Expression Cluster
Expression clusters are listed of genes that are differentially expressed in high throughput expression studies including microarray, tiling array, RNA sequencing, single-cell RNA Sequencing, and proteomics. Expression clusters allow users to get function and tissue expression information for unknown genes in multiple nematode species.
A WormBase curator gets differentially expressed gene lists from supplementary files of publications. To get these data into WormBase, we need to map all the entities into WormBase IDs. These include gene ID, anatomy term, life stage, and molecule ID for chemicals used in the experiments. We also need to know how the authors processed raw data to get these differentially expressed genes. It is critical that authors provide all necessary information to assure that their data is interpreted correctly by curators. Here are some examples of information that we expect to see in published papers.
Software Package (example: DESeq2 v 1.22.16)
Threshold (example: FDR < 0.05 and fold change > 2)
Version of WormBase genome used for mapping (example: WS288)
Life stage of animals studied (example: L4 larva)
Sample Supplementary file for the differentially expressed gene list. This is an example of a single-cell RNASeq study
| Cell Type | Anatomy name | Anatomy term | Gene ID | Gene Name | P value | avg_logFC | Adjusted p value |
|---|---|---|---|---|---|---|---|
| AVF | AVF | Wbbt:0003851 | WBGene00017850 | F27B10.1 | 0 | 4.7088800284 | 0 |
| AVF | AVF | Wbbt:0003851 | WBGene00003752 | nlp-14 | 0 | 3.3727323703 | 0 |
| AVF | AVF | Wbbt:0003851 | WBGene00016114 | flp-27 | 0 | 2.710326377 | 0 |
| Intestine | intestine | Wbbt:0005772 | WBGene00012615 | dct-16 | 0 | 3.2522967876 | 0 |
| Intestine | intestine | Wbbt:0003851 | WBGene00015913 | C17F4.7 | 0 | 1.9188317409 | 0 |
| Intestine | intestine | Wbbt:0003851 | WBGene00022497 | Y119D3B.21 | 0 | 1.876397092 | 0 |
| I5 | I5 neuron | Wbbt:0004740 | WBGene00022144 | pghm-1 | 2.89711642079677E-116 | 0.7731186731 | 5.85565170971444E-112 |
| I5 | I5 neuron | WBbt:0004740 | WBGene00011392 | sbt-1 | 2.60560798327927E-113 | 0.7449088966 | 5.26645485580406E-109 |
| I5 | I5 neuron | Wbbt:0004740 | WBGene00010059 | F54E4.3 | 1.45086508671097E-109 | 0.3023744639 | 2.9324885132602E-105 |
| RMD_LR | RMDL, RMDR | Wbbt:0005037, Wbbt:0005033 | WBGene00012760 | Y41C4A.17 | 4.6219153647023E-60 | 0.8402976236 | 9.34181533513628E-56 |
| RMD_LR | RMDL, RMDR | Wbbt:0005037, Wbbt:0005033 | WBGene00022144 | pghm-1 | 3.05192716357593E-53 | 0.6003905586 | 6.16855518301966E-49 |
| RMD_LR | RMDL, RMDR | Wbbt:0005037, Wbbt:0005033 | WBGene00012853 | Y44A6D.2 | 8.59653038778404E-52 | 0.5616972229 | 1.73753072197891E-47 |
| PHso | phasmid socket cell | WBbt:0008410 | WBGene00009724 | F45D3.4 | 1.05021281935678E-133 | 1.3380881797 | 2.12269015048392E-129 |
| PHso | phasmid socket cell | WBbt:0008410 | WBGene00018250 | F40H3.2 | 7.33293398018014E-131 | 1.0461751837 | 1.48213261607401E-126 |
| PHso | phasmid socket cell | WBbt:0008410 | WBGene00017748 | F23F1.7 | 4.4503443463399E-127 | 2.4747040271 | 8.9950359928222E-123 |
To map your gene names (public name, sequence name or Uniprot IDs) into WormBase IDs, you can use WormBase SimpleMine: https://wormbase.org/tools/mine/simplemine.cgi
To map your cell names into WormBase Anatomy term, you can use this table: http://caltech.wormbase.org/pub/wormbase/spell_download/tables/AnatomyTable.csv
