Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y73F8A.1.1 | Y73F8A.1.1 |
2299
 |
IV: 15227814-15234993 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y73F8A.1 | Y73F8A.1 |
2151
|
IV: 15227942-15228028 |
134 Allele
| Public Name |
|---|
| gk964078 |
| gk964500 |
| gk962765 |
| gk963590 |
| gk963795 |
| gk963948 |
| WBVar01860072 |
| tm10598 |
| WBVar02069873 |
| WBVar02069874 |
| sy606 |
| gk962668 |
| gk962669 |
| gk964526 |
| WBVar01733214 |
| gk219613 |
| gk219629 |
| WBVar01733209 |
| WBVar02022110 |
| WBVar02022109 |
| gk947144 |
| gk947145 |
| WBVar00577113 |
| WBVar00577112 |
| WBVar00577110 |
| WBVar00196630 |
| WBVar00196629 |
| WBVar00196628 |
| WBVar00196634 |
| WBVar00196633 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00004035 | 15227814 | 15234993 | -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_chrIV_15227808..15227813 | 6 | IV: 15227808-15227813 | Caenorhabditis elegans |
77 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
| 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 |
| Transcripts that showed significantly increased expression in pri-1(RNAi) animals comparing to in N2 animals fed with empty vector. | Differential expression analysis was performed quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR ver 3.32.1. FDR < 0.05, fold change > 2. | WBPaper00066418:pri-1(RNAi)_upregulated | |
| Transcripts that showed significantly increased 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_upregulated | |
| 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 | |
| Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in vector control animals. | The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed. | WBPaper00053402:cco-1(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in his-3(RNAi) comparing to in vector control animals. | The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed. | WBPaper00053402:his-3(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:hda-1(ne4752)_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:intestine_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage. | DESeq 2, fold change > 4, adjusted p-value < 0.05. | WBPaper00055013:hmg-3(bar24)_upregulated | |
| Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:eat-2(ad1116)_downregulated | |
| Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage. | DESeq v1.6.3. Fold change > 1.5. | WBPaper00050370:dpy-21(e428)_L3_upregulated | |
| Proteins interacting with HA-PPM-1.D. | N.A. | WBPaper00062498:PPM-1.D_interacting | |
| Proteins identified in extracellular vesicle. | N.A. | WBPaper00062669:extracellular-vesicle_protein | |
| Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult | |
| Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult | |
| Genes with significantly increased expression in eat-2(ad465) treated with 2% DMSO for 72 hours, comparing to in N2 treated with 2% DMSO for 72 hours. | Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes. | WBPaper00048989:eat-2(ad465)_upregulated_in-DMSO | |
| Transcripts that showed significantly increased expression in set-2(zr2012) animals at embryo stage, comparing to in N2 animals. | DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. | WBPaper00060014:set-2(zr2012)_upregulated | |
| Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:daf-2(e1370)_upregulated_neuron | |
| Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:daf-16(mu86)_upregulated_neuron | |
| Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron | |
| Transcripts that showed significantly increased expression in fmi-1(rh308) young adults comparing to in N2 animals. | fold change > 2, p-value < 0.05 | WBPaper00066618:fmi-1(rh308)_upregulated | |
| Genome-wide analysis of developmental and sex-regulated gene expression profile. | self-organizing map | cgc4489_group_14 | |
| EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the second UVC dose (24h). | Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -25h timepoint (just prior to the second UVC dose (24h)). | Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. | WBPaper00041939:EtBr-exposed_vs_UVC-exposed_24h |
| Transcripts that showed significantly increased expression in ints-1(RNAi) animals comparing to control RNAi animals, at late L3 larva stage. | DESeq2, v1.12.0, fold change > 2, FDR < 0.05 | WBPaper00057068:ints-4(RNAi)_upregulated | |
| Genes up-regulated in wdr-23(tm1817) mutants comparing to in N2. | Differentially expressed genes at false discovery rate (FDR) of 0.05 were identified using the Cuffdiff module of the Cufflinks package. | WBPaper00042215:wdr-23(tm1817)_upregulated | |
| Transcripts that showed significantly increased expression in lin-22(icb38) comparing to in N2 at L3 larva. | Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1). | WBPaper00053295:lin-22(icb38)_upregulated | |
| Genes that showed increased mRNA expression in wdr-23(tm1817) comparing to in N2, and was rescued in wdr-23(tm1817);nuIs225[Pmyo-2::GFP, Psnb-1::WDR-23a]. | Differentially expressed genes at false discovery rate (FDR) of 0.05 were identified using the Cuffdiff module of the Cufflinks package. | WBPaper00044743:wdr-23_neuron_upregulated | |
| Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_downregulated_25C |
17 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| PKD-2::GFP transgenes fully rescue the male mating defect of pkd-2(sy606) null mutants. | [pkd-2::gfp] translational fusion. | Expr4254 | pkd-2 is expressed in a subset of male-specific sensory neurons: four CEM neurons in the head, eight pairs of Ray B neurons (1-5 and 7-9, excluding R6B), and the HOB hook neuron in the tail. | Each neuron that expresses PKD-2 has an exposed cilium at the distal ending of the dendrite. In these neurons, PKD-2::GFP localizes predominantly to cell bodies and cilia, and is also observed in small dendritic and axonal puncta. Within the ciliary region, PKD-2::GFP is distributed throughout the cilium, but primarily concentrated at the ciliary base, which corresponds to the distal-most dendrite and transition zone regions. |
