WormMine: Gene WBGene00003622

• WormBase Gene ID: WBGene00003622
• Gene Name: nhr-23
• Sequence Name: C01H6.5
• Brief Description: The nhr-23 gene encodes a nuclear hormone receptor homolog that is required in all larval molts; NHR-23 is highly similar to Drosophila DHR3, an ecdysone-inducible gene product involved in metamorphosis; NHR-23 is required for hypodermal expression of acn-1 and, probably, of dpy-7.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including defense response to Gram-negative bacterium; positive regulation of transcription by RNA polymerase II; and spermatogenesis. Located in nucleus. Part of chromatin. Expressed in several structures, including gonad; hypodermis; oocyte; spermatocyte; and vulval precursor cell. Human ortholog(s) of this gene implicated in idiopathic generalized epilepsy 15 and immunodeficiency 42. Is an ortholog of human RORA (RAR related orphan receptor A); RORB (RAR related orphan receptor B); and RORC (RAR related orphan receptor C).
• Biotype: SO:0001217
• Genetic Position: I :1.84212 ±0.002193
• Length (nt): 6555

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003622

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C01H6.5c.1	C01H6.5c.1	1635	I: 7214745-7221051
Transcript:C01H6.5d.1	C01H6.5d.1	1320	I: 7214967-7220952
Transcript:C01H6.5a.1	C01H6.5a.1	2221	I: 7216784-7221228
Transcript:C01H6.5b.1	C01H6.5b.1	2046	I: 7218786-7221299
Transcript:C01H6.5f.1	C01H6.5f.1	1668	I: 7218823-7220952
Transcript:C01H6.5e.1	C01H6.5e.1	1307	I: 7219318-7220952

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C01H6.5a	C01H6.5a	1767	I: 7216962-7217029
CDS:C01H6.5f	C01H6.5f	1668	I: 7218823-7219177
CDS:C01H6.5b	C01H6.5b	1662	I: 7218823-7219177
CDS:C01H6.5c	C01H6.5c	1314	I: 7214967-7214973
CDS:C01H6.5d	C01H6.5d	1320	I: 7214967-7214973
CDS:C01H6.5e	C01H6.5e	1086	I: 7219631-7219696

64 RNAi Result

• WBRNAi00095482
• WBRNAi00000910
• WBRNAi00002886
• WBRNAi00024444
• WBRNAi00098821
• WBRNAi00084420
• WBRNAi00090757
• WBRNAi00005010
• WBRNAi00027657
• WBRNAi00024445
• WBRNAi00066767
• WBRNAi00039373
• WBRNAi00064887
• WBRNAi00087726
• WBRNAi00111079
• WBRNAi00115755
• WBRNAi00111615
• WBRNAi00107568
• WBRNAi00075403
• WBRNAi00075415
• WBRNAi00075414
• WBRNAi00062004
• WBRNAi00062005
• WBRNAi00117166
• WBRNAi00106466
• WBRNAi00111078
• WBRNAi00098831
• WBRNAi00098830
• WBRNAi00106470
• WBRNAi00106474

79 Allele

• gk962858
• gk962706
• gk963902
• WBVar01432058
• WBVar01432057
• WBVar01432056
• WBVar01432054
• WBVar02069197
• otn91
• otn90
• WBVar01826409
• gk788380
• gk634607
• gk828181
• h3225
• gk585609
• h16094
• gk350938
• h8068
• gk857292
• WBVar01909747
• WBVar01909748
• gk362167
• gk435630
• gk606144
• gk529051
• gk334469
• gk928112
• WBVar01832208
• gk561007

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003622
• Start: 7214745
• End: 7221299
• 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_chrI_7221300..7222290
• Length (nt): 991
• Chromosome Location: I: 7221300-7222290
• Organism: Caenorhabditis elegans

150 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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
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
	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 day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_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 infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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 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
	Top 300 transcripts enriched in excretory duct, excretory pore according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:Excretory_duct_and_pore
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	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 daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Transcripts that showed significantly increased expression in mbl-1(syb4318), referred to as mbl-1short(ex7-), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4318)_upregulated
	Transcripts that showed significantly increased expression in mbl-1(syb4345), referred to as mbl-1long(ex7+), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4345)_upregulated
	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
	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 increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_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 significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased 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_downregulated_hpx-2(dg047)
	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:hypodermis_L1-larva_expressed
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

