WormMine: Gene WBGene00004804

• WormBase Gene ID: WBGene00004804
• Gene Name: skn-1
• Sequence Name: T19E7.2
• Brief Description: skn-1 encodes a bZip transcription factor orthologous to the mammalian Nrf (Nuclear factor-erythroid-related factor) transcription factors; during early embryogenesis, maternally provided SKN-1 is required for specification of the EMS blastomere, a mesendodermal precursor that gives rise to pharyngeal, muscle, and intestinal cells; later, during postembryonic development, SKN-1 functions in the p38 MAPK pathway to regulate the oxidative stress response and in parallel to DAF-16/FOXO in the DAF-2-mediated insulin/IGF-1-like signaling pathway to regulate adult lifespan; in vitro assays indicate that SKN-1 can be directly phosphorylated by the AKT-1, AKT-2, and SGK-1 kinases that lie downstream of DAF-2 in the insulin signaling pathway and in vivo experiments suggest that this phosphorylation is essential for regulation of SKN-1 nuclear accumulation and hence, transcriptional regulator activity; in the early embryo, SKN-1 is detected at highest levels in nuclei of the P1 blastomere and its descendants through the 8-cell stage of embryogenesis; later in embryogenesis, SKN-1 is observed in all hypodermal and intestinal nuclei, with reporter constructs indicating that intestinal expression begins as early as the 50-100-cell stage; in larvae and young adults, SKN-1::GFP reporters are expressed in the intestine and ASI neurons, with expression in intestinal nuclei enhanced under conditions of stress or reduced DAF-2 signaling.
• Organism: Caenorhabditis elegans
• Automated Description: Enables Hsp70 protein binding activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including endoderm development; positive regulation of macromolecule biosynthetic process; and response to stress. Located in endoplasmic reticulum; mitochondrion; and nucleus. Expressed in several structures, including germ line; head ganglion; intestine; neurons; and pharynx. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; liver disease (multiple); obesity; and pulmonary emphysema. Is an ortholog of several human genes including NFE2 (nuclear factor, erythroid 2); NFE2L1 (NFE2 like bZIP transcription factor 1); and NFE2L2 (NFE2 like bZIP transcription factor 2).
• Biotype: SO:0001217
• Genetic Position: IV :2.04386 ±0.029993
• Length (nt): 9346

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004804

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T19E7.2a.1	T19E7.2a.1	2597	IV: 5651039-5660384
Transcript:T19E7.2b.1	T19E7.2b.1	1746	IV: 5651085-5653229
Transcript:T19E7.2d.1	T19E7.2d.1	672	IV: 5651764-5652640
Transcript:T19E7.2c.1	T19E7.2c.1	1602	IV: 5651764-5655605

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T19E7.2d	T19E7.2d	672	IV: 5651764-5651840
CDS:T19E7.2c	T19E7.2c	1602	IV: 5651764-5651840
CDS:T19E7.2a	T19E7.2a	1872	IV: 5651764-5651840
CDS:T19E7.2b	T19E7.2b	933	IV: 5651764-5651840

224 RNAi Result

• WBRNAi00083473
• WBRNAi00083476
• WBRNAi00116227
• WBRNAi00081483
• WBRNAi00084933
• WBRNAi00084939
• WBRNAi00106569
• WBRNAi00106597
• WBRNAi00103038
• WBRNAi00103039
• WBRNAi00113266
• WBRNAi00098226
• WBRNAi00092400
• WBRNAi00067030
• WBRNAi00000466
• WBRNAi00002252
• WBRNAi00053554
• WBRNAi00053555
• WBRNAi00084470
• WBRNAi00059893
• WBRNAi00059894
• WBRNAi00089440
• WBRNAi00089442
• WBRNAi00089444
• WBRNAi00089446
• WBRNAi00072648
• WBRNAi00073616
• WBRNAi00073619
• WBRNAi00102824
• WBRNAi00102825

161 Allele

• gk964500
• gk963722
• gk963417
• gk963150
• gk963375
• gk963416
• tm12203
• WBVar02121205
• WBVar02122599
• WBVar00189064
• WBVar00189065
• WBVar00189066
• gk480996
• gk439627
• gk657962
• gk791387
• gk372481
• gk425185
• gk357342
• gk351127
• gk551726
• gk517430
• gk398719
• gk688118
• gk410281
• gk683993
• gk545366
• gk408410
• gk651862
• gk617854