| Picture: Figure 3A. | Marker27 | Expressed in male specific sensory neurons. | ||
| Picture: Figure 2. Reporter gene fusion type not specified. | Expr7930 | Expressed in more than 10 neuron but ASE. | ||
| Deletion of the PKD-2 N-terminus or the C-terminus does not affect targeting to the somatodendritic or ciliary region. However, deletion of both cytosolic domains results in stable expression only in the ciliary regions. Picture: Fig 1. | Expr7822 | Wild-type PKD-2::GFP localizes to a reticular network in the cell body, the proximal dendrite, and cilium. | ||
| Expr9327 | PKD-2::DsRed2 localizes to cilia and cell bodies of ray, HOB, and CEM neurons. ATP-2::GFP clearly colocalizes with PKD-2::DsRed2 in CEM cilia. In rays and HOB, ciliary colocalization of ATP-2 and PKD-2 was ambiguous due to the expression of ATP-2::GFP in ray neurons, support cells, and hypodermis. | |||
| Expr2408 | PKD-2::GFP4 is expressed in the male-specific sensory neurons of the head (the CEMs), rays, and hook (HOB). | KD-2(+)::GFP4 concentrates in sensory cilia and in a punctate pattern in neuronal cell bodies. Punctate pkd-2::gfp4 expression in ray neuronal cell bodies may be in RER or in Golgi. PKD-2::GFP4 accumulates in a ring around the ciliary transition zones, consistent with plasma membrane localization. | ||
| The overall pattern of alpha-PKD-2 antibody staining is consistent with the expression of the pkd-2::gfp4 fusion gene, although there are a few differences. First, alpha -PKD-2 antibodies label only male-specific neurons, whereas pkd-2::gfp4 is additionally expressed in non-sex-, non-stage-specific nerve ring neurons and occasionally in ray structural cells. Second, alpha-PKD-2 antibodies also recognize axons of male-specific sensory neurons, whereas pkd-2::gfp4 is only weakly expressed in axons. pkd-2(sy606 deletion) mutant animals exhibited no immunoreactivity, demonstrating the specificity of our alpha-PKD-2 polyclonal antibody. | Expr2409 | The alpha-PKD-2 antibodies stained only male-specific sensory neurons in wild-type animals. Based on cell body positions, the PKD-2 protein is detected in the head CEMs, ray (except Ray 6), and hook HOB neurons of wild-type males. | The alpha-PKD-2 antibodies labeled the entire neuron (cilia, dendrite, cell body, and axon). Cytoplasmic, nonnuclear staining in cell bodies and dendrites is punctate, suggesting that one pool of PKD-2 is located in intracellular membranes of the ER, Golgi apparatus, and/or transport vesicles while another is found in sensory cilia. | |
| Expr3490 | In the wild-type, PKD-2::GFP localizes throughout neuronal cell bodies and in small, discrete puncta in cilia of male-specific CEM, RnB, and HOB neurons. In wild-type rays, PKD-2::GFP normally localizes to ciliated endings on dendrites of RnB neurons. In the head of a wild-type male, PKD-2::GFP normally localizes to the ciliary transition zone and small, finger-like ciliary projections emanating from the transition zone of the four CEM neurons. | |||
| Reporter gene fusion type not specified. The basodendritic localization of PKD-2::GFP2 (which contains membrane-spanning regions) is identical to that of LOV-1::GFP1. | Expr1149 | PKD-2 is localized to the same male-specific sensory neurons as LOV-1. Rarely, very faint non-sex- and non-stage-specific expression of pkd-2::gfp1 is observed in nerve-ring cell bodies. Expression of pkd-2::gfp1 (which lacks transmembrane domains) is uniform throughout the HOB, ray and CEM neurons. | cell body | |
| Expr14407 | In wild-type neurons, PKD-2::GFP is localized to somatodendritic (ER in the cell body and puncta along the dendrite) and ciliary regions of 4 CEM, 16 RnB, and the HOB male-specific sensory neurons. PKD-2::GFP localizes to the ciliary base (corresponding to the distal most dendrite and ciliary transition zone) in all neurons and in 56% of the cilium proper of neurons examined. | |||
| Expr14408 | In wild-type neurons, PKD-2::GFP is localized to somatodendritic (ER in the cell body and puncta along the dendrite) and ciliary regions of 4 CEM, 16 RnB, and the HOB male-specific sensory neurons. PKD-2::GFP localizes to the ciliary base (corresponding to the distal most dendrite and ciliary transition zone) in all neurons and in 56% of the cilium proper of neurons examined. | |||
| Expr11947 | A pkd-2-gfp fusion vector, that partially rescued the response phenotype of pkd-2-mutant males, was expressed in the CEM neurons, HOA, HOB, and sensory ray neurons and in the rays. Developmental regulation of expression was seen, appearing at L4 and peaking in adult males. | |||
| Expr11948 | A polyclonal anti-polycystin-2 peptide antibody confirmed expression of polycystin-2 in the cytoplasm of the cell bodies and neuronal processes of 4 male-specific cephalic neurons in the head. In the male tail, staining was seen in the cell bodies of both sets of 9 neurons that innervate the sensory rays on each side of the tail as well as in the HOA and HOB neurons that innervate the hook, used to detect the hermaphrodite vulva. | |||
| Expr2014947 | 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). | |||
| Expr1015403 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1161794 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2033182 | 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). |
41 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in |
14 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
41 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIV_15234994..15235181 | 188 | IV: 15234994-15235181 | Caenorhabditis elegans |
