr15297
• Pattern: Both ceh-20 and ceh-40 are expressed broadly in an overlapping fashion during embryogenesis.

• Primary Identifier: Expr3498
• Pattern: Expression not detected.

• Primary Identifier: Expr3858
• Pattern: Broad expression in many nuclei, including most ventral nerve cord neurons. Authors specifically identified expression in P11.aaap, which undergoes programmed cell death in a ceh-20-dependent fashion.
• Subcellular Localization: Expressed in nuclei.

32 GO Annotation

18 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000443
• Start: 6979884
• End: 6981785
• Strand: 1

32 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1902

1 Sequence Ontology Term