Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F58F9.9a.1 | F58F9.9a.1 |
1043
 |
IV: 6240293-6241558 |
| Transcript:F58F9.9b.1 | F58F9.9b.1 |
847
|
IV: 6240306-6241426 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F58F9.9a | F58F9.9a |
861
|
IV: 6240306-6240365 |
| CDS:F58F9.9b | F58F9.9b |
810
|
IV: 6240306-6240365 |
61 Allele
| Public Name |
|---|
| gk964500 |
| gk963722 |
| gk963417 |
| gk963416 |
| WBVar02124590 |
| WBVar01728405 |
| WBVar01581179 |
| WBVar01728403 |
| WBVar01728404 |
| WBVar01728397 |
| WBVar01728398 |
| WBVar01728395 |
| WBVar01728396 |
| WBVar01728401 |
| WBVar01728402 |
| WBVar01728399 |
| WBVar01728400 |
| gk203373 |
| gk203374 |
| gk203372 |
| WBVar02119475 |
| WBVar02124698 |
| WBVar01900901 |
| gk956161 |
| WBVar02122600 |
| WBVar02103645 |
| WBVar02103644 |
| WBVar00189393 |
| h6198 |
| h7617 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00044307 | 6240293 | 6241558 | 1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIV_6241559..6241854 | 296 | IV: 6241559-6241854 | Caenorhabditis elegans |
11 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 decreased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_downregulated_25C | |
| Bacteria infection: Photorhabdus luminescens | Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_TilingArray |
| Transcripts that showed significantly increased expression in xpf-1(tm2842) comparing to in N2 animals. | DESeq2 1.14.1, fold change > 2, FDR < 0.01. | WBPaper00062497:xpf-1(tm2842)_upregulated | |
| Transcripts enriched in male him-5(e1490 animals, comparing to in N2 hermaphrodite animals from L3 larva to young adult stages. | DESeq FDR < 0.01. | WBPaper00050231:male_enriched | |
| Genes that showed significantly decreased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control. | Fold change > 1.2 or < 0.8. | WBPaper00042477:rsr-2(RNAi)_downregulated_TilingArray | |
| Fungi infection: Harposporium sp. | Genes with increased expression after 24 hours of infection by Harposporium 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:Harposporium_24hr_upregulated_RNAseq |
| Transcripts expressed in male seminal vesicle, according to RNA tomography. | RNA tomography | WBPaper00055648:male-seminal-vesicle_expressed | |
| Transcripts that showed significantly increased expression in postdauer adults comparing to adult animals that bypassed the dauger stage. | DESeq 2, FDR < 0.05. | WBPaper00064494:postdauer_upregulated_WholeAnimal | |
| Transcripts that showed significantly decreased expression in spe-44(fx110) comparing to in control male animals. | DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression. | WBPaper00064502:spe-44(fx110)_downregulated |
4 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2022635 | 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). | |||
| Expr1152773 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2004412 | 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). | |||
| Expr1017167 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |