Genomics
11 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:R13H8.1h.1 | R13H8.1h.1 |
1626
 |
I: 10750498-10775050 |
| Transcript:R13H8.1i.1 | R13H8.1i.1 |
1548
|
I: 10750632-10775050 |
| Transcript:R13H8.1f.1 | R13H8.1f.1 |
2016
|
I: 10750632-10775993 |
| Transcript:R13H8.1k.1 | R13H8.1k.1 |
1458
|
I: 10750960-10775050 |
| Transcript:R13H8.1d.1 | R13H8.1d.1 |
1920
|
I: 10750960-10775987 |
| Transcript:R13H8.1b.1 | R13H8.1b.1 |
2698
|
I: 10763103-10776702 |
| Transcript:R13H8.1c.1 | R13H8.1c.1 |
2704
|
I: 10763103-10776702 |
| Transcript:R13H8.1l.1 | R13H8.1l.1 |
1224
|
I: 10763654-10775050 |
| Transcript:R13H8.1m.1 | R13H8.1m.1 |
1218
|
I: 10763654-10775050 |
| Transcript:R13H8.1a.1 | R13H8.1a.1 |
2765
|
I: 10771508-10776703 |
| Transcript:R13H8.1e.1 | R13H8.1e.1 |
912
|
I: 10772999-10775050 |
Other
11 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:R13H8.1h | R13H8.1h |
1626
|
I: 10750498-10750509 |
| CDS:R13H8.1i | R13H8.1i |
1548
|
I: 10750632-10750655 |
| CDS:R13H8.1f | R13H8.1f |
1554
|
I: 10750632-10750655 |
| CDS:R13H8.1b | R13H8.1b |
1527
|
I: 10763103-10763347 |
| CDS:R13H8.1m | R13H8.1m |
1218
|
I: 10763654-10763706 |
| CDS:R13H8.1a | R13H8.1a |
1593
|
I: 10771508-10772149 |
| CDS:R13H8.1e | R13H8.1e |
912
|
I: 10772999-10773121 |
| CDS:R13H8.1c | R13H8.1c |
1533
|
I: 10763103-10763347 |
| CDS:R13H8.1d | R13H8.1d |
1464
|
I: 10750960-10750984 |
| CDS:R13H8.1k | R13H8.1k |
1458
|
I: 10750960-10750984 |
| CDS:R13H8.1l | R13H8.1l |
1224
|
I: 10763654-10763706 |
294 RNAi Result
348 Allele
| Public Name |
|---|
| gk962858 |
| gk962706 |
| gk963849 |
| otn10712 |
| h11872 |
| h10765 |
| h6567 |
| h7349 |
| h13683 |
| h10766 |
| cxTi8911 |
| mgDf50 |
| mu86 |
| gk823618 |
| WBVar01900340 |
| WBVar01432854 |
| WBVar01432855 |
| WBVar01432856 |
| WBVar01432852 |
| WBVar01432858 |
| WBVar01432859 |
| mu54 |
| gk426214 |
| gk677837 |
| gk437965 |
| gk676772 |
| gk866558 |
| gk747776 |
| gk504647 |
| gk386322 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00000912 | 10750498 | 10776703 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrI_10776704..10781277 | 4574 | I: 10776704-10781277 | Caenorhabditis elegans |
175 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 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 | |
| Bacteria infection: Enterococcus faecalis | Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50. | For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. | WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| 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 | |
| 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 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 | |
| Bacteria infection: Photorhabdus luminescens | Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection. | MAANOVA and BRB-Array-Tools. | WBPaper00030985:Photorhabdus_luminescens_downregulated |
| Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic. | 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_SM | |
| 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 | |
| Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. | Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:S.aureus-4h_upregulated_N2 |
| Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours. | The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. | WBPaper00065373:Cisplatin_downregulated_WT | |
| Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. | DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. | WBPaper00062159:hda-2(ok1479)_upregulated | |
| Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Psora-Allantoin_downregulated | |
| Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Metformin_downregulated | |
| Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with heat killed E. coli OP50. | Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2. | WBPaper00059824:rnp-6(dh1127)_regulated_OP50 | |
| Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin-Allantoin_downregulated |
32 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| No detailed description on expression pattern in other life stage. | Expr4483 | Expressed in lateral hypodermal cells from L2 to L4, vulval muscle in some adult animals, anterior neurons (not individually identified in this study) from L2 to L4, posterior neurons in some L2/L3 and adult animals, body wall muscle from L2 to adult. | ||
