Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C08C3.3.1 | C08C3.3.1 |
1103
 |
III: 7776835-7783454 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C08C3.3 | C08C3.3 |
603
|
III: 7777269-7777391 |
101 Allele
| Public Name |
|---|
| gk964518 |
| gk963887 |
| WBVar01607135 |
| WBVar01710144 |
| WBVar00066558 |
| mu14 |
| WBVar02053403 |
| WBVar00066563 |
| e1936 |
| WBVar00061464 |
| WBVar01446864 |
| WBVar00061469 |
| WBVar01645532 |
| WBVar01645533 |
| WBVar00061474 |
| WBVar00061479 |
| WBVar01838108 |
| WBVar01838107 |
| WBVar00061484 |
| WBVar01838105 |
| WBVar00061489 |
| WBVar00061494 |
| WBVar00061499 |
| WBVar01408916 |
| ok5304 |
| WBVar01408915 |
| WBVar00061504 |
| WBVar00061509 |
| bx54 |
| WBVar00061514 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003102 | 7776835 | 7783454 | -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_7776034..7776834 | 801 | III: 7776034-7776834 | Caenorhabditis elegans |
161 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
| 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 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 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 that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141) | |
| Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141) | |
| 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 | |
| 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 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 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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. | Sleuth | WBPaper00051558:aging_regulated | |
| 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 | |
| Gamma irradiation 100 mGY per hour for 72 hours since L1 larva. | Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage. | DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3. | WBPaper00058958:100mGy-irradiation-72h_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:A-class-motor-neurons_L2-larva_expressed | |
| Reduced humidity (98% relative humidity). | Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis. | Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001. | WBPaper00044578:reduced-humidity_downregulated_microarray |
| 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 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:GABAergic-motor-neurons_L2-larva_expressed | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:hypodermis_L3-L4-larva_expressed | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:PVD-OLL-neurons_L3-L4-larva_expressed | |
| Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. | DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. | WBPaper00062159:hda-2(ok1479)_upregulated |
21 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031467 | Tiling arrays expression graphs | |||
| LacZ expression in posterior of the worm-consistent with in situ pattern. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr694 | Expression observed in cells of Q lineage, at first expression is specific for the left Q cell lineage; No expression in QR or its descendants. mab-5::lacZ is not expressed in QL during initial mab-5 independent phase of its migration but is switched on in QL during the course of its migration. beta-galactosidase expression is strongest after first division and persists throughout the migration of the QL descendants. QL moves into a region of the body where ectodermal, mesodermal and endodermal cells express mab-5-lacZ, QR migrates anteriorly into a region where only the juvenile neurons express mab-5-lacZ. After Q cell migration is complete expression observed in QL at low-level but not in QR. After Q cells have divided, QL descendants express high levels of the fusion. Staining persists in all QL descendants throughout migration and to end of L1. There is no expression in QR descendants. 0-2 hours after hatching No expression in Q cell. 2-3h expression observed in QL cells migrating up over V5. Expression observed in all posterior cells in which mab-5 function is predicted genetically, as well as the posterior intestine and juvenile neurons. | ||
| Clone: pUL#JRH10H7 | Expr7424 | Expression observed from early embryo to adult. Weak general expression in early embryo, weak anterior and ventral expression in mid embryo. Later expression in dorsal nerve cord, ventral nerve cord, other nerves in head and tail. In L1 can see expression in all body wall muscles. After L1 can see weak (possibly artifactual) expression in head muscles and also in posterior intestine. | ||
| Expr16258 | For lin-39 and mab-5, previous work reported their partially overlapping expression in the ventral cord motor neurons (MNs). In this study, we used two fosmid reporters wgIs18[lin39::EGFP] and wgIs27[mab-5::EGFP] to map their expression to the single-cell resolution among the 75 motor neurons (MNs), which include 54 cholinergic MNs, 19 GABAergic MNs, and 2 serotonergic MNs with stereotypical positions. These MNs can be further classified into eight neuron classes (DA, DB, VA, VB, AS, VC, DD, and VD). By crossing the GFP reporters with mCherry strains labelling cholinergic or GABAergic neurons in the ventral cord, we identified lin-39 expression in DA2-5, DB2-7, VA3-8, VB4-9, AS2-8, VC1-6, DD2-6, and VD3-12 and mab-5 expression in DA4-8, DB5-7, VA6-11, VB8-11, AS5-11, VC3-6, DD2-6, and VD2-12. Both lin-39 and mab-5 expression were generally weaker in more anterior MNs. Interestingly, for cholinergic MNs, mab-5 and lin-39 expression only overlapped in a set of mid-body MNs; MNs more anterior to this region expressed only lin-39 and MNs more posterior expressed only mab-5. For GABAergic MNs (DD and VD), however, lin-39and mab-5 expression overlapped entirely. Outside of the ventral nerve cord, lin-39 was expressed in AQR and AIYL/R in the head and AVM, SDQL/R, PDEL/R, and PVDL/R neurons along the body; mab-5 was expressed in the AVL in the head, SDQL in the mid-body region, and PQR neuron in the tail. | |||
