New ERGO Feature: MetaCyc/EcoCyc/BioCyc Pathway Database Integration

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We’re always aiming to improve the breadth and depth of data we provide to our clients. This is why we’ve integrated SRI’s MetaCyc* and EcoCyc* databases into ERGO. This adds over 3000 new pathways to ERGO. BioCyc functional assignments are computed for every genome in the ERGO database.

The pathway diagrams are drawn using a subset of the System Biology Graphical Notation. The pathway diagrams are completely interactive and can be customized and rearranged to your preference. Each pathway has a summary description and background so that the researcher can completely understand its context.

RNA-Seq and other expression data can be interactively projected onto the BioCyc pathways. BioCyc is also one of the ontologies available for Gene Set Enrichment Analysis (GSEA) and on differential gene expression plots.

ERGO’s differential analysis and GSEA plots can help you quickly identify which pathways are changing under your experimental conditions.

 

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*BioCyc TM pathway/genome databases under license from SRI International. (https://www.biocyc.org).

New ERGO Feature: Violin Plots for Expression Analysis

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We’ve added to ERGO’s rich visualizations with a new plot type: the violin plot. A violin plot is a way to visualize an underlying distribution of values (in our case, log fold change). Similar in utility to a box plot, a violin plot has a few advantages. Instead of just representing the median, quartiles, minimum and maximum, a violin plot uses a kernel density estimation algorithm to visualize the distribution of underlying points.

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New ERGO Feature: Gene Set Enrichment Analysis

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New ERGO Feature: Gene Set Enrichment Analysis

Quickly identify significantly up and down regulated pathway and functional categories using ERGO’s gene set enrichment analysis (GSEA). Gene set enrichment analysis detects concordant movement of gene sets between two phenotypes, usually experimental conditions. In this way the researcher can identify the statistically significant pathways and infer the effect the experimental conditions had upon their organism of study.

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