Genomics
7 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:M6.1b.1 | M6.1b.1 |
3859
 |
X: 642156-650107 |
| Transcript:M6.1d.1 | M6.1d.1 |
1979
|
X: 642156-645724 |
| Transcript:M6.1e.1 | M6.1e.1 |
4020
|
X: 642214-654821 |
| Transcript:M6.1f.1 | M6.1f.1 |
2119
|
X: 643108-645708 |
| Transcript:M6.1a.2 | M6.1a.2 |
4016
|
X: 643108-650108 |
| Transcript:M6.1a.1 | M6.1a.1 |
4317
|
X: 643108-654904 |
| Transcript:M6.1c.1 | M6.1c.1 |
2097
|
X: 646066-650092 |
Other
27 RNAi Result
153 Allele
| Public Name |
|---|
| gk963652 |
| gk963725 |
| rh90 |
| rh105 |
| gk226 |
| gk898071 |
| WBVar01690010 |
| WBVar01600338 |
| WBVar01600339 |
| WBVar01600341 |
| WBVar01600340 |
| WBVar00074375 |
| WBVar00074374 |
| WBVar00074377 |
| WBVar00074376 |
| WBVar01979042 |
| WBVar01823969 |
| WBVar01823970 |
| WBVar01823972 |
| WBVar01823971 |
| gk902802 |
| gk898070 |
| gk361206 |
| gk564273 |
| gk431133 |
| gk486853 |
| gk759454 |
| gk919958 |
| gk495610 |
| gk619802 |
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_chrX_641541..642155 | 615 | X: 641541-642155 | Caenorhabditis elegans |
292 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 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 | |
| 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 |
| TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood. | SAM | WBPaper00031040:TGF-beta_adult_upregulated | |
| 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 |
| 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 | |
| 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 |
| Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq. | DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison. | WBPaper00045934:wrn-1(gk99)_upregulated | |
| 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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day11_vs_Day1_downregulated | |
| Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(cmh15)_downregulated | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:NMDA-neuron_expressed | |
| Genes up regulated in alg-1(gk214) comparing to in N2. | Differential expression was assessed using an empirical Bayes statistics using the eBayes function. | WBPaper00040823:alg-1(gk214)_upregulated | |
| 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 Late reproduction stage (96 hours at 24 centigrade). | Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118. | WBPaper00040858:eQTL_regulated_reproductive | |
| Bacteria infection: Bacillus thuringiensis | Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304. | N.A. | WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated |
| 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 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h |
| Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. | Fold change > 2. | WBPaper00064306:Agaro-oligosaccharides_upregulated | |
| 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 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h |
| Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage. | EdgeR, fold change > 2, FDR < 0.001. | WBPaper00056290:hsp-6(mg585)_downregulated | |
| Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. | DESeq2(v1.32.0), FDR < 0.05. | WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs |
17 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031209 | Tiling arrays expression graphs | |||
| Expr15269 | The immunofluorescence whole mount microscopy on embryos, larvae and adults, using the ECP-1 antibody, revealed a strong staining of the excretory cells, including the canals and the cell bodies, the pharynx, the pharyngeal-intestinal valve as well as of the intestinal-rectal valve. These results confirmed the specificity of our ECP-1 antibody and reveal that the excretory cell specific expression of ECP-1 was different from the intestinal expression of the IFC-2 protein, while the pharynx and the two intestinal valves contain both these ECP-1 and IFC-2 proteins. | |||
| Expr15272 | The promoter/GFP-reporter 1 was expressed in the pharynx, the pharyngeal-intestinal valve, the intestinal-rectal valve and also weakly in the uterus. | |||
| Expr2260 | Double staining with C2 and desmosomal MH27 antibodies shows that C2 is located in the cytoplasm of intestinal cells and at desmosomes in intestine and pharynx of the larva, late embryo and adults. MH27 antibody additionally stained the hypodermal and all other epithelial desmosomes. | cytoplasm | ||