22 Expression Patterns

• Primary Identifier: Expr2871
• Pattern: The mRNAs for lin-42, nhr-23, and nhr-41a exhibit a low-high (peak)-low profile during the L1 intermolt that is precisely reiterated at later stages. The mRNAs for nhr-25a, nhr-25b, and nhr-41b have a high-low-high (peak) expression profile during the L1 stage (and into early L2) that is also reiterated. nhr-25a and nhr-41b also show a downward trend in baseline expression as development proceeds. For all six mRNAs, there are peaks of expression that occur at precise intervals relative to the molt at all larval stages: nhr-25b and nhr-41b peak at the beginning of the intermolt; nhr-23 peaks at mid-intermolt, slightly preceding the intermolt peak in lin-42 expression; and nhr-25a and nhr-41a peak at the time the larval molts occur. Two mRNAs, nhr-6 and nhr-85a, show a more irregular expression pattern with respect to the molt; however, it should be noted that nhr-6 mRNA has consistent relatively lower expression values at the times the molt takes place. nhr-67 also does not display a reiterated, oscillating expression pattern, although two early peaks are observed at the end of the L1 stage and at the beginning of L2.

• Primary Identifier: Expr1031668
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1429
• Pattern: Epidermal expression of nhr-23 reporter genes can be achieved with as little as 600 bp of sequence upstream of exon I provided that intron I sequences are also included (construct #4281). However, this construct shows additional expression in nuclei of the pharynx and distal 4-6 nuclei of the intestine, two common sites of ectopic expression. Expression was completely eliminated by removing intron I (construct #4298) and only ectopic (pharynx and intestine) Expression was observed when mostly intron I sequences (construct #4282) were used to drive expression. Reporter gene constructs that begin at least 1.6 kb upstream of exon I and include all of intron I were consistently expressed in epidermal cells and their precursors. Expression in epidermal cells and precursors was clearly evident by the comma stage of embryogenesis and continued through larval stages. Construct #3306 showed the earliest expression, beginning at about the 50-cell stage in one or two unidentified nuclei. Based on the lineage of epidermal cells, it is possible that these early nuclei are Cpa and Caa; however, authors have been unable to confirm this independently.

• Primary Identifier: Expr9736
• Pattern: GFP expression was seen from embryo through to adulthood, in hypodermal and intestinal nuclei, as well as some head neurons. The first 3 images are of UL3202, while image 4 is of UL3201.

• Primary Identifier: Expr9760
• Pattern: GFP was seen, from embryo to adult, in hypodermal nuclei over the whole worm. GFP expression was stronger in the head and tail and GFP was observed occasionally in intestinal nuclei.

• Primary Identifier: Expr16424
• Pattern: We found a similar pulse of NHR-23::mScarlet in L4.3 vulval precursor cells as that reported by Kinney et al.. nhr-23::mScarlet was also detectable in seam and hypodermal cells at this stage, epithelial cells that synthesize cuticular components. NHR-23::mScarlet was detected in pachytene nuclei in L4 animals and its zone of expression became restricted in young adult animals. This expression pattern is again similar to NHR-23::GFP::AID*::3xFLAG (Ragle et al. 2020). However, we also observed some interesting differences compared to NHR-23::GFP::AID*::3xFLAG. In our previous work, we observed that NHR::23::GFP became undetectable in ovulating adults (Ragle et al. 2020). In contrast, NHR-23::mScarlet appears to be diffusely expressed in young adult residual bodies and spermatocytes. This diffuse expression persists into ovulating adults, and appears restricted to the spermatheca. The NHR-23::mScarlet signal is specific to nhr-23::mScarlet::3xMyc animals as no diffuse expression in the germline is observed in wild-type animals. One can observe the diffuse expression pattern in L4.5 germlines several rows of cells after NHR-23::mScarlet::3xMyc localization is lost from nuclei.

• Primary Identifier: Expr15791
• Pattern: NHR-23::GFP expression was observed in hypodermal and seam cells of developing larvae.

• Primary Identifier: Expr1200149
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr9749
• Pattern: GFP expression looks the same as for other nhr-23::gfp fusions of this series (see UL3202, UL3486 and UL3582), only much weaker. The hypodermal nuclear-localized GFP expression was apparent, but not the intestinal expression. Two more lines were generated and showed the same GFP expression pattern as UL3409, but were lost.

• Primary Identifier: Expr9781
• Pattern: The GFP expression in hypodermal nuclei over the whole worm, looks like that for the nhr-23::gfp fusion constructed in this series with gfp inserted before the stop codon (see UL3202), but probably lacking the intestinal expression component. The GFP expression was mostly very weak but slightly stronger than in UL3409 which had the fusion specifically to transcript nhr-23a.