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004804
• Start: 5651039
• End: 5660384
• 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

138 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
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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
	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) and age at old adults stage (214 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_aging
	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 old adults stage (214 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_regulated_aging
	Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_developing
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in nuo-6(qm200) 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:nuo-6(qm200)_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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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)
	Transcripts that showed significantly decreased expression after exposure of to 10 mg per liter of SiNPs for 24 h.	Fold change and Welcht-test performed between probes per gene and were applied to selectdifferentially expressed genes (DEGs): the fold change threshold was 2-fold and the significance level was p < 0.05.	WBPaper00057098:SiO2-nanoparticles_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
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_TilingArray
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:sin-3(tm1276)_upregulated

21 Expression Patterns

• Primary Identifier: Expr2034064
• 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: Expr11548
• Pattern: Expressed in head neurons, pharynx.

• Primary Identifier: Expr572
• Remark: early embryo(author) = blastula embryo(curator).
• Pattern: SKN-1 protein first becomes visible in oocyte and sperm pronuclei before the first mitotic division of the zygote. SKN-1 becomes cytoplasmic as AB and P1 enter mitosis. P2 and EMS have more SKN-1 than AB daughters. By the 8-cell stage, the granddaughters of AB do not stain for SKN-1, but P1 granddaughters do. SKN-1 is not detectable by the 12-cell stage.
• Subcellular Localization: After the first cleavage, SKN-1 protein locates at the nuclei of AB and P1. As AB and P1 enter mitosis, SKN-1 protein is distributed throughout cytoplasm.

• Primary Identifier: Expr15938
• Pattern: SKN-1B::GFP is expressed in ASI neurons. DiI staining confirms SKN- 1B::GFP in the ASI neurons and identified two of these additional neurons as being the ADLs.

• Primary Identifier: Expr2646
• Remark: Gene_regulation: A promoter fusion transgene in which only the SKN-1 N terminus was linked to GFP (SknPro GFP) was constitutively expressed at high levels in all intestinal cells, suggesting that SKN-1 expression or localization might also be regulated posttranscriptionally by oxidative stress. Gene_regulation: After exposure to either paraquat or heat, neither the location nor intensity of SKN-1 GFP was detectably altered in the ASI neurons, but in a high percentage of animals, elevated levels of SKN-1 GFP appeared in intestinal cell nuclei, particularly anteriorly and posteriorly, where GCS-1 GFP is most robustly expressed. SKN-1 GFP accumulated in intestinal nuclei within 5 min after treatment with 50 mM sodium azide, which induces oxidative stress by blocking mitochondrial electron transport.
• Reporter Gene: [skn-1::gfp] translational fusion. skn-1 gfp promoter fusion construct (SknPro GFP) was created by ligating GFP vector pPD95.67 and a PCR-amplified 2.1-kb clone containing the promoter region and 38 amino acids from the first ATG codon of the skn-1 gene from cosmid T19E7. To generate the SKN-1 GFP translational fusion construct, the 5.7-kb EcoRI DNA fragment that rescues the maternal skn-1 phenotype and encodes the 533-amino-acid SKN-1 protein was amplified from cosmid B0547. A ClaI site was created immediately 3' to the SKN-1 C terminus by the QuikChange method (Stratagene), which was used for all site-directed mutagenesis. This EcoRI fragment was subcloned into pUC18, which contained the upstream 1.3-kb SphIEcoRI fragment from SknPro GFP. A 0.8-kb ClaI fragment that contained the GFP open reading frame (amplified from plasmid pPD114.35) was then cloned into the ClaI site to generate an in-frame exon fusion of GFP to the SKN-1 C terminus.
• Pattern: In larvae and young adults, SKN-1 GFP was usually present at very low levels in intestinal nuclei. SKN-1 GFP was readily detectable in the ASI neurons, but not in other cells in the head. In late-stage embryos, SKN-1 GFP was also present in intestinal nuclei but not in the hypodermis. Nuclear SKN-1 GFP was uniformly detected in intestinal precursors beginning at the 50100-cell stage, then in both the intestine and hypodermis.
• Subcellular Localization: nuclei

• Primary Identifier: Expr12625
• Remark: The authors used RNA interference (RNAi) feeding clones corresponding to the unique 5' end of either skn-1b or skn-1c to knock down each isoform separately in GFP reporter strains, and determined that skn-1b is expressed in the ASI neurons but not detectably in the gut, and skn-1c is expressed in the gut but not detectably in the ASI neurons.
• Pattern: skn-1b is expressed in the ASI neurons but not detectably in the gut.