| Expr15629 | ||||
| Expr1200084 | Data from the TransgeneOme project | |||
| early + mid embryo(author) = gastrulating + enclosing embryo(curator). | Expr585 | At the 200-cell stage, four posterior ventral cells stain, AB.p(r/)lpppp(a/p). At about 350 cells, their eight descendants, and about 12 other cells including lateral and ventral epidermal blast cells, show expression. By the 1.5-fold stage, additional cells stain, e.g., posterior ventral cord neuronal precursors. Most of the cells continue to stain at L1, with the notable exception of the eight descendants of the four cells that show initial staining. | Muscle sarcomeres and nuclear localization. Staining is nuclear localized. | |
| Expr10501 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr10502 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr11558 | Expressed in ventral cord neurons, anchor cell, tail neuron. | |||
| Expr1516 | About 8 hour after hatching, P cells descend into the ventral nerve cord and interdigitate to form a single row of cells of P1-P12. In both sexes, mab-5 was detected in P7-P10. In older larva, mab-5 was detected in P7-P12, but not more anterior cells. In hermaphrodites, expression pattern was similar to males with two exceptions. The p(9-11).app cells and p(9-11).p cells no longer express MAB-5 by L2. In male, descendants of P10 consistently express high levels of MAB-5, those of P9 and P11 express low levels, and those of P7 and P8 express barely detectable levels. P12 descendants express MAB-5 only until the division of P12.a. The descendants of P cells express comparable levels of MAB-5 with exceptions to Pn.p cells, they express lower levels than their neighbors. Expression levels in P descendants were similar to those seen in the neighboring juvenile motoneurons. Both sets of cells expressed MAB-5 in a graded pattern, tapering off toward the anterior. In newly hatched larva, in both sexes, mab-5 was detected consistently in nuclei of P9/10 and P11/12, but not more anterior P cells. mab-5 was also detected at high levels in the posterior juvenile motoneurons, located ventrally. MAB-5 is localized to the posterior of the body, including P7-P12 in the P lineage but not in more anterior cells. Within P7-P12, MAB-5 expression was graded with the highest levels in the P10 descendants. The descendants of any one P cell expressed comparable levels of MAB-5. | |||
| Expr9685 | Expression of the Wnt target gene mab-5 was examined in Q neuroblasts after initial migration but before Q.d cell migration. Expression of mab-5 was quantified using smFISH in Q neuroblasts and was plotted against the position of the Q neuroblasts on the anteroposterior axis. In wild type animals, mab-5 was expressed at an average of 30 ± 7.1 (mean ± SD, n = 32) transcripts per cell in QL, and 3 ± 2.9 transcripts per cell in QR (n = 28). We found that the average mab-5 expression level was similar in QL and QR (p > 0.1, t-test). Importantly, we observed that mab-5 expression correlated with the position of the Q neuroblasts on the anteroposterior axis after initial migration. Thus, mab-5 transcript counts were significantly higher in posteriorly positioned Q neuroblasts than in Q neuroblasts that had migrated toward the anterior. | |||
| Expr1021791 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr14629 | In wild type animals, less than five mab-5 transcripts were detected in QR. This number decreased in QR.p and no mab-5 transcripts could be detected in QR.pa. | |||
| Expr13570 | In WT, mab-5 expression was detected at the posterior end of the animal and specific localisation to the posterior V5 daughter cell after the first L2 division. | |||
| Expr2013328 | 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). | |||
| Expr2031560 | 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). | |||
| Expr1144149 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr695 | L1-L3 High level of expression observed between the anus and a position roughly midway the anus and gonad. Lower level of staining extends further anteriorly between this region and head, anterior body region or the tail (posterior to anus) | ||
| Expr12590 | The middle-body Hox gene mab-5 is not detectably expressed in either ALM or PLM. | |||
| Expr1170023 | 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 |
24 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| results_in_movement_of(WBbt:0004056),happens_during(GO:0002119) | involved_in |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00001170) | involved_in |
| located_in | |
| part_of | |
| enables | |
| enables | |
| acts_upstream_of | |
| has_input(WB:WBGene00001170) | contributes_to |
| acts_upstream_of | |
| acts_upstream_of | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables |
16 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
24 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| results_in_movement_of(WBbt:0004056),happens_during(GO:0002119) | involved_in |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00001170) | involved_in |
| located_in | |
| part_of | |
| enables | |
| enables | |
| acts_upstream_of | |
| has_input(WB:WBGene00001170) | contributes_to |
| acts_upstream_of | |
| acts_upstream_of | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables |
1 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Binding targets of MAB-5, according to ChIP-Seq analysis. | N.A. | WBPaper00037946:MAB-5_interacting |
21 Strains
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_7783455..7793445 | 9991 | III: 7783455-7793445 | Caenorhabditis elegans |
