Workflow of BioTranslator Comparative Analysis
Version 1

Workflow Type: Galaxy
Stable

This workflow is based on the idea of comparing different gene sets through their semantic interpretation. In many cases, the user studies a specific phenotype (e.g. disease) by analyzing lists of genes resulting from different samples or patients. Their pathway analysis could result in different semantic networks, revealing mechanistic and phenotypic divergence between these gene sets. The workflow of BioTranslator Comparative Analysis compares quantitatively the outputs of pathway analysis, based on the topology of the underlying ontological graph, in order to derive a semantic similarity value for each pair of the initial gene sets. The workflow is available in a Galaxy application and can be used for 14 species. The algorithm accepts as input a batch of gene sets, such as BioTranslator, for the same organism. It performs pathway analysis according to the user-selected ontology and then it compares the derived semantic networks and extracts a matrix with their distances, as well as a respective heatmap.

Inputs

ID Name Description Type
Input sets of genes Input sets of genes Input file format: Tab or csv delimited file with a specific gene set in each column. The header is used for gene set labels. n/a
input input runtime parameter for tool Comparative Analysis n/a

Steps

ID Name Description
0 Input sets of genes Input file format: Tab or csv delimited file with a specific gene set in each column. The header is used for gene set labels.
1 BioTranslator Comparative Analysis The algorithm consists of two sequential tasks: 1. Pathway Analysis of the input gene sets, using the selected ontology 2. Comparison of the derived semantic sets, using the topology of ontological graph Outputs: 1. The distance matrix in tsv format 2. A heatmap (png format) which illustrates the agglomerative clustering of input sets, based on the respective semantic distances comparative_analysis

Outputs

ID Name Description Type
ds ds n/a tsv
hm hm n/a png
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Created: 26th Sep 2021 at 19:20

Last updated: 26th Sep 2021 at 19:21

Last used: 17th Oct 2021 at 04:09

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Version 1 Created 26th Sep 2021 at 19:20 by thodk

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