• Primary Identifier: Expr15874
• Pattern: The translational fusion protein expressed by skn-1::GFP is expressed in the ASI neurons and the intestine.

• Primary Identifier: Expr13359
• Pattern: skn-1::EGFP is highly expressed in neurons in the lateral, ventral and dorsal ganglia, and to a lesser extent in the anterior ganglia. Furthermore, skn-1::EGFP clearly colocalizes with the specific AIY marker ttx-3::RFP, confirming that skn-1 is indeed expressed in AIY interneurons.

• Primary Identifier: Expr1032384
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr561
• Remark: This maternal RNA was absent from somatic cells at the 28-cell stage. Subsequent somatic accumulation is presumably due to embryonic transcription.
• Pattern: At 1 to 28-cell stage, staining was maintained in germ line and progressively lost from somatic cells. At comma through pretzel stage, the gut stained.

• Primary Identifier: Expr12626
• Remark: The authors used RNA interference (RNAi) feeding clones corresponding to the unique 5' end of either skn-1b or skn-1c to knock down each isoform separately in GFP reporter strains, and determined that skn-1b is expressed in the ASI neurons but not detectably in the gut, and skn-1c is expressed in the gut but not detectably in the ASI neurons.
• Pattern: skn-1c is expressed in the gut but not detectably in the ASI neurons.

• Primary Identifier: Expr12666
• Pattern: SKN-1A is expressed in the intestine.

• Primary Identifier: Expr1200037
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr699
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Staining is first detected after fertilization in both the oocyte and sperm pronuclei shortly before the first mitotic division. After the first cleavage, the nuclei of both AB and P1 blastomeres appear to contain equivalent levels of the protein. During the first embryonic cell cycle, the protein appears to accumulate to much higher levels in the nucleus of P1 than in the AB nucleus. As AB and P1 enter mitosis, the protein is distributed throughout the cytoplasm. After the nuclei of the AB daughters re-form, both appear to have equivalent levels of the protein and similarly with the P1 daughters but at a much higher level.. During the second cell cycle the level of the protein increases in the nuclei of both P1 daughters. Late in the cell cycle the level of protein begins to decrease in both P1 daughters and in both AB daughters and in many embryos the two AB daughters have no detectable protein. After the third cleavage (8-cell stage), there is no detectable protein in any of the AB granddaughters but staining is detected throughout the P1 granddaughters. By the 12-cell stage, there is no staining in any blastomere. Peak levels of SKN-1 detected at 4-cell stage in EMS and P2. Little or no expression are detected in ABa and ABp.

• Primary Identifier: Expr1200113
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr11497
• Pattern: In animals expressing the skn-1a construct, fluorescence was observed in many tissues, as previously reported, as well as in cholinergic neurons of the ventral cord and GABAergic neurons.

• Primary Identifier: Expr9129
• Remark: No specific staining was observed in primary DA neurons or other cells from animals in which skn-1 mRNA levels were reduced using RNAi. Furthermore, SKN-1-associated DA neuron immunoreactivity was not observed following co-incubation of the cultures with the SKN-1 antibody and the complementary antigenic peptide, providing further proof that the antibody is binding to the SKN-1 protein in the DA neurons. Taken together, these results indicate that SKN-1 is expressed in DA neurons, and that a reduction in the transcription factor mRNA levels by RNAi results in a significant loss of SKN-1 immunoreactive protein expression in the DAergic cells. Picture: Fig 5, Fig S2.
• Pattern: SKN-1 immunoreactivity is observed in all dopaminergic (DA) neurons.

• Primary Identifier: Expr2015831
• 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: Expr1157117
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1016708
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr14853
• Subcellular Localization: Each form of SKN-1 is expressed at approximately similar levels and is nuclear-localized.

