WormMine: Gene WBGene00000914

• WormBase Gene ID: WBGene00000914
• Gene Name: daf-19
• Sequence Name: F33H1.1
• Brief Description: daf-19 is the sole C. elegans member of the RFX family of transcriptionfactors, and is required for sensory neuron cilium formation; DAF-19 isexpressed in ciliated sensory neurons during the period that their ciliaare generated, and probably functions as an common transcriptionalactivator of many genes that specifically encode cilial structures insensory neurons; daf-19 mutants lack sensory cilia, have abnormal amphids,are strongly dauer-constutive, lack normal openings of the amphids to theexternal environment (i.e., fail to show dye-filling), and are highlydefective in their ability to taste or smell; DAF-19 regulates bbs-5,che-2, che-13, dyf-3, osm-1, osm-6, and xbx-1 expression, and probablyregulates ~200 other genes (e.g., bbs-2, bbs-7 and bbs-8); thelocalization of DAF-6 is aberrant in daf-19 mutants.
• 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. Involved in several processes, including defense response to Gram-negative bacterium; male mating behavior; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within serotonin biosynthetic process. Located in nucleus. Expressed in several structures, including body wall musculature; excretory cell; intestine; neurons; and somatic nervous system. Is an ortholog of human RFX3 (regulatory factor X3).
• Biotype: SO:0001217
• Genetic Position: II :2.15653 ±0.013324
• Length (nt): 11827

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000914

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F33H1.1d.1	F33H1.1d.1	2493	II: 10157520-10164452
Transcript:F33H1.1b.1	F33H1.1b.1	2874	II: 10157521-10169345
Transcript:F33H1.1a.1	F33H1.1a.1	2799	II: 10157522-10169346
Transcript:F33H1.1c.1	F33H1.1c.1	2035	II: 10157953-10161673
Transcript:F33H1.1e.1	F33H1.1e.1	1917	II: 10157953-10163576

Other

5 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F33H1.1a	F33H1.1a	2343	II: 10157953-10158087
CDS:F33H1.1c	F33H1.1c	1869	II: 10157953-10158087
CDS:F33H1.1e	F33H1.1e	1917	II: 10157953-10158087
CDS:F33H1.1b	F33H1.1b	2418	II: 10157953-10158087
CDS:F33H1.1d	F33H1.1d	1986	II: 10157953-10158087

7 RNAi Result

• WBRNAi00046226
• WBRNAi00063121
• WBRNAi00014256
• WBRNAi00092895
• WBRNAi00102068
• WBRNAi00115749
• WBRNAi00115748

192 Allele

• gk963801
• gk963053
• otn10886
• gk962682
• rh1024
• sa190
• sa232
• WBVar02068174
• WBVar01604571
• h7187
• h10066
• n4132
• m86
• tm5562
• WBVar01559668
• ttTI36198
• WBVar01394031
• WBVar01394032
• WBVar01243741
• WBVar01405534
• WBVar01243745
• WBVar01895148
• WBVar01895149
• WBVar01253528
• WBVar01895146
• gk942124
• WBVar01895147
• WBVar00174938
• sm129
• m336

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000914
• Start: 10157520
• End: 10169346
• 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_chrII_10156223..10157519
• Length (nt): 1297
• Chromosome Location: II: 10156223-10157519
• Organism: Caenorhabditis elegans

200 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
	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
	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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	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 expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_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
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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 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
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa 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:ASE_parent
	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 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 sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	Transcripts that showed significantly increased expression in isp-1(qm150) 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:isp-1(qm150)_upregulated
	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:dopaminergic-neurons_L3-L4-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

17 Expression Patterns

• Primary Identifier: Expr1030575
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr10789
• Pattern: daf-19 is expressed broadly in neurons but also in the intestine

• Primary Identifier: Expr9767
• Pattern: GFP expression was first seen in embryos and persists throughout all stages, in many neurons and potentially other cells in the head, both inside and outside of the pharynx. GFP was also observed in the pharyngeal-intestinal valve and possibly head muscle. The expression pattern includes components seen in UL3399 and UL3833 (transgenic for reporter gene fusions with gfp inserted immediately after the daf-19c and daf-19d start codons, respectively) but with additional components. Several tail cells, possibly neurons, and occasionally ventral cord nerve cells, body wall muscle and hypodermis show GFP expression.

• Primary Identifier: Expr8518
• Remark: Authors stained gfp reporter lines, which mark subgroups of neurons, with anti-GFP and with AbDAF19N antibodies to determine whether they label the same neurons. For example, ceh-23::gfp is expressed in many ciliated sensory neurons and the nonciliated neurons AIY and CAN. DAF-19A/B were detected in AIY and CAN but not in ciliated sensory neurons. Similarly, the nonciliated neurons marked with nmr-1::gfp stained with AbDAF-19N and therefore express DAF-19A/B. Picture: Figure 3.
• Pattern: DAF-19A/B were expressed only in nonciliated neurons and not in ciliated sensory neurons. In summary, DAF-19A/B are expressed in 200 to 240 nonciliated neurons.

• Primary Identifier: Expr7537
• Remark: Clone: pUL#JRH6E8
• Pattern: The expression in early and comma stage embryos is mostly anterior and ventral. From late embryo to adult, expression is seen in many tissues but most strongly in the pharynx and muscles of the body wall, head, rectum and vulva. Other tissues showing expression include the intestine, excretory cell, seam cells, dorsal and ventral nerve cord and other nerves in the head.

