WormMine: Gene WBGene00000447

• WormBase Gene ID: WBGene00000447
• Gene Name: ceh-24
• Sequence Name: F55B12.1
• Brief Description: ceh-24 encodes an NK class homeodomain protein orthologous to human NK2 Homeobox 1 (NKX2-1; OMIM:600635) which is expressed in the thyroid, lung, and bronchial epithelia and which, when mutated, leads to disease.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell differentiation; regulation of transcription by RNA polymerase II; and regulation of transcription elongation by RNA polymerase II. Predicted to be located in nucleus. Expressed in head muscle; intestine; neurons; non-striated muscle; and ventral nerve cord. Human ortholog(s) of this gene implicated in choreatic disease and papillary thyroid carcinoma. Is an ortholog of human NKX2-1 (NK2 homeobox 1) and NKX2-4 (NK2 homeobox 4).
• Biotype: SO:0001217
• Genetic Position: V :5.59946 ±0.002711
• Length (nt): 2120

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000447

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F55B12.1.1	F55B12.1.1	1056	V: 13813231-13815350

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F55B12.1	F55B12.1	900	V: 13813309-13813323

16 RNAi Result

• WBRNAi00107685
• WBRNAi00107686
• WBRNAi00048448
• WBRNAi00107516
• WBRNAi00073119
• WBRNAi00073118
• WBRNAi00073120
• WBRNAi00027721
• WBRNAi00107517
• WBRNAi00015693
• WBRNAi00107549
• WBRNAi00107116
• WBRNAi00107065
• WBRNAi00107499
• WBRNAi00107466
• WBRNAi00107333

38 Allele

• gk963271
• gk963706
• gk963301
• gk964458
• gk964459
• WBVar02062099
• tm1103
• WBVar01744151
• gk252439
• WBVar00013965
• gk252440
• gk252437
• gk252438
• gk252436
• h4795
• WBVar00013970
• h3450
• gk443761
• cc539
• gk876953
• gk419867
• gk792009
• gk903854
• gk930605
• gk377827
• gk769620
• gk410087
• gk482681
• gk854491
• gk470929

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000447
• Start: 13813231
• End: 13815350
• 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_chrV_13815351..13815373
• Length (nt): 23
• Chromosome Location: V: 13815351-13815373
• Organism: Caenorhabditis elegans

96 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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	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 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 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 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 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 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
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_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
	Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis.	Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction.	WBPaper00040560:hpl-2_embryo_downregulated
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly decreased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_downregulated
	Transcripts that showed significantly increased expression in dpy-7(e88) animals comparing to N2 animals.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:up_at_dpy-7(e88)
	Total muscle depleted genes (complete list of non-overlapping genes from the 0hr and 24hr muscle depleted datasets).	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:total_muscle_depleted
	Transcripts that showed significantly decreased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_downregulated
	Transcripts that showed significantly decreased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_downregulated
	Genes that showed flat 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:flat_dev_expression
	Transcripts that did not alter expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, but their mRNAs co-purify with SMG-2.	edgeR	WBPaper00053308:SMG-2_associated_NMD(-)_unaltered_ClassII
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage.	Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00065158:AFD_enriched
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly increased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_upregulated_hpx-2(dg047)
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly decreased expression in mter-4(syb3662 syb3403) comparing to in N2.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00061995:mter-4(syb3662syb3403)_downregulated

18 Expression Patterns

• Primary Identifier: Expr2009871
• 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: Expr1030254
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7584
• Remark: Clone: pUL#JRHAD8
• Pattern: Expression observed from late embryo to adult. Three pairs of nerves in head all on ventral side of posterior pharyngeal bulb, one pair slightly more anterior to the other two. Also ventral nerve cord and two pairs of nerves in tail with processes to head. Another single nerve in ventral tail with process posterior ventrally to tail tip then anterior along dorsal side to one third along body axis. Possibly artifactual expression in head muscles and posterior intestine.

• Primary Identifier: Expr1440
• Pattern: In adult animals, expression was seen in three distinct areas: in the eight vulval muscles, in 8-10 ventral neurons in the head and in the most posterior pharyngeal muscle cell, m8. Expression in vulval muscle cells was seen from the L4 larval stage onward, starting just before these cells began contractile activity. Vulval muscle cells are born in the late L3 larval stage. Two sex myoblast cells present in the L3 larval stage are the precursors to the eight vulval and eight uterine muscles. No ceh-24 reporter activity was seen in the sex myoblasts or uterine muscles. Expression in the pharynx was limited to a single cell, the donut-shaped muscle cell m8. This unique cell forms the rear of the pharynx. m8 expression was first seen in the embryo, beginning approximately 400 minutes after the first cell cleavage. This activity continued throughout the life of the animal. The ceh-24 reporter construct was active in SMDVL, SMDVR, SIBVL, SIBVR, SIBDL and SIBDR. There are another four neurons with ceh-24 promoter activity appear to belong to the SI/SM class of sublateral neurons.

• Primary Identifier: Expr1200027
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr11281
• Remark: Feature : "ceh-24.vulval"
• Pattern: A 452 bp sequence from the vulval enhancer region of ceh-24 activated the minimal pes-10 promoter in all eight vulval muscle cells. This fragment was capable of enhancement in either orientation.

• Primary Identifier: Expr15576

• Primary Identifier: Expr13324
• Pattern: ceh-24 is expressed in the sublateral SMB, SIB, and SIA neurons as well as in the m8 muscle cells.

• Primary Identifier: Expr11282
• Remark: Feature : "ceh-24.pm8"
• Pattern: A 117bp fragment from ceh-24 activated expression in the pharyngeal muscle cell m8. Enhancement by this segment was not seen in any other cell.

• Primary Identifier: Expr13507
• Pattern: Embryonic and postembryonic (from late comma stage and on). SMDV, SIAV, SIAD, SIBV, SIBD.

• Primary Identifier: Expr15324

• Primary Identifier: Expr1152237
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2028111
• 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: Chronogram1381
• Remark: Original chronogram file: chronogram.2624.xml
• Reporter Gene: [F55B12.1:gfp] transcriptional fusion.

• Primary Identifier: Chronogram1382
• Remark: Original chronogram file: chronogram.2625.xml
• Reporter Gene: [F55B12.1:gfp] transcriptional fusion.

• Primary Identifier: Expr1026957
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1170045
• 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: Expr1441
• Pattern: ceh-24 transcripts were first detected approximately 400 minutes after the first cell cleavage, and were seen in ventral head neurons. RNA transcripts could be detected in these cells until hatching. Authors did not obtain reproducible permeabilization of differentiated pharyngeal or vulval muscles.

13 GO Annotation

22 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000447
• Start: 13813231
• End: 13815350
• Strand: 1

13 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2120

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00030580
• WBStrain00030582
• WBStrain00030581
• WBStrain00048954
• WBStrain00051837
• WBStrain00008317

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_13811824..13813230
• Length (nt): 1407
• Chromosome Location: V: 13811824-13813230
• Organism: Caenorhabditis elegans