| No detailed description on expression pattern in other life stage. | Expr4484 | Expressed in anterior neurons (not individually identified in this study) from L2 to L4, posterior neurons from L2 to L4, body wall muscle from L2 to adult. | ||
| Expr1030573 | Tiling arrays expression graphs | |||
| Expr3931 | The daf-16a promoter::gfp fusion construct (pPV199) was expressed in all life stages of C. elegans transformants. Bright fluorescence was seen in cells of the body wall, muscles, intestine and neurons but not in the pharynx or gonad. | |||
| Reporter gene fusion type not specified. | Expr1457 | Transgenic daf-16a::GFP animals show strong GFP fluorescence in most cells including ectoderm, muscles, intestine and neurons. The broad expression pattern of daf-16a::GFP is also seen in late embryos, larvae and dauer larvae. No expression was seen in the pharynx. | ||
| Expr15897 | DAF-16 was reported to be distributed in the ectoderm, myocytes, cells of the intestine and neurons in resting state wild-type worms [Libina et al., 2003], and we found that the broad expression pattern of DAF-16::GFP is in muscles, intestine and neurons in our experiments. | |||
| Expr11868 | GFP::DAF-16 protein localized to neurons, hypodermis, intestine, and body wall muscles. | |||
| Expr16365 | We found that DAF-16::GFP was expressed ubiquitously in most or all somatic tissues, such as neurons, intestine, BWM, and hypodermis, and also in the germ cells and oocytes. Germline expression of DAF-16::GFP was not detected by earlier transgene reporters.Temporally, ubiquitous expression of DAF-16::GFP from the endogenous locus was detected from the embryonic bean stage to adulthood. | |||
| Expr1738 | The functional GFP::DAF-16B fusion protein fluorescence was first detected in early embryos, prior to morphogenesis. After hatching and in all later developmental stages, transgenic larvae showed GFP in the pharynx and in many neurons throughout the body. From the late L3 stage onward, GFP was also detected in somatic gonads. | |||
| Clone: pUL#JRH7G3 | Expr7644 | Expression is observed from early embryogenesis to adult. Early embryonic expression is in peripheral cells. From late embryogenesis to adult, expression is seen in the pharynx, rectal glands, a subset of ventral nerve cord cells, a single neuron with a cell body in the tail and processes along the ventral side to the nerve ring. There is also expression in the vulva and somatic gonad, possibly the distal tip cells, and possibly the germ line. | ||
| Expr9886 | DAF-16B is expressed in AIY. | |||
| Expr12364 | daf-16d/f expression is dramatically increased at the level of transcription during the young adult stage in the intestine. | |||
| Expr11340 | In the germline itself, DAF-16::GFP is barely detectable, indicating that daf-16 is expressed at low levels in this tissue. DAF-16::GFP, however, is expressed at high levels in the somatic gonadal sheath cells, localizing to the nuclei of these cells under normal fed conditions. | localizes to the nuclei of these cells under normal fed conditions. | ||
| Expr9833 | GFP expression was observed in many tissues from early embryo to mature adult. GFP fluorescence was particularly strong in many neurons in the nerve ring and tail, and in some neurons in the ventral nerve cord. One unidentified neuron in the tail showed particularly strong expression such that its axon, projecting towards the anterior, was also visibly fluorescing. GFP was mainly diffuse and spread throughout the cells in which it was expressed, but in some individuals the fluorescence in some tissues, such as the seam cells, was much brighter in the nucleus. | |||
| Expr11684 | daf-16 is enriched in the gonad. | |||
| Expr14747 | daf-16a::gfp was mainly expressed in neuronal and hypodermal cells in the head and tail body regions. | |||
