Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F13D11.2a.1 | F13D11.2a.1 |
4478
 |
X: 5822142-5827755 |
| Transcript:F13D11.2b.1 | F13D11.2b.1 |
2883
|
X: 5823132-5826361 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F13D11.2a | F13D11.2a |
2949
|
X: 5822277-5822279 |
| CDS:F13D11.2b | F13D11.2b |
2883
|
X: 5823132-5823178 |
79 RNAi Result
75 Allele
| Public Name |
|---|
| gk393245 |
| gk849124 |
| gk936978 |
| gk886877 |
| gk366972 |
| gk546873 |
| gk750146 |
| gk515148 |
| gk894950 |
| gk670159 |
| gk766396 |
| gk346291 |
| gk424510 |
| gk688957 |
| gk730485 |
| gk551369 |
| gk551834 |
| gk437159 |
| gk602377 |
| gk605335 |
| gk411429 |
| gk669308 |
| gk738226 |
| gk631962 |
| gk493905 |
| gk454576 |
| gk859322 |
| gk859323 |
| gk829881 |
| gk344824 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001824 | 5822142 | 5827755 | 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_chrX_5827756..5829434 | 1679 | X: 5827756-5829434 | Caenorhabditis elegans |
268 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 |
| 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 |
| 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:bodywall-muscle_L1-larva_expressed | |
| Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_upregulated_25C | |
| 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 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_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin_upregulated | |
| Transcripts that showed significantly increased 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_upregulated | |
| 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 that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248) | |
| 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 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 that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. | DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. | WBPaper00056169:rrf-3(pk1426)_upregulated_embryo | |
| Bacteria: Pseudomonas donghuensis HYS | Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to OP50. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00068216:FUR_vs_OP50_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 |
| 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 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h |
| 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 | |
| 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 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h |
| 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 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 | |
| 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 |
15 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031071 | Tiling arrays expression graphs | |||
| Picture: Figure 2. Reporter gene fusion type not specified. | Expr7911 | Expressed in more than 10 neurons but not ASE. | ||
| Clone: pUL#JRH/AG5 | Expr7503 | From late embryo to adult, expression is seen in muscles of head, body, vulva and rectum. Expression is also seen in ten nerves in the head, six nerves in the post-anal tail, and one nerve on ventral side of the pre-anal tail. | ||
| Expr12968 | hbl-1 showed pan-germline expression. Reporter expression was observed in the distal region of the germline, in mitotic progenitor cells, as well as in the syncytial region, in the germline bend, in oocytes, and in embryos. The hbl-1 reporter expression was faint in all regions of the germline. No expression was observed in sperm, consistent with the findings of Seydoux and co-workers that suggests sperm expression is governed via transcriptional regulation at the promoter, rather than post-transcriptionally through 3'UTR level. | |||
| Same construct used in Expr542. | Expr2602 | HBL-1::GFP expression was observed in the hypodermal syncitial cells (e.g., hyp7), in the ventral hypodermal cells (P cells), and weakly in the lateral hypodermal seam cells (H, V, and T cells). By the L2 stage, HBL-1::GFP was no longer expressed in the seam cells but was still observed in P cell descendants and weakly in the non-seam cell hypodermis. By the L3 stage, HBL-1::GFP was virtually absent in the hypodermis and Pn.p cell descendants, but was still highly expressed in the ventral nerve cord (generated from Pn.a cells) (100%, n=40) and other unidentified neurons. Early L4 animals express high HBL-1::GFP levels in the VNC (76%, n=26), while late L4 and adult animals express HBL-1::GFP very weakly in the VNC (100%, n=40). In some adult VNCs, expression is undetectable. As judged by this HBL-1::GFP fusion, HBL-1 expression is downregulated during the course of postembryonic development, with highest expression in L1 animals and lowest expression in adults. | ||
| Expr13377 | During WT development, hbl-1::GFP is highly expressed in the hypodermis upon hatching and throughout the L1, but is down-regulated as development proceeds, becoming undetectable by the L3. | |||
| Expr542 | Expressed in hypodermal precursors, primordial pharynx, and cells surrounding developing buccal and rectal openings at comma stage embryo. Found in P1/2 - P11/12, V1L/R - V6L/R, H0L/R - H2L/R, hyp4, hyp6, and hyp7 cells at comma to 1.5-fold stage embryo. First detected at ~500-cell stage in hypodermal precursor cells and several unidentified cells in the developing tail. Comma-stage and 1.5-fold stage, Expression in many hypodermal precursor cells including P1-12, V1-6 (QV5), H0-H2, hyp4, hyp6, hyp7 cells as well as several presumptive hypodermal cells clustered in the tail. Expression at this stage is also observed in the primordial pharynx as well as in the arcade cells encircling the forming buccal cavity. Posterior expression is detected in cells surrounding the forming rectum and in other cells likely to be neuronal precursors. Later in embryogenesis, GFP detected in majority of pharyngeal cells as well as in neurons with no difference in expression in the cells of the hypodermis. In larvae, GFP observed predominantly in neurons. Staining in ventral nerve cord (first detected in L1 prior to migration of P-cells and is later observed in many cells of the ventral nerve cord from L2-L4). Staining is also detected in hermaphrodite-specific neurons HSN beginning around L2 stage and in the canal associated neurons beginning around L3. Staining is also seen in many neurons of the anterior nerve ring, the dorsal nerve cord and several neurons in the tail. In young adult, weak expression observed in muscle cells. | |||
| Expr12657 | hbl-1 was not detected in the AC before or during the time of invasion, but was expressed in the ventral nerve cord and underlying vulval cells (VPCs) at earlier stages of development. | |||
| Expr9939 | hbl-1 promoter is expressed at significantly higher levels in DD neurons than in VD neurons. | |||
| Expr2030610 | 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). | |||
| Expr2012374 | 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). | |||
| Expr1148445 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1170020 | Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191 | |||
| Expr1012633 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr770 | High level of expression in the mixed-stage embryonic population. Present at low levels in pregastrulation embryo stage. Present in all larval stages at low levels decreasing progressively with age. |
22 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00002285) | involved_in |
| has_input(WB:WBGene00003015) | involved_in |
| enables | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in |
22 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00002285) | involved_in |
| has_input(WB:WBGene00003015) | involved_in |
| enables | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_5822035..5822141 | 107 | X: 5822035-5822141 | Caenorhabditis elegans |