• Primary Identifier: Expr8517
• Remark: Picture: Supplemental Figure 2F.
• Pattern: The expression was restricted to a small set of neurons in the head and the tail, a pattern reminiscent of ciliated sensory neurons. In summary, DAF-19C is expressed in 60 ciliated sensory neurons.

• Primary Identifier: Expr1150114
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1075
• Pattern: Expressed in all ciliated sensory neurons. GFP expression began around the 2-fold stage of embryogenesis, continued at high levels through the L1 and L2 larval stages, and then weakened or was absent. In occasional animals that expressed GFP at higher levels than regularly observed, expression was noticed in a few additional neurons as well as hypodermal and intestinal cells.
• Subcellular Localization: Expression was seen in a pattern of nuclei consistent with those of all ciliated sensory neurons.

• Primary Identifier: Expr9796
• Pattern: GFP was observed in nuclei of a few neurons in the head, probably in the nerve ring, and 1 or 2 neurons in the tail. The GFP expression was only seen in the L1 and was extremely faint, much weaker than seen in strains, such as UL3509 or UL3404, transgenic for reporter gene fusions with gfp inserted immediately after the daf-19a/b or daf-19c start codon.

• Primary Identifier: Expr9783
• Pattern: No GFP expression was observed.

• Primary Identifier: Expr9747
• Pattern: GFP expression was observed in all stages in approximately 5 neurons, probably sensory neurons, slightly posterior of the anterior pharyngeal bulb, and many neurons in the nerve ring. Some GFP was seen in the processes of the sensory neurons whereas in nerve cells in the nerve ring, the GFP appeared more nuclear-localized. No expression was observed in the tail.

• Primary Identifier: Expr9270
• Pattern: In hermaphrodites, P4daf-19m::GFP is expressed in IL2 neurons. In the male, P4daf- 19m::GFP is expressed in IL2 and CEM head neurons, and HOB and RnB tail neurons. The 22-bp sequence acts remotely as a daf-19m CEM/IL2 element. In core IL2s, P4daf-19m::GFP is expressed throughout development in males and hermaphrodites. In male-specific CEMs, P4daf-19m::GFP expression commences in the mid to late L4 male, a stage that coincides with pkd-2 expression and the onset of sexual maturity.

• Primary Identifier: Expr9269
• Pattern: P1daf-19m::GFP is specifically expressed in the male tail HOB and RnB neurons but not in male-specific CEM head neurons or other ciliated neurons.
• Subcellular Localization: DAF-19M is nuclear localized.

• Primary Identifier: Expr2010767
• 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: Expr1013986
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029004
• 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: Expr1200378
• Pattern: Data from the TransgeneOme project

17 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000914
• Start: 10157520
• End: 10169346
• Strand: -1

17 Ontology Annotations

10 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at L1 larva stage.	BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).	WBPaper00053550:daf-19(m86)_downregulated_L1
	Genes that showed significantly increased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 3-fold embryo stage.	BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).	WBPaper00053550:daf-19(m86)_upregulated_3-fold-embryo
	Candidate daf-19 up regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a class comparisons tool from BRB Array Tools.	BRB Array Tools (version 3.3) was subsequently used to identify genes with a statistically significant variation in expression when comparing between the two classes defined in this study. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically different. Genes with a signal variation of 1.5-fold or greater were selectively identified for use in all subsequent experiments. To reduce the chances of false discoveries, a class comparison test was conducted using a multivariate permutation test with the confidence level of 97%.	WBPaper00039866:ClassComp_daf-19_upregulated
	Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 2-day post-L4 adult hermaphrodite stage.	BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).	WBPaper00053550:daf-19(m86)_downregulated_AdultDay2
	Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a class comparisons tool from BRB Array Tools.	BRB Array Tools (version 3.3) was subsequently used to identify genes with a statistically significant variation in expression when comparing between the two classes defined in this study. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically different. Genes with a signal variation of 1.5-fold or greater were selectively identified for use in all subsequent experiments. To reduce the chances of false discoveries, a class comparison test was conducted using a multivariate permutation test with the confidence level of 97%.	WBPaper00039866:ClassComp_daf-19_downregulated
	Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 3-fold embryo stage.	BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).	WBPaper00053550:daf-19(m86)_downregulated_3-fold-embryo
	Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM).	Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison.	WBPaper00039866:SAM_daf-19_downregulated
	Genes that showed significantly increased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 2-day post-L4 adult hermaphrodite stage.	BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).	WBPaper00053550:daf-19(m86)_upregulated_AdultDay2
	Genes that showed significantly increased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at L1 larva stage.	BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).	WBPaper00053550:daf-19(m86)_upregulated_L1
	Candidate daf-19 up regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM).	Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison.	WBPaper00039866:SAM_daf-19_upregulated

1 Sequence

• Length: 11827

1 Sequence Ontology Term

• Name: gene

10 Strains

• WBStrain00022829
• WBStrain00029254
• WBStrain00029253
• WBStrain00029252
• WBStrain00051991
• WBStrain00052538
• WBStrain00006259
• WBStrain00006178
• WBStrain00006383
• WBStrain00006236

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_10169347..10171267
• Length (nt): 1921
• Chromosome Location: II: 10169347-10171267
• Organism: Caenorhabditis elegans