Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y54F10BM.20.1 | Y54F10BM.20.1 |
911
 |
III: 2308256-2309706 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y54F10BM.20 | Y54F10BM.20 |
906
|
III: 2308256-2308344 |
63 Allele
| Public Name |
|---|
| gk962532 |
| gk964281 |
| WBVar02122456 |
| WBVar01327303 |
| gk581884 |
| gk795934 |
| gk366768 |
| gk461832 |
| gk692400 |
| gk393662 |
| gk442744 |
| gk683087 |
| gk444777 |
| h17932 |
| h13210 |
| h8309 |
| WBVar02074043 |
| gk958821 |
| gk961396 |
| WBVar00097370 |
| WBVar02102339 |
| WBVar02102338 |
| WBVar01565594 |
| WBVar01565595 |
| WBVar01709456 |
| WBVar01709455 |
| WBVar01709457 |
| WBVar01709448 |
| WBVar01709447 |
| WBVar01709450 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00206486 | 2308256 | 2309706 | 1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_2309707..2309791 | 85 | III: 2309707-2309791 | Caenorhabditis elegans |
9 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 signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. | FDR < 0.05, fold change > 2 | WBPaper00067368:pabp-2(RNAi)_upregulated_N2 | |
| Transcripts of coding genes that showed significantly increased expression in muscle. | DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. | WBPaper00062325:muscle_enriched_coding-RNA | |
| Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage. | DESeq2, FDR < 0.05 | WBPaper00058691:cfp-1(tm6369)_upregulated | |
| Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage. | DESeq2, FDR < 0.05 | WBPaper00058691:sin-3(tm1276)_upregulated | |
| Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:daf-2(e1370)_upregulated_neuron | |
| Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:daf-16(mu86)_upregulated_neuron | |
| Diet: supplemented with milk fat-containing protein powder from L1 to day 2 adult stage. | Transcripts that showed significantly decreased expression in N2 animals fed with OP50 supplemented with milk fat-containing protein powder from L1 to day 2 adult stage. | Differential expression analysis between two conditions (three biological replicates per condition) was performed using DESeq2. Genes with p-value < 0.05 and Fold Change > 2 found by DESeq2 were assigned as differentially expressed. | WBPaper00067530:Milk-protein_downregulated |
| Transcripts that showed significantly increased expression in DA116[eat-2(ad1116)] comparing to in N2. | The DESeq2 package (v1.24.0) was used to identify differentially expressed genes (DEGs). Fold change > 2, FDR < 0.05. | WBPaper00061040:eat-2(ad1116)_upregulated |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2026159 | 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). | |||
| Expr1160848 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2007917 | 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_2308127..2308255 | 129 | III: 2308127-2308255 | Caenorhabditis elegans |