• Primary Identifier: Expr15793
• Pattern: NHR-23::GFP somatic cell expression persisted in L4 larvae, specifically in hypodermal cells of the head, vulval precursor cells of hermaphrodites, and hypodermal and tail cells of males. Notably, NHR-23::GFP was also expressed in the sperm-producing germlines of males and L4 hermaphrodites, but not in hermaphrodites producing only oocytes. Previous studies missed this spermatocyte expression as transgenes are frequently silenced in the germline (Kelly et al., 1997) and immunolabeling was limited to embryos (Kostrouchova et al., 1998, 2001).

• Primary Identifier: Expr10509
• Pattern: Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/

• Primary Identifier: Expr1428
• Pattern: nhr-23 RNA is easily detectable in the germline and oocytes. nhr-23 RNA is also detected in 2- and 4-cell embryos but then becomes undetectable in subsequent stages of early embryogenesis. By the comma stage of embryogenesis, a faint in situ signal for nhr-23 appears on the surface of embryos, consistent with expression in the epidermis.

• Primary Identifier: Expr15792
• Pattern: NHR-23::GFP somatic cell expression persisted in L4 larvae, specifically in hypodermal cells of the head, vulval precursor cells of hermaphrodites, and hypodermal and tail cells of males. Notably, NHR-23::GFP was also expressed in the sperm-producing germlines of males and L4 hermaphrodites, but not in hermaphrodites producing only oocytes. Previous studies missed this spermatocyte expression as transgenes are frequently silenced in the germline (Kelly et al., 1997) and immunolabeling was limited to embryos (Kostrouchova et al., 1998, 2001).

• Primary Identifier: Expr15794
• Pattern: In males (and sperm-producing hermaphrodites), NHR-23::GFP was first observed in early pachytene spermatocytes, increased in intensity through late pachytene and became undetectable during late meiotic prophase with onset of chromatin condensation. NHR-23 was undetectable in meiotically dividing spermatocytes or mature spermatids.
• Subcellular Localization: NHR-23::GFP labeled most chromosomes along their entire length yet failed to label a region of DNA in each pachytene stage spermatocyte. Presumably NHR-23 is not labeling the X chromosome, which is transcriptionally silent during spermatocyte meiosis (Kelly et al., 2002).

• Primary Identifier: Expr15790
• Pattern: NHR-23::GFP expression was observed in epidermal cell nuclei of 1.5-stage embryos.

• Primary Identifier: Expr1023690
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1580
• Remark: C01H6.5 = CHR3 in this article.
• Pattern: CHR3 is most highly expressed in adult worms, although it can be seen in larval stages L3 and L4. The 2.7kb transcript was more highly expressed in the L3 stage while the 3.2 kb transcript showed much greater expression in adult worms.

• Primary Identifier: Expr1245
• Pattern: High level expression of CHR3(nhr-23) was observed in embryos and persisted in newly hatched larvae, then decreased to a minimum at 4-6 hours after synchronized-hatched L1 larvae were first fed, in the period preceding the first molt. Similarly, an elevation in nhr-23 expression was observed between successive molts, and minimal values were observed at each molt. nhr-23 transcript is present throughout development, with intermolt peaks reaching two to five times higher levels than the minimal values at the molts.

• Primary Identifier: Expr1143488
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2014139
• 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: Expr2032379
• 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).

24 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003622
• Start: 7214745
• End: 7221299
• Strand: 1

24 Ontology Annotations

5 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in nhr-23(kry61);spe-44(fx110) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:nhr-23(kry61);spe-44(fx110)_downregulated
	Transcripts that showed significantly increased expression in nhr-23(kry61);spe-44(fx110) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:nhr-23(kry61);spe-44(fx110)_upregulated
	Transcripts that showed significantly increased expression in nhr-23(kry61) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:nhr-23(kry61)_upregulated
	Genes that showed decreased expression in nhr-23 RNAi experiment.	Microarray chip data was collected and analyzed by both Affymetrix MAS 5.0 suite software (>= 1.6-fold change in mRNA expression) and Robust Multichip Average (RMA) (>= 1.2-fold change in mRNA expression) as part of the Partek genomics suite software package, all with a p-value less than or equal to 0.05. Normalized data was further analyzed and visualized with Genespring software (Agilent Technologies, Santa Clara, CA).	WBPaper00040185:nhr-23(RNAi)_downregulated
	Transcripts that showed significantly decreased expression in nhr-23(kry61) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:nhr-23(kry61)_downregulated

1 Sequence

• Length: 6555

1 Sequence Ontology Term