| Expr1021117 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr9815 | GFP expression was observed in many tissues from early embryogenesis to the mature adult. Expression was particularly strong in many neurons in the nerve ring and tail. In well fed worms the GFP was mainly diffuse and throughout the cells but the GFP became more nuclear-localized upon starvation. | |||
| Expr2010765 | 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). | |||
| Expr1739 | GFP was first detected in comma-stage embryos. After hatching, transgenic animals showed high levels of GFP expression in almost all somatic cells. In contrast to the daf-16b fusion gene, little GFP was detected in somatic gonad or pharynx (except occasionally in one or two unidentified cells in the terminal bulb). | |||
| Expr14746 | At the late L4 larval and young adult stages when IIS begins to affect lifespan, daf- 16d/f::gfp was expressed in almost all somatic cells of both sexes, mainly in the cytoplasm, but nuclear presence was also detectable, and at significantly higher levels in XX hermaphrodites than in XO males | |||
| Expr1155591 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| This result is consistent with the idea that localisation of DAF-16 in the nucleus is the mechanism by which starvation confers oxidative stress resistance. | [daf-16a::gfp] translational fusion. An integrated DAF-16a::GFP construct that rescues daf-16 activity. | Expr3860 | In L1s hatched in the presence of food, as previously reported, DAF-16a::GFP was located in both the nucleus and the cytoplasm. However, in over 70% of L1s hatched in liquid culture and starved for one day, DAF-16a::GFP was localised solely to the nucleus. | |
| No GO_term assigned. No detailed description on cellular expression patterns. | Expr1740 | DAF-16::GFP is first visible in late embryos just before hatching and exposure to the external environment and is present throughout the life of the animal. DAF-16::GFP is expressed in most cell types, with the exception of pharyngeal cells. | Under standard culture conditions, the fusion protein is predominantly unlocalized and is strongly expressed in many neuronal cells. The expression pattern and subcellular localization of DAF-16::GFP does not change with age. In well-fed old worms, DAF-16::GFP remains unlocalized. | |
| Expr14683 | ||||
| Expr14684 | ||||
| Expr14685 | ||||
| Expr14686 | ||||
| Expr3117 | Under reproductive conditions, DAF-16 is found in both the cytoplasm and the nucleus, whereas upon activation by the IGF-1 or the TGF- pathways the protein is accumulated in the nucleus. In L3 larvae grown on cholesterol, DAF-16::GFP showed diffuse fluorescence throughout many cells, as reported previously. In contrast, in the second generation of worms grown on lophenol, DAF-16::GFP is localised in nuclei of neurons of the pharynx, ventral cord, and tail. Lophenol had a very weak effect on the accumulation of DAF-16 in the nuclei of other cells. | |||
| Expr1962 | In daf-16(mgDf47), GFP::DAF-16B was predominantly cytoplasmic. |
94 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| has_input(WB:WBGene00004027) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00006926) | enables |
| enables | |
| has_input(WB:WBGene00006926) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| part_of(GO:0034599) | enables |
| enables | |
| enables | |
| enables |
20 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
94 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| has_input(WB:WBGene00004027) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00006926) | enables |
| enables | |
| has_input(WB:WBGene00006926) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| part_of(GO:0034599) | enables |
| enables | |
| enables | |
| enables |
31 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. | DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. | WBPaper00048971:daf-16(mgDf50)_downregulated_L1 | |
| Genes regulated by DAF-16, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12. | Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons. | WBPaper00050801:DAF-16_dauer_regulome | |
| Transcripts that showed significantly increased expression in daf-16(mu86);fer-15(b26ts) comparing to in fer-15(b26ts) at 2-day or 3-day post L4 adult hermaphrodite stage. | DESeq2 (v1.18.1), ajusted p-value < 0.05 | WBPaper00056218:daf-16(mu86)_upregulated_Day3 | |
