WormMine: Gene WBGene00002004

• WormBase Gene ID: WBGene00002004
• Gene Name: hsf-1
• Sequence Name: Y53C10A.12
• Brief Description: hsf-1 encodes the C. elegans heat-shock transcription factor ortholog; HSF-1 functions as a transcriptional regulator of stress-induced gene expression whose activity is required for heat-shock and proteotoxicity response, larval development, innate immunity, and regulation of adult lifespan; HSF-1 binds bovine calmodulin in vitro in a calcium-dependent manner.
• Organism: Caenorhabditis elegans
• Automated Description: Enables several functions, including calmodulin binding activity; identical protein binding activity; and promoter-specific chromatin binding activity. Involved in several processes, including ascaroside biosynthetic process; positive regulation of metabolic process; and response to stress. Located in cytoplasm; nuclear body; and nuclear stress granule. Part of chromatin. Expressed in several structures, including hypodermis; intestine; neurons; pharyngeal muscle cell; and somatic cell. Human ortholog(s) of this gene implicated in Huntington's disease and cataract 5 multiple types. Is an ortholog of human HSF1 (heat shock transcription factor 1) and HSF2 (heat shock transcription factor 2).
• Biotype: SO:0001217
• Genetic Position: I :13.0131 ±0.000976
• Length (nt): 9579

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002004

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y53C10A.12.2	Y53C10A.12.2	2478	I: 11953507-11963085
Transcript:Y53C10A.12.1	Y53C10A.12.1	2326	I: 11953509-11961984

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y53C10A.12	Y53C10A.12	2016	I: 11953797-11953889

117 RNAi Result

• WBRNAi00084937
• WBRNAi00084943
• WBRNAi00084555
• WBRNAi00070400
• WBRNAi00067333
• WBRNAi00067363
• WBRNAi00067553
• WBRNAi00067882
• WBRNAi00067999
• WBRNAi00057239
• WBRNAi00026806
• WBRNAi00026807
• WBRNAi00078327
• WBRNAi00063650
• WBRNAi00078303
• WBRNAi00068415
• WBRNAi00068417
• WBRNAi00068416
• WBRNAi00068418
• WBRNAi00068883
• WBRNAi00068884
• WBRNAi00004706
• WBRNAi00097032
• WBRNAi00076810
• WBRNAi00093191
• WBRNAi00093188
• WBRNAi00071065
• WBRNAi00093223
• WBRNAi00093220
• WBRNAi00093219

276 Allele

• gk962706
• gk963849
• gk962859
• gk964175
• h13384
• h12557
• gk963906
• gk506415
• gk506910
• gk685422
• gk327307
• gk436125
• gk933619
• gk900998
• gk473491
• gk365877
• gk834239
• gk341388
• gk567564
• gk395753
• gk931387
• gk890959
• gk324764
• gk861408
• gk324629
• gk625749
• gk852402
• gk384206
• gk500505
• gk780749

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002004
• Start: 11953507
• End: 11963085
• 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_11953155..11953506
• Length (nt): 352
• Chromosome Location: I: 11953155-11953506
• Organism: Caenorhabditis elegans

115 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
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_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
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	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 decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Transcripts that were regulated by both set-6(ok2195) and baz-2(tm0235) at 2-day post L4 adult hermaphrodite stage.	N.A.	WBPaper00059356:set-6(ok2195)_baz-2(tm0235)_regulated
	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 (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
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point on the non pathogenic strain Bt407 compared to E. coli OP50.	Cuffdiff	WBPaper00060358:B.thuringiensis_non-pathogen_regulated_elt-2(RNAi)
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 altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
	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)

13 Expression Patterns

• Primary Identifier: Expr1031169
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9596
• Pattern: The GFP fluorescence expressed under the con­trol of the hsf-1 promoter was detected in nearly all cells. Substantial fluorescence was detected in body wall muscles and intes­tine, whereas relatively dim expression was observed in neurons.

• Primary Identifier: Expr15900
• Pattern: HSF-1::GFP expression was observed in all cell types examined. In unstressed worms, HSF-1::GFP was predominantly localized diffusely in the nucleus and was visible in all cells examined including hypodermal cells, intestinal cells, pharyngeal muscle cells, amphid neurons, phasmid neurons, and germ cells. Interestingly, HSF-1::GFP was observed to form nuclear stress bodies throughout the germline including both the distal and proximal ends as well as the loop, even though the worms were not exposed to any external stressors.

• Primary Identifier: Expr9954
• Pattern: HSF-1-GFP was observed in intestinal cells, body wall muscle cells, and hypodermal cells, as well as many neurons in the head and tail.
• Subcellular Localization: The HSF-1-GFP is evenly distributed between the nucleus and cytoplasm before heat shock in intestinal cells. In response to 30 min of heat shock, an accumulation of HSF-1-GFP was observed in the intestinal nuclei.

