Welcome to OBELiX (Ochre Bio Encyclopedia for Liver Xploration), Ochre's software for the generation of gene reports and recommendation reports. This fork of the software contains the gene report functionality, where you are able to (i) explore the expression associations of 15,000 genes with liver cellular, histological, and clinical phenotypes from over 1000+ livers and (ii) mechanistically study the proprietary and public signatures these genes enrich for with their knockdown in human hepatocytes cultured under baseline and steatohepatitis conditions.

To start, enter one or more genes (their symbols or Ensembl Gene IDs), or import a list of genes, and click "View Gene Report". Each report contains four interactive sections with plots that can be downloaded as individual PNGs or a single PDF.

1. The first section contains general information describing the gene, together with links to useful external resources.
2. The second section contains a single-cell UMAP plot visualising the gene's expression across 20 liver cell populations taken from 6h biopsies of 50 perfused livers.

The barplot allows you to visualise how this changes with sex, age, steatosis score, inflammation score and ballooning scores.
3. The third section contains expression associations with histological and clinical traits from Ochre’s 1000-liver atlas.

It also contains perturbation signature associations with its knockdown in human hepatocytes cultured under baseline and steatohepatitis conditions.

The signatures are either biological (gene ontologies, public or proprietary signatures) or Ochre’s knockdown signatures of the genes upregulated or downregulated with a gene’s knockdown.

The perturbation association plot also displays the effect of the knockdown on gene expression.
4. Clicking on any associations in the above plots opens up a volcano plot of all genes associated with that phenotype or signature.

Clicking on any gene on the volcano plot will open its respective gene report.

 

Recommendation Report

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