Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:B0244.2.1 | B0244.2.1 |
2591
 |
III: 5755539-5765816 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:B0244.2 | B0244.2 |
2304
|
III: 5755595-5755664 |
167 Allele
| Public Name |
|---|
| gk964518 |
| gk175338 |
| gk175339 |
| gk175340 |
| gk175341 |
| gk175342 |
| gk175343 |
| gk175344 |
| gk175345 |
| gk175346 |
| gk175347 |
| gk175348 |
| gk175349 |
| gk175350 |
| gk175351 |
| gk175352 |
| gk175353 |
| gk175354 |
| gk175355 |
| gk175356 |
| gk175357 |
| gk175358 |
| gk175359 |
| gk175360 |
| gk175361 |
| gk175362 |
| gk964338 |
| gk964339 |
| tm334 |
| ok409 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00002048 | 5755539 | 5765816 | 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_chrIII_5765817..5769899 | 4083 | III: 5765817-5769899 | Caenorhabditis elegans |
304 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 | |
| Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage. | 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_larva_enriched | |
| Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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 |
| Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:AVE-neuron_L1-larva_expressed | |
| 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 | |
| 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 |
| 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 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 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 | |
| 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 | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| 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 |
| 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 | |
| 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 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 |
| 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 | |
| Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. | 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_N2-background | |
| Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. | DESeq2 version 1.22.2, p < 0.05 | WBPaper00064716:paraquat_downregulated | |
| Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. | DESeq | WBPaper00053302:stavudine_24h_regulated | |
| Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. | DESeq2, fold change > 2, adjusted p-value < 0.01 | WBPaper00058598:sin-3(tm1276)_downregulated |
14 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031202 | Tiling arrays expression graphs | |||
| Reporter gene fusion type not specified. To analyze ida-1 gene expression in males, the pida-1::GFP transgenic strain BL5715 was crossed with the him-8 (high incidence of males) mutant strain BW1663. cgc6469 mentioned that this reporter gene is transcriptional fusion. | Expr843 | The ida-1 gene promoter-driven GFP expression pattern in males differs from hermaphrodites, especially in the tail, where many more fluorescent cells are observed. Male larvae appear very similar to hermaphrodite larvae, the only difference being that the PVP neurons in the preanal ganglion showed higher GFP expression levels. It was concluded that all neurons expressing GFP in the hermaphrodite pharyngeal nerve ring and in the tail also express GFP in males. In adult males, additional fluorescence is seen in neurons anterior to the nerve ring, in the ventral cord and many more in the tail. The four additional GFP-expressing cells in the procorpus just anterior to the pharyngeal bulb have not been identified. Expression in the male-specific CEM neurons at the anterior end of the nerve ring appeared variable. The hermaphrodite-specific cells VC, HSN, and uv1 observed to express GFP are not found in males. Nonetheless, several cell bodies in the male ventral cord expressed GFP. Dorsally directed processes emanate from them, which identifies them as CAn, a set of eight motoneurons. As in hermaphrodites, PDE weakly expressed GFP. In the male tail, about 20 neurons express GFP. They include PHA, PHB, PHC, and PVP in the preanal ganglion, which are already seen in larvae. Some of the rays contain GFP-filled axons that extend all the way to the tip of the ray. Rays 2, 8, and 9 show the highest expression levels; axons of rays 1, 4, and 6 fluoresce more weakly. No GFP expression is observed in the spicules. | ||
| Reporter gene fusion type not specified. cgc6469 mentioned that this reporter gene is transcriptional fusion. | Expr842 | GFP expression was observed in about 30 neurons of adult hermaphrodite worms. pida-1::GFP 7.6 expression was prominent in a subset of neurons in the head nerve ring, around the vulva, in a few cells in the ventral cord, and in the tail. Although the GFP was concentrated in the nucleus, the whole cell body including axons was labelled. Labeled processes included two lateral and one dorsal axon and a bundle of ventral axons running the length of the body, a pair of lateral axon bundles running from the head to the tip of the nose, and a pair of axons running from the anal region to the tip of the tail. GFP expression was observed as early as in late embryos. Larvae showed expression in the head and the tail, whereas GFP expression near the vulva and in the ventral cord was only seen in late L4 and adult animals. The expression pattern in dauer larvae was similar to that in other larval stages. Males exhibited many more GFP-expressing cells in the tail and additional cells in the head, and expression in the ventral cord differed from that observed in hermaphrodites. The GFP-expressing neurons in the hermaphrodite head were identified as ADE, ALA, ASI, ASK, AUA, ASG, AVH, and AVJ. Expression