Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y75D11A.6.1 | Y75D11A.6.1 |
120
 |
X: 1748403-1748576 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y75D11A.6 | Y75D11A.6 |
120
|
X: 1748403-1748430 |
20 Allele
| Public Name |
|---|
| gk963725 |
| gk964444 |
| gk964445 |
| gk963977 |
| otn10330 |
| otn9081 |
| otn12563 |
| otn11605 |
| otn16665 |
| otn3605 |
| otn949 |
| WBVar02123948 |
| otn20215 |
| otn4540 |
| otn19071 |
| otn13509 |
| otn5541 |
| WBVar02123610 |
| otn18450 |
| otn6861 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00044561 | 1748403 | 1748576 | -1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_1746218..1748402 | 2185 | X: 1746218-1748402 | Caenorhabditis elegans |
6 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 | |
| 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 dpy-21(e428) comparing to in N2 during L3 stage. | DESeq v1.6.3. Fold change > 1.5. | WBPaper00050370:dpy-21(e428)_L3_upregulated | |
| Genes that showed flat mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. | The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. | WBPaper00044736:flat_dev_expression | |
| Genes identified by ChIP-Seq analysis that are detected in both klf-1 overexpressor worms and isp-1;ctb-1 mutants | N.A. | WBPaper00059194:KLF-1_interacting | |
| 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 |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2026669 | 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). | |||
| Expr1010390 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1161895 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_1748577..1756158 | 7582 | X: 1748577-1756158 | Caenorhabditis elegans |
