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New Blast2GO Version 3.3

Major Release Version 4

(Release Date: 13/09/2016) We are very happy to announce the release of Blast2GO 4. This new version contains many new bioinformatic features like Differential Expression Analysis, Gene Finding or Gene Set Enrichment Analysis. Blast2GO will update automatically if activated. Otherwise please download the latest version online from here. Feedback, questions, as well as feature requests, are most welcome. Please write

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Functional Analysis of Pancreatic Cancer Expression Profiles

This use case shows how to perform a functional analysis of pancreatic cancer expression data with Blast2GO. The performed steps are explained more in detail with short video tutorial linked to each section. Malignant (PDAC), benign (CP) and normal tissue (NP) gene lists are compared against each other. The human genome functional annotation data is retrieved via BioMart and used

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How to perform a Gene Set Enrichment Analysis (GSEA)

This articles explains what a Gene Set Enrichment Analysis (GSEA) is, how it works and how it can be performed with OmicsBox. What is an enrichment analysis? An enrichment analysis is a bioinformatics method which identifies enriched or over-represented gene sets among a list of ranked genes. Gene sets are groups of genes that are functionally related according to current

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How to use PSORTb

This tutorial shows how to assign subcellular localizations with PSORTb in OmicsBox/Blast2GO. We also explain how to merge the obtained results to the existing functional annotations of a Blast2GO project. OmicsBox/Blast2GO allows to assigns sub-cellular localization sites to proteins based on their amino acid sequence via PSORTb. PSORTb is an algorithm which can be applied to bacteria or archaea protein sequences

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Coloured Graphs: How to combine multiple functional GO profiles

The Coloured Graph option is a function in Blast2GO which allows to combine and visualize multiple functional profiles within one GO graph. For each group or profile a different color can be assigned and the resulting GO graph can be filtered and colored accordingly. This video shows how to create a text files to generate a Coloured Graph for three

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How to select sequences by function and create ID lists

This tutorial shows how to use the Generic Table and the “Select” functions in Blast2GO to identify sequences based on its biological functions and how to create and combine ID lists. These lists can be saved and used in downstream analysis like e.g. enrichment analysis. In Blast2GO, sequences are shown in table format. Per default, annotation projects use the Blast2GO

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How to perform a Fisher’s Exact Test

OmicsBox allows performing functional enrichment analysis with a Fisher’s Exact Test. It is a statistical test based on contingency tables to study the significance of the association between two kind of classifications. OmicsBox allows to apply this test to Gene Ontology functional annotations and other labels and to compare different gene lists against each other. This is used to identify

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How to use BioMart and GO-Slim

This short video shows how to use BioMart and GO-Slim to download and review the whole human genome functional annotation with Blast2GO. BioMart allows you to download the functional annotations of many different organisms directly into Blast2GO. BioMart offers many different identifiers like e.g. UniProt, Ensembl, HGNC, etc. Additionally to the annotations, it is also possible to obtain the protein

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