| Transcripts that showed significantly increased expression in daf-16(mu86);fer-15(b26ts) comparing to in fer-15(b26ts) at 4-day or 5-day post L4 adult hermaphrodite stage. | DESeq2 (v1.18.1), ajusted p-value < 0.05 | WBPaper00056218:daf-16(mu86)_upregulated_Day5 | |
| Transcripts that showed significantly increased expression in daf-16(mu86);fer-15(b26ts) comparing to in fer-15(b26ts) at 6-day or 7-day post L4 adult hermaphrodite stage. | DESeq2 (v1.18.1), ajusted p-value < 0.05 | WBPaper00056218:daf-16(mu86)_upregulated_Day7 | |
| Genes upregulated in daf-2(-) compared to daf-16(-); daf-2(-) | Significance Analysis of Microarray (SAM) was performed to identify genes that were differentially regulated in each of the comparisons.For DAF-16 regulated genes, 1% median false positive discovery rate was used. | WBPaper00035479:daf-16(RNAi)_downregulated | |
| Transcripts up regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to daf-2(e1370). | DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05. | WBPaper00048988:daf-16(mu86)_upregulated_neuron | |
| Genes that showed significantly changed expression in daf-16(mgDF50) starved vs N2 starved animals at L1 larva. | Normalized log2 GCRMA values were used to assess significance of expression changes with the LIMMA/GCRMA empirical Bayes test. A threshold for significance at a q-value (FDR) of less than 0.05 was used to determine if a gene is differentially expressed. | WBPaper00053236:daf-16(mgDF50)_regulated_Starved | |
| Transcriptions that showed significantly decreased expression in daf-16(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:daf-16(RNAi)_downregulated | |
| Transcripts that showed significantly decreased expression in daf-16(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:daf-16(RNAi)_downregulated | |
| Transcripts up regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to N2. | DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05. | WBPaper00048988:daf-2(e1370)_daf-16(mu86)_upregulated_neuron | |
| Transcripts that showed significantly decreased expression in daf-16(mu86);fer-15(b26ts) comparing to in fer-15(b26ts) at 6-day or 7-day post L4 adult hermaphrodite stage. | DESeq2 (v1.18.1), ajusted p-value < 0.05 | WBPaper00056218:daf-16(mu86)_downregulated_Day7 | |
| Genes that were regulated by DAF-16 in response to germline loss, identified by comparing differentially expression genes between glp-1(e2141ts, 25C) vs. glp-1(e2141ts, 20C) and daf-16;glp-1(e2141ts, 25C) vs. daf-16;glp-1(e2141ts, 20C). | All lists used an Fs:Ptab 0.01 cutoff. | WBPaper00040412:germline-regulated_daf-16_target | |
| Transcriptions that showed significantly increased expression in daf-16(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:daf-16(RNAi)_upregulated | |
| DAF-16 binding DNA target identified by chromatin profiling by DNA adenine methyltransferase identification (DamID). | DAM methylation profiles derived from three biological replicates fed on daf-2 RNAi (no heat shock) showed a high degree of correlation between replicates. Sequences was identified with methylation peaks in the top 1% of smoothed log2 ratios (log2 ratio > 1.5) and within the gene boundary or 2kb upstream of the translational start. This defined 1135 methylation peaks and 907 associated genes, with a false discovery rate of <5%. | WBPaper00037055:DAF-16_binding_DNA | |
| The cluster contains genes that are upregulated with daf-16 RNAi treatment and downregulated with daf-2 RNAi treatment and in daf-2 pathway mutants. | hierarchical clustering | [cgc5976]:class_2 | |
| Transcripts that showed significantly increased expression by DAF-16 by comparing glp-1(e2141ts) with daf-16(mu86);glp-1(e2141ts) animals. | The Cuffdiff Differential Gene Expression tool (version 0.0.5) was used to calculate differential gene expression using a false discovery rate of 0.05, a minimum alignment count of 100 and with bias correction to obtain gene and transcript expression level data along with fold change (in log2 scale) and P values (raw and corrected for multiple testing). | WBPaper00049217:DAF-16_upregulated | |
