WormMine: Gene WBGene00003675

• WormBase Gene ID: WBGene00003675
• Gene Name: nhr-85
• Sequence Name: W05B5.3
• Brief Description: nhr-85 encodes a nuclear receptor of the NR1 subfamily that is orthologous to the insect E75 nuclear receptors that regulate molting and metamorphosis, and human NR1D1, which is involved in mammalian circadian rhythms; by homology, NHR-85 likely functions as a transcription factor that,based upon RNAi experiments, is required for development of the egg-laying system and formation of SDS-resistant dauer larvae; an nhr-85 reporter fusion is expressed in the hypodermis, the excretory and rectal epithelia, and the vulva; nhr-85 mRNA is expressed in an oscillating manner throughout larval development, in a pattern that is slightly irregular with respect to the timing of larval molts.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and nuclear receptor activity. Predicted to be involved in cell differentiation; hormone-mediated signaling pathway; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Expressed in excretory duct cell; hypodermis; vulva; and vulval precursor cell. Human ortholog(s) of this gene implicated in several diseases, including alcoholic liver cirrhosis; brain small vessel disease; and type 2 diabetes mellitus. Is an ortholog of human NR1D1 (nuclear receptor subfamily 1 group D member 1) and NR1D2 (nuclear receptor subfamily 1 group D member 2).
• Biotype: SO:0001217
• Genetic Position: I :17.1507 ±0.010426
• Length (nt): 6922

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003675

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W05B5.3a.1	W05B5.3a.1	2516	I: 13055201-13062122
Transcript:W05B5.3b.1	W05B5.3b.1	1325	I: 13056091-13059625

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W05B5.3a	W05B5.3a	1545	I: 13056151-13056462
CDS:W05B5.3b	W05B5.3b	1011	I: 13056151-13056462

9 RNAi Result

• WBRNAi00054818
• WBRNAi00072233
• WBRNAi00063691
• WBRNAi00004432
• WBRNAi00004567
• WBRNAi00036299
• WBRNAi00063672
• WBRNAi00063673
• WBRNAi00063681

256 Allele

• gk963849
• gk964175
• otn10735
• h9683
• WBVar02120914
• WBVar02120442
• gk963138
• WBVar02123874
• tm11184
• WBVar01434159
• WBVar01434160
• WBVar01434161
• WBVar01434166
• WBVar01434167
• WBVar01434168
• WBVar01434169
• WBVar01434162
• WBVar01434163
• WBVar01434164
• WBVar01434165
• WBVar01434170
• WBVar01434171
• gk126280
• gk126279
• gk126282
• gk126281
• gk126276
• gk126275
• gk126278
• gk126277

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003675
• Start: 13055201
• End: 13062122
• 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

139 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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
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 that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_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 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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Coexpression clique No. 60, 176662_at-Y53F4B.16, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:176662_at-Y53F4B.16
	Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_upregulated
	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 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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_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 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 increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_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 animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:oocyte_vs_mitosis_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
	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:A-class-motor-neurons_L2-larva_expressed
	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

9 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: Expr1031706
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1019249
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr16423
• Pattern: We were able to reproduce the NHR-85::GFP peak in expression in vulval precursor cells from L4.0 to L4.9. We also observed the reported expression in hypodermal cells as well as in seam cells. Interestingly, we did not observe NHR-85::GFP expression in the L4 or adult germline.

• Primary Identifier: Expr2864
• Remark: Reporter gene fusion type not specified.
• Pattern: The nhr-85DGFP reporter is expressed in the developing vulva, the hypodermis, and specialized epithelia of the rectum and excretory duct.

• Primary Identifier: Expr1158359
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr16425
• Subcellular Localization: NHR-85::GFP expression is nuclear and excluded from nucleoli.

• Primary Identifier: Expr2014236
• 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: Expr2032477
• 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).

16 GO Annotation

42 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003675
• Start: 13055201
• End: 13062122
• Strand: -1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6922

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00032354

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_13062123..13066623
• Length (nt): 4501
• Chromosome Location: I: 13062123-13066623
• Organism: Caenorhabditis elegans