WormMine: Gene WBGene00000920

• WormBase Gene ID: WBGene00000920
• Gene Name: daf-28
• Sequence Name: Y116F11B.1
• Brief Description: daf-28 encodes a beta-type insulin, mostly similar to INS-4 and INS-6and homologous to human insulin; DAF-28 inhibits dauer formation; daf-28mutants arrest as dauers and have downregulated signals through theDAF-2/insulin pathway; in young animals, daf-28 is expressed in ASI andASJ neurons, which regulate dauer formation; in older animals, daf-28expression spreads to other head neurons and to the somatic gonad;daf-28 expression is reduced by pheromone signalling, or in daf-1,daf-7, daf-11, or daf-22 mutant dauers; daf-28 mutants are dominantnegative, and are suppressed by excess wild-type DAF-28, INS-4, orINS-6; normal loss-of-function daf-28 alleles are expected to have anormal phenotype because C. elegans' 38 insulin genes are likely to beredundant; daf-28 expression is increased in daf-6, osm-1, or tax-4mutants; the transmembrane protein-tyrosine phosphatase IDA-1 isrequired for DAF-28 function; a ida-1 null allele enhancesdaf-28(sa191), with double mutants forming 50% dauers at 22.5 deg. C.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable insulin receptor binding activity. Involved in several processes, including insulin receptor signaling pathway; negative regulation of dauer entry; and regulation of synaptic assembly at neuromuscular junction. Acts upstream of with a negative effect on protein import into nucleus. Located in extracellular space and synapse. Expressed in several structures, including distal tip cell; egg-laying apparatus; neurons; pharynx; and ventral nerve cord.
• Biotype: SO:0001217
• Genetic Position: V :23.5308 ±0.014333
• Length (nt): 1322

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000920

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y116F11B.1.1	Y116F11B.1.1	752	V: 19815133-19816442
Transcript:Y116F11B.1.2	Y116F11B.1.2	641	V: 19815405-19816454

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y116F11B.1	Y116F11B.1	294	V: 19815445-19815646

4 RNAi Result

• WBRNAi00055471
• WBRNAi00107945
• WBRNAi00036623
• WBRNAi00087976

58 Allele

• gk963271
• gk964176
• gk962705
• gk963489
• gk963304
• WBVar02124642
• gk963809
• gk963637
• WBVar02063201
• WBVar02063200
• gk962717
• WBVar00071643
• WBVar00071644
• WBVar00071642
• WBVar00071647
• WBVar00071648
• WBVar00071645
• WBVar00071646
• sa191
• WBVar01978291
• gk962751
• WBVar01543685
• WBVar01543684
• gk950030
• WBVar02047640
• gk642985
• gk411072
• gk874382
• gk565392
• gk684942

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000920
• Start: 19815133
• End: 19816454
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_19816455..19820566
• Length (nt): 4112
• Chromosome Location: V: 19816455-19820566
• Organism: Caenorhabditis elegans

172 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
	Single-cell RNA-Seq cell group 84_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:84_0
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
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
	Single-cell RNA-Seq cell group 71_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:71_0
	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
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
	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 that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 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 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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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 increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
	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
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster3
	Transcripts that showed significantly decreased expression in npr-8(ok1439) animals with 24 hour exposure to P. aeruginosa PA14, comparing to N2 animals with 24 hour exposure to P. aeruginosa PA14.	DESeq2, fold change > 1.5, FDR < 0.05.	WBPaper00058948:npr-8(ok1439)_downregulated_PA14
	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
	Transcripts that showed significantly increased expression among animals treated with 400mM sucrose and 500 mg per ml stearic acid from L1 to L4 larva stage comparing to animals grown up on control plates.	CuffDiff, FDR <= 0.05, fold change >= 2.	WBPaper00059253:sucrose_stearic-acid_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:coelomocytes_L2-larva_expressed
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly decreased expression in rbr-2(tm3141) comparing to in N2 animals.	Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05).	WBPaper00050080:rbr-2(tm3141)_downregulated

13 Expression Patterns

• Primary Identifier: Expr10838
• Remark: Supplemental Table S4.

• Primary Identifier: Expr13308
• Pattern: The DAF-28::mCherry expression followed the reported expression pattern of pdaf-28::GFP transcriptional reporter, with fluorescent protein detected in head and tail neurons, pharynx, hypodermis, and other tissues. DAF-28::mCherry was efficiently secreted upon expression in L1 stage, as detected by its uptake by endocytic scavenger cells, coelomocytes. Interestingly, compared to the DAF-28::mCherry fusion protein, the previously described DAF-28::GFP protein was not efficiently secreted, as judged by coelomocyte fluorescence, and instead appeared to accumulate in neuronal cell bodies. This may be due to misfolding of the GFP moiety.
• Subcellular Localization: Confocal imaging showed that DAF-28::mCherry protein is predominantly found in a punctate pattern reminiscent of the secretory vesicles in mammalian cells expressing insulin or IGF, with some puncta found in a regularly spaced pattern adjacent to the ASI axons. DAF-28::mCherry was efficiently secreted upon expression in L1 stage, as detected by its uptake by endocytic scavenger cells, coelomocytes.

• Primary Identifier: Expr13511
• Pattern: daf-28 is expressed in ASK neurons.

• Primary Identifier: Expr11265
• Pattern: In wild-type animals DAF-28::GFP was detected in its producing cells, (the ASI and ASJ neurons and the posterior intestine)as well as in the coelomocytes. In wild-type animals DAF-28::GFP wasdetected in its producing cells, (the ASI and ASJ neurons and the posterior intestine)as well as in the coelomocytes.
• Subcellular Localization: In wild-type animals DAF-28::GFP was detected surrounding the periphery of the nucleus as well as in the axons. In wild-type animals the DAF-28::GFP is detected in the ER as well as in the axons.

• Primary Identifier: Expr2445
• Pattern: From late L1 to L2, Pdaf-28 GFP is strongly expressed in two pairs of ciliated sensory neurons: ASI and ASJ. This expression pattern continues through L3, L4, and early adult stages. Pdaf-28 GFP is also expressed in the hindgut as well as a tail neuron identified as PQR. From late embryogenesis to early L1, Pdaf-28 GFP was seen in many cell types including pharyngeal muscle, hypodermal, and many head cells.

• Primary Identifier: Expr11926

• Primary Identifier: Expr15282
• Pattern: DAF-28::GFP is found in the coelomocytes, in the posterior intestine and in the anterior sensory neurons.

• Primary Identifier: Expr11266
• Pattern: In wild-type worms, in addition to being in the amphid neurons and the gut, the protein is also found in coelomocytes. In the coelomocytes,the full-length DAF-28::GFP protein was present in vacuoles that have been shown to take up the endocytosis marker FM4-64 (Fares and Greenwald, 2001). daf-28::gfp transcriptional reporters are not expressed in coelomocytes (Li et al., 2003) (G.K., S.T., and P.N., unpublished data). The presence of DAF-28::GFP in coelomocytes,therefore, is the result of uptake of the protein from the psuedocoelomic fluid rather than that of transcription of daf-28 in these cells.

• Primary Identifier: Expr2010772
• 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: Expr1158982
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1022985
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029009
• 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: Expr11886
• Subcellular Localization: DAF-28 was co-localized with SNB-1/synaptobrevin at the synaptic region in ASJ neurons.

26 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000920
• Start: 19815133
• End: 19816454
• Strand: 1

26 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1322

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00022782
• WBStrain00040866
• WBStrain00007937

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_19811830..19815132
• Length (nt): 3303
• Chromosome Location: V: 19811830-19815132
• Organism: Caenorhabditis elegans