Genomics
9 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T24H10.7a.1 | T24H10.7a.1 |
1447
 |
II: 9113157-9132218 |
| Transcript:T24H10.7b.1 | T24H10.7b.1 |
1311
|
II: 9116617-9132217 |
| Transcript:T24H10.7f.1 | T24H10.7f.1 |
1284
|
II: 9118423-9132215 |
| Transcript:T24H10.7h.1 | T24H10.7h.1 |
762
|
II: 9120190-9131865 |
| Transcript:T24H10.7i.1 | T24H10.7i.1 |
651
|
II: 9120806-9131865 |
| Transcript:T24H10.7g.1 | T24H10.7g.1 |
528
|
II: 9122313-9131865 |
| Transcript:T24H10.7d.1 | T24H10.7d.1 |
902
|
II: 9127337-9132223 |
| Transcript:T24H10.7e.1 | T24H10.7e.1 |
870
|
II: 9129391-9132219 |
| Transcript:T24H10.7c.1 | T24H10.7c.1 |
750
|
II: 9130759-9132231 |
Other
9 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T24H10.7a | T24H10.7a |
960
|
II: 9113291-9113402 |
| CDS:T24H10.7b | T24H10.7b |
900
|
II: 9116676-9116727 |
| CDS:T24H10.7i | T24H10.7i |
651
|
II: 9120806-9120918 |
| CDS:T24H10.7d | T24H10.7d |
468
|
II: 9127413-9127627 |
| CDS:T24H10.7c | T24H10.7c |
306
|
II: 9130837-9130889 |
| CDS:T24H10.7e | T24H10.7e |
495
|
II: 9129412-9129653 |
| CDS:T24H10.7f | T24H10.7f |
804
|
II: 9118553-9118580 |
| CDS:T24H10.7g | T24H10.7g |
528
|
II: 9122313-9122492 |
| CDS:T24H10.7h | T24H10.7h |
762
|
II: 9120190-9120296 |
33 RNAi Result
304 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk962682 |
| gk962798 |
| tm11436 |
| WBVar01696088 |
| WBVar01696089 |
| WBVar01696090 |
| WBVar01604409 |
| WBVar01438985 |
| WBVar01438982 |
| WBVar01438980 |
| WBVar01438981 |
| WBVar01377122 |
| WBVar01377133 |
| WBVar01377100 |
| WBVar01377111 |
| WBVar01377089 |
| h8476 |
| h7382 |
| WBVar01826611 |
| cxTi10060 |
| WBVar01935182 |
| WBVar01935179 |
| gk551 |
| gk557 |
| gk150264 |
| gk150263 |
| WBVar01393940 |
| gk450332 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00012005 | 9113157 | 9132231 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
208 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 | |
| Genes that were upregulated in lin-15B(n744). | For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. | WBPaper00038168:lin-15B(n744)_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 that showed significantly increased expression in eft-2(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2 | |
| 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 increased expression in hsf-1(sy441) vs. in N2 day 1 adults without heat shock. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00066900:hsf-1(sy441)_upregulated | |
| 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 altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector. | p-value <= 0.05 | WBPaper00066902:cat-1(RNAi)_regulated | |
| 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 | |
| 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 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 | |
| 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 detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| 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 | |
| Transcripts that showed significantly increased expression in exos-8(RNAi) animals. | fold change > 2, FDR < 0.05 | WBPaper00068292:exos-8(RNAi)_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 | |
| 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 signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. | FDR < 0.05, fold change > 2 | WBPaper00067368:pabp-2(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. | Sleuth | WBPaper00051558:aging_regulated | |
| Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:A-class-motor-neurons_L2-larva_expressed | |
| 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:all-neurons_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2. | Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. | WBPaper00053810:nuo-6(qm200)_upregulated |
14 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr9764 | GFP was expressed at a very low level in body wall muscle, pharyngeal-intestinal valve, intestine and possibly the excretory cell and rectal muscle from L1 to adult. GFP may have been present in all muscle cells. The GFP was weakly nuclear- localized with some cytoplasmic. | The GFP was weakly nuclear-localized with some cytoplasmic. | ||