63 GO Annotation

18 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004804
• Start: 5651039
• End: 5660384
• Strand: -1

63 Ontology Annotations

13 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in skn-1(lax188) gain of function comparing to in N2 at day 2 adult stage.	fold change > 2	WBPaper00058711:skn-1(lax188)_downregulated
	Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in skn-1(RNAi) animals comparing to vector controls, after both were exposed to 300mM NaCl for 24 hours.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:down_by_skn-1(RNAi)_at_24h-NaCl
	Transcripts that showed significantly decreased expression in skn-1(RNAi) animals comparing to in control animals.	Using the Cufflink package and CuffDiff application from Galaxy, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated and tested for differential expression with a FDR score of 5%.	WBPaper00050332:skn-1(RNAi)_downregulated
	Transcriptions that showed significantly decreased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_downregulated
	Transcripts that showed significantly increased expression in skn-1(lax188) gain of function comparing to in N2 at day 2 adult stage.	fold change > 2	WBPaper00058711:skn-1(lax188)_upregulated
	Transcripts that showed significantly decreased expression in skn-1(RNAi);dpy-7(e88) animals comparing to dpy-7(e88) vector controls.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:down_by_skn-1(RNAi)_at_dpy-7(e88)
	Genes with >0.67 fold decreased expression in skn-1(RNAi) animals comparing to in N2 control at 25 centigrade. fold change = N2 + skn-1 RNAi vs. N2 + vector.	Fold change > 4.0 for glp-1(ts) regulated genes, and fold change < 0.67 for skn-1(RNAi) regulated genes.	WBPaper00047132:skn-1(RNAi)_downregulated
	Genes with < 0.67 fold decreased expression in skn-1(RNAi) animals comparing to in N2 control at 25 centigrade. Fold change = glp-1(ts) + skn-1 RNAi vs. glp-1(ts) + vector	Fold change > 4.0 for glp-1(ts) regulated genes, and fold change < 0.67 for skn-1(RNAi) regulated genes.	WBPaper00047132:skn-1(RNAi)_downregulated_glp-1(ts)-dependent
	Transcripts that showed significantly altered expression in skn-1gf(lax188) comparing to in WT animals in ASI neuron.	DESeq2, p-value < 0.05.	WBPaper00066256:skn-1gf(lax188)_regulated
	Transcripts that showed significantly decreased expression in skn-1(RNAi) animals comparing to vector controls, after both were exposed to 300mM NaCl for 3 hours.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:down_by_skn-1(RNAi)_at_3h-NaCl
	Genes with >4.0 fold increased expression in glp-1(ts) animals comparing to in N2 control at 25 centigrade, and the change was dependent on skn-1(RNAi). fold change FC1 > 4.0 for glp-1(ts) + vector vs. N2 + vector; fold change FC2 < 0.67 for glp-1(ts) + skn-1 RNAi vs. glp-1(ts) + vector	Fold change > 4.0 for glp-1(ts) regulated genes, and fold change < 0.67 for skn-1(RNAi) regulated genes.	WBPaper00047132:glp-1(ts)-25C_upregulated_skn-1-dependent
	Transcripts that showed significantly decreased expression in skn-1(RNAi) animals comparing to vector controls.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:down_by_skn-1(RNAi)

1 Sequence

• Length: 9346

1 Sequence Ontology Term

• Name: gene

28 Strains

• WBStrain00022470
• WBStrain00024180
• WBStrain00024183
• WBStrain00024182
• WBStrain00024188
• WBStrain00024186
• WBStrain00024125
• WBStrain00024124
• WBStrain00031273
• WBStrain00031272
• WBStrain00034419
• WBStrain00034420
• WBStrain00036863
• WBStrain00043864
• WBStrain00051964
• WBStrain00005860
• WBStrain00007250
• WBStrain00007253
• WBStrain00007254
• WBStrain00007251
• WBStrain00007252
• WBStrain00007255
• WBStrain00007966
• WBStrain00005115
• WBStrain00007257
• WBStrain00007258
• WBStrain00005061
• WBStrain00007249

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_5660385..5661140
• Length (nt): 756
• Chromosome Location: IV: 5660385-5661140
• Organism: Caenorhabditis elegans