Welcome to the Ahringer lab C. elegans regulatory atlas

Explore and mine C. elegans developmental and tissue-specific regulatory elements and genes

Single gene information

Gene not found. Please enter a valid gene locus (e.g. hlh-1) or WormBaseID (e.g. WBGene00001948)

Quick gene information:


Wormbase description:


Additional resources:

Temporal and spatial gene expression profiles

Associated accessible elements and tissue-specific accessibility values

Input a list of genes to determine:

(1) their overlap with the gene expression classes defined in Serizay et al. (submitted);

(2) their expression in different young adult (YA) tissues;

(3) the tissue-specific accessibility of the associated accessible chromatin loci;

(4) the GO terms enriched in the gene list.

Long lists will take a while to be processed

Intersection of query genes with adult gene expression classes from Serizay et al. (submitted)


Download full tissue-specific datasets

Search ATAC-seq data

Search RNA-seq data

General Information

Data availability

The tissue-specific accessibility and expression data displayed in this application are from Serizay et al, submitted; raw data are available from GEO accession number GSE141213. Processed data are downloadable from the "Explore/Download datasets" of this application. Developmental time course accessibility and expression data are from Janes et al, 2018 (DOI: 10.7554/eLife.37344e). Tissue-specific expresssion at the L2 stage are from single cell sequencing data in Cao et al, 2017 (DOI: 10.1126/science.aam8940).

Genome version

Gene and regulatory element coordinates are in the WBcel235/ce11 version of the genome. Genome sequence and gene annotations were obtained from Ensembl release 92.

Additional information

Background RNA contamination

We found that RNA from some highly expressed tissue-specific genes was unexpectedly detected in all sorted tissue samples. This appears to be due to contamination by cytoplasmic mature RNA released during nuclear isolation. This RNA, released from all of the tissues of the animal, may have adhered to the outside nuclei, and thus be carried over into all samples. We found that the carry-over is primarily detectable for highly expressed genes (e.g, muscle myosin unc-54).

Background removal

To estimate and remove background contamination in our RNA-seq samples, we used the DSA 1.0 package [Zhong et al., BMC Bioinformatics 2013] in R with default parameters and the linear regression method. The corrected gene expression values are displayed in the "Look-up gene" tab (third barplot).
The DSA package estimates tissue-specific gene expression from mixed samples (e.g. complex tissues or samples with contamination) using profiles of "pure" genes known to be expressed in a single tissue. DSA normalisation improves profiles for tissue-specific genes, but introduce tissue biases for broadly expressed genes.

The following genes were used as "pure" tissue-specific genes for the DSA-based background correction:
- Germline: maph-1.2, prom-1, zim-3, htp-2, xnd-1;
- Neuron: ncx-4, tsp-7, oig-8, Y106G6G.6, Y106G6G.2, C35E7.2, F32B4.5, ttr-39;
- Muscle: B0379.1, srp-3, ttr-36, Y97E10AR.2, C13C4.7, tsp-11, lev-8;
- Hypodermis: fip-5, osm-8, ptr-16, F36H9.5, nipi-4, R07E3.7;
- Intestine: Y106G6H.1, F46A8.11, ugt-6, T02B5.3.

App development

This app was built in R 3.5.1 "Feather Spray", with Shiny 1.1.0. The source code of this app is available on Github.

Contact information

Jacques Serizay

Developer of RegAtlas

Ahringer lab

Gurdon Institute, University of Cambridge, UK