| Transcripts that showed significantly increased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. | DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. | WBPaper00048971:daf-16(mgDf50)_upregulated_L1 | |
| Transcripts down regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to N2. | DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05. | WBPaper00048988:daf-2(e1370)_daf-16(mu86)_downregulated_neuron | |
| Genes downregulated in daf-2(-) compared to daf-16(-); daf-2(-) | Significance Analysis of Microarray (SAM) was performed to identify genes that were differentially regulated in each of the comparisons.For DAF-16 regulated genes, 1% median false positive discovery rate was used. | WBPaper00035479:daf-16(RNAi)_upregulated | |
| Transcripts that showed significantly decreased expression by DAF-16 by comparing glp-1(e2141ts) with daf-16(mu86);glp-1(e2141ts) animals. | The Cuffdiff Differential Gene Expression tool (version 0.0.5) was used to calculate differential gene expression using a false discovery rate of 0.05, a minimum alignment count of 100 and with bias correction to obtain gene and transcript expression level data along with fold change (in log2 scale) and P values (raw and corrected for multiple testing). | WBPaper00049217:DAF-16_downregulated | |
| The cluster contains genes that are upregulated with daf-2 RNAi treatment and in daf-2 pathway mutants, and downregulated with daf-16 RNAi treatment. | hierarchical clustering | [cgc5976]:class_1 | |
| Proteins related to protein metabolism that, compared with N2, display reduced abundance in the daf-2(e1370) proteome, and are suppressed by daf-16. | Over and under-representation analysis (ORA) and GSEA were performed using web-based tool GeneTrail. Significance cutoff P < 0.05) was determined by a hypergeometric distribution test using all C. elegans genes as background with a 5% FDR multiple testing correction. Genes with a 1.3-fold change in daf-2(e1370) mutants relative to wild type were included in the analysis. The results of the ORA were subsequently confirmed by GSEA, a method that is independent of any fold change cutoff. | WBPaper00042552:daf-2(e1370)_downregulated_daf-16-dependent | |
| Transcripts that showed significantly decreased expression in daf-16(mu86);fer-15(b26ts) comparing to in fer-15(b26ts) at 4-day or 5-day post L4 adult hermaphrodite stage. | DESeq2 (v1.18.1), ajusted p-value < 0.05 | WBPaper00056218:daf-16(mu86)_downregulated_Day5 | |
| Top 50 down regulated genes by DAF-16 based on reanalysis 75 previously published experiments. | Authors reanalyzed raw genome-wide expression data from five studies (McElwee et al., 2003; McElwee et al., 2004; Murphy et al., 2003; Shaw et al., 2007; Troemeletal.,2006) encompassing 75 genome-wide expression profiles, which authors used to construct 46 explicit contrasts between conditions with differing levels of DAF-16 activity. After complete reprocessing of the raw data (array-specific standardization, normalization, and remapping of probes), a log-fold-change and corresponding standard error were calculated for each transcript on each array (or array pair for single-channel technologies). Together, these were converted into a vote value between 1 (highly likely to be downregulated) and +1 (highly likely to be upregulated). The total voting score for each gene was computed as the sum of voting scores for individual experiments, which is robust in the sense that the influence of any individual experiment is limited to a single full vote. An empirical null distribution based on random permutation was created, and all genes were ranked from consistently upregulated (class I) to consistently downregulated (class II). The area under the null distribution (p value) for each gene that served as the basis for assigning genes to class I or class II at a 5% false discovery rate. | WBPaper00044005:DAF-16_downregulated | |
| Transcripts down regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to daf-2(e1370). | DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05. | WBPaper00048988:daf-16(mu86)_downregulated_neuron | |