• Primary Identifier: Expr13252
• Pattern: HSF-1::GFP is localized to the nuclei of all major somatic tissues in L2 and young adult animals.

• Primary Identifier: Expr2012610
• 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: Expr10595
• Subcellular Localization: Single copy HSF-1::GFP localized predominantly to the nucleus under basal conditions (20 C).

• Primary Identifier: Expr1017824
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr16169
• Pattern: Our results indicate that hsf-1 expression steadily declines during development as hsf-1 mRNA transcripts were most abundant during embryonic development (in eggs), less in L2, even less in L4 larvae, while the least amount of hsf-1 mRNA was detected in young adults.

• Primary Identifier: Expr16170
• Pattern: Our results showed that HSF-1 is more abundant in L2 larvae than in their L4 counterparts in both supernatant and pellets, indicating that not only hsf-1 expression level is elevated in L2 larval stage but also the amounts of HSF-1 protein.

• Primary Identifier: Expr2030846
• 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: Expr1160675
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr13567
• Subcellular Localization: Consistent with its essential role in development, C. elegans HSF-1, as detected by an antibody specific for endogenous C. elegans HSF-1 and by the localization of green fluorescent protein (GFP)-tagged HSF-1, is constitutively present in nuclei. Although we occasionally observed HSF-1 nuclear bodies in the vicinity of the nuclear pore complex (NPC) in germline nuclei, they did not colocalize with NPCs under any of our conditions.

56 GO Annotation

19 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002004
• Start: 11953507
• End: 11963085
• Strand: -1

56 Ontology Annotations

13 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in hsf-1(RNAi) animals comparing to in control animals, without heat shock.	Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).	WBPaper00049942:hsf-1(RNAi)_downregulated
	Transcripts that showed significantly increased expression in hsf-1(RNAi) animals comparing to in control animals, without heat shock.	Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).	WBPaper00049942:hsf-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in hsf-1(RNAi) comparing to in ash-2 animals injected with vector.	Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed.	WBPaper00066232:hsf-1(RNAi)_downregulated_ash-2
	Transcripts that showed significantly decreased expression in hsf-1(RNAi) comparing to in wild type animals injected with vector.	Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed.	WBPaper00066232:hsf-1(RNAi)_downregulated_WT
	Transcripts that showed significantly increased expression in strain AGD1289 with pan-neuronall expression of HSF-1, comparing to in N2 animals.	DESeq2 v1.22.2, p-value < 0.05 and fold change > 2.	WBPaper00062118:neural-HSF-1_upregulated
	Transcripts that showed significantly increased expression in hsf-1(RNAi) comparing to in wild type animals injected with vector.	Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed.	WBPaper00066232:hsf-1(RNAi)_upregulated_WT
	Transcripts that showed significantly increased expression in hsf-1(RNAi) comparing to in ash-2 animals injected with vector.	Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed.	WBPaper00066232:hsf-1(RNAi)_upregulated_ash-2
	Transcriptions that showed significantly decreased expression in hsf-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:hsf-1(RNAi)_downregulated
	Transcriptions that showed significantly increased expression in hsf-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:hsf-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in strain AGD1289 with pan-neuronall expression of HSF-1, comparing to in N2 animals.	DESeq2 v1.22.2, p-value < 0.05 and fold change > 2.	WBPaper00062118:neural-HSF-1_downregulated
	MicroRNAs that showed significantly altered expression in hsf-1(+);+HS vs hsf-1(RNAi);+HS. Worms remained on RNAi plates until the L4 larval-stage before being heat shocked by submerging plates in a 33C water bath for 30 minutes.	The Benjamini-Hochberg correction for multiple testing was then used to determine significantly altered miRNAs between each treatment condition. Micro RNAs with q-value < 0.05 was considered differentially expressed.	WBPaper00052959:hsf-1(RNAi)_regulated_miRNA_HS-dependent
	Transcripts that showed significantly decreased expression in hsf-1(ok600) comparing to in N2.	Cuffdiff	WBPaper00050199:hsf-1(ok600)_downregulated
	Transcripts that showed significantly increased expression in hsf-1(ok600) comparing to in N2.	Cuffdiff	WBPaper00050199:hsf-1(ok600)_upregulated

1 Sequence

• Length: 9579

1 Sequence Ontology Term

• Name: gene

20 Strains

• WBStrain00026688
• WBStrain00029269
• WBStrain00029268
• WBStrain00029267
• WBStrain00029266
• WBStrain00029271
• WBStrain00029264
• WBStrain00029263
• WBStrain00030516
• WBStrain00030519
• WBStrain00030520
• WBStrain00030522
• WBStrain00030521
• WBStrain00030901
• WBStrain00037656
• WBStrain00047522
• WBStrain00050114
• WBStrain00054876
• WBStrain00000108
• WBStrain00007673

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_11963086..11966270
• Length (nt): 3185
• Chromosome Location: I: 11963086-11966270
• Organism: Caenorhabditis elegans