| Expr9780 | Compared to the other jun-1 reporter gene fusions constructed in this series (e.g. see UL3240, UL3496 and UL3512), GFP expression was quite strong, from embryo to adult, in the pharyngeal-intestinal valve, spermathecae, and probably all muscle cells. The GFP was weakly nuclear-localized with some cytoplasmic. | |||
| Clone: pUL#IAH10D8 | Expr7681 | Strong consistent expression in all 7 lines. Expression is probably constitutive, but in more mosaic lines, more of the individual components could be seen. Stronger expression seen in the excretory cell, the pharynx and the spermathecae. Expression was also seen in the uterus, body wall muscle cells and nervous system. | ||
| Expr9782 | GFP expression was observed from embryo through to adulthood. In L1s, mostly non-nuclear localized patches of GFP were seen. In adults, the pattern looked more complex. GFP that was partly nuclear-localized and partly cytoplasmic, was seen in the pharynx and pharyngeal-intestinal valve, bodywall and tail muscle, and maybe vulval muscle, and spermathecae. In several cells in the head expression was nuclear-localized. | |||
| Expr9740 | Widespread GFP expression was observed, in all stages, with many components. But in all strains obtained, individuals only showed a few components, presumably due to a high degree of mosaicism. Weak GFP expression was seen in many head neurons and tail neurons. Much weaker GFP expression was found in body wall muscle, intestine and spermathecae. GFP expression was weaker than for reporter gene fusions that tagged different specific jun-1 transcripts at the start of the protein coding region. The absence of some expression pattern components that could be seen with transcript specific reporter gene fusion constructions might be due to the low level of expression seen with this fusion with gfp inserted at the end of the protein coding region. | |||
| Expr9763 | Nuclear-localized GFP expression in many nerve ring neurons, and sometimes very weakly in intestine and head muscle. | |||
| Expr1200330 | Data from the TransgeneOme project | |||
| Expr11363 | JUN-1::GFP was nuclear-localized and expressed in all cells of the developing and young adult spermatheca as well as the spermatheca-uterine junction core cells (sujc) in L4, which forms part of the spermatheca-uterine valve. Expression in the spermatheca-uterine valve was not observed in young adults. | |||
| Expr9768 | Weak, nuclear-localized GFP in the developing gonad in larval stages. | |||
| Expr1157629 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2031132 | 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). | |||
| Expr1028025 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2012898 | 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). | |||
| Expr1035307 | Tiling arrays expression graphs |
28 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041) | involved_in |
| happens_during(WBls:0000041) | involved_in |
| involved_in | |
| has_input(WB:WBGene00002008)|has_input(WB:WBGene00013441) | involved_in |
| happens_during(WBls:0000041),has_input(WB:WBGene00002013),happens_during(GO:0042594) | involved_in |
| part_of | |
| part_of(WBbt:0008218) | located_in |
| located_in | |
| located_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041),happens_during(GO:0042594) | involved_in |
| happens_during(WBls:0000041),happens_during(GO:0042594) | involved_in |
| involved_in | |
| enables | |
| enables | |
| enables |
7 Homologues
| Type |
|---|
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
28 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041) | involved_in |
| happens_during(WBls:0000041) | involved_in |
| involved_in | |
| has_input(WB:WBGene00002008)|has_input(WB:WBGene00013441) | involved_in |
| happens_during(WBls:0000041),has_input(WB:WBGene00002013),happens_during(GO:0042594) | involved_in |
| part_of | |
| part_of(WBbt:0008218) | located_in |
| located_in | |
| located_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041),happens_during(GO:0042594) | involved_in |
| happens_during(WBls:0000041),happens_during(GO:0042594) | involved_in |
| involved_in | |
| enables | |
| enables | |
| enables |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_9112959..9113156 | 198 | II: 9112959-9113156 | Caenorhabditis elegans |
