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Worm Perturb-Seq
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We applied Worm Perturb-Seq (WPS), a high-throughput RNAi and RNA-seq method, to ~900 metabolic genes in the nematode Caenorhabditis elegans and derive a metabolic gene regulatory network (mGRN) in which the knockdown of 365 metabolic genes is connected to 9,414 genes by more than 110,000 interactions. The mGRN reveals a highly modular network structure, characterized by distinct clusters of perturbations and co-regulated gene modules affected by these clusters. This website provides a user-friendly interface for exploring the mGRN. We also applied WPS to 103 nuclear hormone receptors (NHRs), with the data searchable and downloadable from this website.

WPS portal version 0.04 - Walhout Lab

Search a gene from metabolic or NHR Gene Regulatory Network (GRN)

Download Table

Interactive plot of perturbation clusters

Tip: click any dot to view the heatmap of all DEGs and their Wald statistics within the selected cluster. Use Box Select tool to enlarge an area for details.
This 2-D layout was generated by densMap (Narayan et al., Nat. Biotech. 2021), where the local density proxies variability of the cluster perturbations.
Download DEG Table for Selected Cluster

Search a Gene Expression Program (GEP)

By a GEP name
By a gene residing in a GEP

Gene set enrichment for genes in selected GEP

1. GEP Wald statistic is a test statistic following standard normal distribution and describing the GEP changes in a perturbation.
2. Larger dots indicate significant change (adjusted p-value < 0.05) of the GEP in the corresponding perturbation.
Bubble plot of metabolic perturbation clusters versus GEPs
Heatmap of clicked bubble
Download data of heatmap
Bubble size indicates -log10(p.adj) of the cluster-level GEP change. P.adj less than 0.001 is shown as 0.001 (bubble size of 3).

Original heatmap

Search Heatmap

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Selected sub-heatmap

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Click the button below to turn the sub-heatmap into an interactive app.

Export values in sub-heatmaps as a text table.

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Download Tables

Click to download DEG table of WPS on metabolic genes with FDR < 0.1 and FC > 1.5

DEG Table_metabolic

Click to download read-count table of WPS on metabolic genes

Read-count Table_metabolic

Click to download Wald statistics table for all metabolic WPS

Wald Statistics Table

Click to download DEG table of WPS on NHR genes with FDR < 0.1 and FC > 1.5

DEG Table_NHR

Click to download read-count table of WPS on NHR genes

Read-count Table_NHR