in ASG, AVH, and AVJ was not as bright as in other cells and was variable from individual to individual. A few other GFP-expressing anterior neurons could not be identified unequivocally. The fluorescent cells in the midsection of the animal were identified as the vulval motoneurons VC and HSN and the vulval uv1 cells. These are all hermaphrodite-specific and GFP expression was not observed until the late L4 larval stage. A lateral pair of neurons in the posterior half of the animal with weak GFP expression was identified as PDE. They possess ventrally directed processes entering the ventral nerve cord. In the preanal ganglion a pair of neurons with weak GFP expression was identified as PVP. Three pairs of GFP-expressing cells in the tail were identified as PHA, PHB, and PHC. Corresponding cells for the dorsal axon and a preanal structure have not been identified. The latter short process originates from the ventral nerve cord and peters out and terminates at the hypodermis. | GFP was concentrated in the nucleus, the whole cell body including axons was also labelled. | |
| CeIA-2 = ida-1. | Expr2900 | CeIA-2::GFP was easily detected in a restricted set of 13 neurons. CeIA-2::GFP was strongest in the ALA neuron and easily detectable in the VCs, HSNs, and PHCs. A lower level of GFP was also detected in the uv1 secretory cells. The pattern of GFP expression from this reporter gene likely under-represents the normal CeIA-2 distribution because of previous transcriptional reporter results and very faint GFP that can be observed in additional neurons under certain conditions. The expression pattern of the integrated strain was similar to that seen with extrachromosomal arrays. Despite integration, there was still a degree of mosaic expression, most notably in the VC motor neurons. | Pida-1CeIA-2::GFP was observed in neuronal cell bodies and in puncta along the length of axons of neurons in which it was expressed. Animals expressing this CeIA-2::GFP transgene were stained with an antibody against synaptotagmin. The punctate GFP reporter pattern in axons colocalized with synaptotagmin staining, suggesting clustering of CeIA-2::GFP to synaptic regions. | |
| Expr2970 | Expression was prominent in the ALA neuron in the dorsal ganglion of the pharyngeal nerve ring, the hermaphrodite-specific vulval motoneurons HSN, VC4 and VC5, the neuroendocrine-like uv1 cells, the tail neuron pair PHC, was also present in the ventral cord neurons VC1, VC2, VC3, VC6, and was somewhat variable in a few amphid neurons. | Cytoplasmic GFP fluorescence was high in cell bodies and extended into the nerve processes in a distinct punctate pattern. The subcellular distribution of IDA-1::GFP was similar to that of IDA-1 as observed by immunofluorescence microscopy of wild-type animals (see Expr2969), as best observed in the ALA lateral process and PHC. | ||
| Expr2969 | Immunofluorescence microscopy of wild-type hermaphrodites using anti-IDA-1 antibodies revealed strong immunoreactivity within the pharyngeal nerve ring, around the vulva and the tail, and variable staining at the nose tip. Males showed weaker staining of the nerve ring and intense staining of male-specific tail neurons. Immuno-reactivity was detectable from the L1 larval stage onwards. The observed cellular expression pattern matches that of a transcriptional pida-1::GFP reporter construct (see Expr843). | At the subcellular level, the antigen was localized to cell bodies exterior to the nucleus and to neuronal processes. These included amphid sensory dendrites, ALA lateral processes, processes of the ventral and dorsal nerve cords and PHC neurons in the tail spike. Staining along the processes was punctate in appearance and distributed among a large number of small individual elements and a few brighter, apparently larger objects. | ||
| Reporter gene fusion type not specified. cgc6469 mentioned that this reporter gene is transcriptional fusion. | Expr808 | Examination of transgenic animals showed expression of GFP exclusively in neuronal tissues and in particular in the ventral nerve cord, preanal ganglia, and in the nerve ring. Expression was first observed during early embryonic elongation (1.5-fold stage) and continued through adulthood. A nuclear localized version of the reported gene (GFP linked to a nuclear localization signal under control of the C. elegans promoter) showed mosaic expression in ventral cord neurons. Examination of many animals showed that all neurons of the ventral nerve cord could express both reporter constructs, suggesting expression is pan-neuronal. | ||
| Expr13791 | ida-1::mCherry expression was observed in HSN, VC, and the uv1 neuroendocrine cells in L4.7-8 animals. | |||
| Expr1021027 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr13337 | IDA- 1::GFP translational fusion produces punctate fluorescence in the uv1 cells. | |||
| Expr2012668 | 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). | |||
| Original chronogram file: chronogram.2585.xml | [B0244.2:gfp] transcriptional fusion. | Chronogram1339 | ||
| Expr1142998 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2030904 | 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). |
21 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| occurs_in(WBbt:0003850),happens_during(GO:0007419) | involved_in |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
7 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
21 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| occurs_in(WBbt:0003850),happens_during(GO:0007419) | involved_in |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_5755432..5755538 | 107 | III: 5755432-5755538 | Caenorhabditis elegans |
