Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y25C1A.9b.1 | Y25C1A.9b.1 |
1159
 |
II: 3087942-3091368 |
| Transcript:Y25C1A.9a.1 | Y25C1A.9a.1 |
954
|
II: 3088474-3091296 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y25C1A.9b | Y25C1A.9b |
1002
|
II: 3088027-3088078 |
| CDS:Y25C1A.9a | Y25C1A.9a |
954
|
II: 3088474-3088650 |
126 Allele
| Public Name |
|---|
| gk964317 |
| gk963801 |
| gk962754 |
| h7164 |
| gk963671 |
| gk964487 |
| gk964488 |
| WBVar02124761 |
| WBVar01695166 |
| WBVar01436808 |
| WBVar01244496 |
| WBVar02106401 |
| WBVar01948707 |
| gk137576 |
| WBVar01235055 |
| WBVar01765310 |
| gk137575 |
| WBVar01235056 |
| gk137578 |
| gk137577 |
| WBVar01235059 |
| WBVar01235060 |
| gk137574 |
| WBVar01765311 |
| WBVar01235057 |
| gk137573 |
| WBVar01765312 |
| WBVar01235058 |
| gk137583 |
| WBVar01235061 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00005178 | 3087942 | 3091368 | -1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_3087683..3087941 | 259 | II: 3087683-3087941 | Caenorhabditis elegans |
12 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
| 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 | |
| Heat shock: 34C 30min. | Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min. | DESeq2 v 1.18.1, fold change > 2, FDR < 0.01. | WBPaper00058955:heatshock_upregulated_CE |
| Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron | |
| Transcripts that showed significantly increased expression in hpl-2(tm1489) comparing to in N2 animals. | DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. | WBPaper00054493:hpl-2(tm1489)_upregulated | |
| Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control. | Fold change > 1.2 or < 0.8. | WBPaper00042477:rsr-2(RNAi)_upregulated_TilingArray | |
| Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. | Student's t-test, fold change > 2, p-value < 0.05. | WBPaper00055386:daf-2(e1370)_downregulated | |
| Transcripts that showed significantly increased expression in drh-3(rrr2) comparing to in N2. | edgeR, log2 fold change > 2 or < -2. | WBPaper00053888:drh-3(rrr2)_upregulated | |
| Coexpression clique No. 282, srj-21-srh-32, on the genome-wide coexpression clique map for the nematode GPL200 platform. | All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. | WBPaper00061527:srj-21-srh-32 | |
| Genes predicted to be upregulated more than 2.0 fold in rde-3(ne298) mutant worms as compared to wild-type animals (t-test P-value < 0.05). | A t-test (5% confidence) was applied to the triplicate sample data for each transcript in each mutant to identify genes significantly elevated or decreased compared with the wild type. | WBPaper00027111:rde-3(ne298)_upregulated | |
| Single-cell RNA-Seq cell group 99_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:99_0 | |
| Transcripts that showed significantly decreased expression in cnd-1(ju29) comparing to in N2. | DESeq2 1.16.1 (R3.4.1) | WBPaper00059932:cnd-1(ju29)_downregulated |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2034547 | 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). | |||
| Expr2016320 | 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). | |||
| Expr1159261 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
5 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in |
5 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_3091369..3091502 | 134 | II: 3091369-3091502 | Caenorhabditis elegans |