| Expr14340 | Labeled EXC-2 is located at the lumen of the excretory canal, in the corpus, posterior bulb, and pharyngeal-intestinal valve of the pharynx, as well as in the uterine seam and intestinal-rectal valve. | Labeled EXC-2 is located apical to canal cytoplasm, as determined via cross-sectional fluorescence intensity measurements. This result was confirmed by evaluating the subcellular location of EXC-2 relative to a known apical membrane protein, ERM-1 (Gbel et al. 2004). The results demonstrate that EXC-2 and ERM-1 show overlapping expression at the canal apical (luminal) membrane. | ||
| Expr15267 | IFC-2a/e::YFP is localized in the intestine, the excretory canal, corpus and posterior bulb of the pharynx, pharyngeal-intestinal valve and interfacial uterine cells. | |||
| Expr15268 | No intestinal expression can be observed for IFC-2a/b/c, which instead presents a very prominent localization in the intestinal-rectal valve. Expression is also observed in the excretory canal, corpus and posterior bulb of the pharynx, pharyngeal-intestinal valve and interfacial uterine cells. | |||
| Picture: Fig. 1. | Expr8185 | Anti-IFB-2 fluorescence was detectable diffusely in the cytoplasm of intestinal cells accumulating over time in the sub-apical domain next to the newly forming lumen (e.g., plum stage). Anti-IFC-2 antibodies reacted only very weakly with the intestinal cells at plum stage although co-distribution with anti-IFB-2 was detectable in some sub-apical areas. The major IFC-2 immunofluorescence, however, was seen in hypodermal cells presenting a multipunctate staining of cell borders indicating a junctional localization. In subsequent stages, anti-IFB-2 reactivity further concentrated in the periluminal compartment, i.e., in the electron-dense endotube ultrastructure. Strongest immunofluorescence was noted in junctional regions due to the localization of IFB-2 along the entire junctional complex. In addition, multiple cytoplasmic puncta were seen that had not been described previously. These fluorescent structures began to accumulate in L3-larvae and were most abundant in old adults with a predilection for the posterior intestine. The anti-IFC-2-staining gradually increased in the intestine becoming quite prominent in L3-larvae in which it presented a very similar distribution to anti-IFB-2 fluorescence although diffuse cytoplasmic and junctional staining were more pronounced. In adult intestines anti-IFC-2 fluorescence was essentially identical to that of anti-IFB-2. | ||
| Expr15273 | The resulting promoter/GFP-reporter 2 expression was monitored in the intestine in agreement with the intestinal staining obtained with the IFC-2-specific antibody, which however also revealed, in addition, the staining of the pharynx. | |||
| Expr14279 | Animals grown on control bacteria (OP50, control JM103) reach adulthood and display smooth periluminal localization of IFC-2a::YFP in the intestine indistinguishable from IFB-2a::CFP. | |||
| Expr2012682 | 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). | |||
| Expr1154745 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2030918 | 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). | |||
| Expr14343 | Labeled EXC-2 is located apical to canal cytoplasm, as determined via cross-sectional fluorescence intensity measurements. This result was confirmed by evaluating the subcellular location of EXC-2 relative to a known apical membrane protein, ERM-1 (Gbel et al. 2004). The results demonstrate that EXC-2 and ERM-1 show overlapping expression at the canal apical (luminal) membrane. | |||
| Original chronogram file: chronogram.646.xml | [M6.1:gfp] transcriptional fusion. | Chronogram1728 | ||
| Expr1010980 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr15159 | To optimize comparative imaging of all canal cIFs and their isoforms during canal lumenogenesis, ifa-4, ifb-1b, ifc-2a, and ifc-2b cDNAs were cloned behind the canal-specific sulp-5 promoter and fused to different fluorophores. All localized to expanding larval and fully expanded adult lumenal membranes adjacent to but distinct from lumenal ERM-1. Thus, all C. elegans canal cIFs and their isoforms are located at the lumen. |
16 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in |
13 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
16 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_654905..656183 | 1279 | X: 654905-656183 | Caenorhabditis elegans |