| Genes showing significantly decreased expression in daf-16(mgDf50);daf-2(e1370) comparing to daf-2(e1370), but not in daf-2(m577). | Raw microarray data (cel files) were normalized, fold-changes between genotypes were determined, and global statistical analysis was performed, using a slightly modified version of the recently described Goldenspike methodology implemented in R (version 2.0.1) (Choe et al. 2005). Briefly, this procedure performs eight different normalization routines, which are then used to produce an average fold-change difference and false-discovery rate (q-value) between different genotypes that takes into consideration the variance of probe set intensity across the different normalizations. The Goldenspike methodology has been shown to out-perform most commonly used normalization methods (Choe et al. 2005). The Goldenspike protocol was altered slightly to exclude absent probe sets (those probe sets called absent in all hybridizations by MAS5) prior to the final probe-set-level Loess normalization. This alteration was found to reduce the number of false positives associated with the absent probe sets (Schuster et al. 2007). | WBPaper00031486:daf-16_upregulated | |
| Top 50 up regulated genes by DAF-16 based on reanalysis 75 previously published experiments. | Authors reanalyzed raw genome-wide expression data from five studies (McElwee et al., 2003; McElwee et al., 2004; Murphy et al., 2003; Shaw et al., 2007; Troemeletal.,2006) encompassing 75 genome-wide expression profiles, which authors used to construct 46 explicit contrasts between conditions with differing levels of DAF-16 activity. After complete reprocessing of the raw data (array-specific standardization, normalization, and remapping of probes), a log-fold-change and corresponding standard error were calculated for each transcript on each array (or array pair for single-channel technologies). Together, these were converted into a vote value between 1 (highly likely to be downregulated) and +1 (highly likely to be upregulated). The total voting score for each gene was computed as the sum of voting scores for individual experiments, which is robust in the sense that the influence of any individual experiment is limited to a single full vote. An empirical null distribution based on random permutation was created, and all genes were ranked from consistently upregulated (class I) to consistently downregulated (class II). The area under the null distribution (p value) for each gene that served as the basis for assigning genes to class I or class II at a 5% false discovery rate. | WBPaper00044005:DAF-16_upregulated | |
| Genes that showed significantly changed expression in daf-16(mgDF50) fed vs N2 fed animals at L1 larva. | Normalized log2 GCRMA values were used to assess significance of expression changes with the LIMMA/GCRMA empirical Bayes test. A threshold for significance at a q-value (FDR) of less than 0.05 was used to determine if a gene is differentially expressed. | WBPaper00053236:daf-16(mgDF50)_regulated_Fed | |
| Genes showing significantly decreased expression in daf-16(mgDf50);daf-2(e1370) comparing to daf-2(e1370), but not in daf-2(m577). | Raw microarray data (cel files) were normalized, fold-changes between genotypes were determined, and global statistical analysis was performed, using a slightly modified version of the recently described Goldenspike methodology implemented in R (version 2.0.1) (Choe et al. 2005). Briefly, this procedure performs eight different normalization routines, which are then used to produce an average fold-change difference and false-discovery rate (q-value) between different genotypes that takes into consideration the variance of probe set intensity across the different normalizations. The Goldenspike methodology has been shown to out-perform most commonly used normalization methods (Choe et al. 2005). The Goldenspike protocol was altered slightly to exclude absent probe sets (those probe sets called absent in all hybridizations by MAS5) prior to the final probe-set-level Loess normalization. This alteration was found to reduce the number of false positives associated with the absent probe sets (Schuster et al. 2007). | WBPaper00031486:daf-16_downregulated |