Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T04A6.4.1 | T04A6.4.1 |
564
 |
III: 7608570-7609268 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T04A6.4 | T04A6.4 |
564
|
III: 7608570-7608938 |
14 Allele
| Public Name |
|---|
| gk964518 |
| gk963887 |
| gk854247 |
| gk385794 |
| gk342944 |
| gk774537 |
| gk891079 |
| WBVar01837931 |
| WBVar00060910 |
| gk178582 |
| gk178581 |
| WBVar01837930 |
| WBVar01446788 |
| otn11086 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00194734 | 7608570 | 7609268 | -1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_7608324..7608569 | 246 | III: 7608324-7608569 | Caenorhabditis elegans |
10 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066485:ogt-1(ok1474)_upregulated_neuron | |
| Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. | Student's t-test, fold change > 2, p-value < 0.05. | WBPaper00055386:daf-2(e1370)_upregulated | |
| Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. | N.A. | WBPaper00026929:sir-2.1_overexpression_regulated | |
| Genes enriched in AMsh glia. | Two different statistical methods were used for differential gene expression analysis, DESeq and voom. For DEseq analysis, DESeq2 was applied to normalize count matrix and to perform differential gene expression on the counts using negative binomial distribution; for voom analysis, edgeR was applied to normalize count matrix, and voom was applied for gene differentiation analysis. Significant genes from both analyses were combined. To identify transcripts enriched in AMsh glia compared to other cells (control AMsh versus control non-AMsh), authors used a fold change of 3.5 and an adjusted p value threshold of <0.05. | WBPaper00049489:AMsh-glia_enriched | |
| Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. | N.A. | WBPaper00026929:Resveratrol_regulated_daf-16 | |
| Germline-enriched and sex-biased expression profile cluster D. | hierarchical clustering | [cgc6390]:Cluster_D | |
| spermatogenesis-enriched | Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. | [cgc6390]:spermatogenesis-enriched | |
| Genes with more than 2 fold increase of expression after 500 mg/l acrylamide treatment comparing with control. | Two-sided t-test, p < 0.005. | WBPaper00031184:acrylamide_upregulated | |
| Transcripts that showed significantly increased expression in eat-2(ad465) comparing to in N2. | Student's t-test, fold change > 2, p-value < 0.05. | WBPaper00055386:eat-2(ad465)_upregulated | |
| Genome-wide analysis of developmental and sex-regulated gene expression profile. | self-organizing map | cgc4489_group_10 |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1155961 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2005795 | 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). | |||
| Expr2024012 | 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). |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_7609269..7612107 | 2839 | III: 7609269-7612107 | Caenorhabditis elegans |
