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Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

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Keeping you up-to-date with the latest in NGS, Bioinformatics Analysis, and cancer genomics with blogs on Array Suite, OncoLand (TCGA and more), ImmunoLand, and more.

[New Feature] Geneset Analysis Functionality: integrated with Omicsoft Land databases

Vivian Zhang

Gene Set Analysis is a powerful tool to help users who have their own gene signatures and would like to identify comparisons or other signatures containing similar gene set enrichment from both tens of thousands of comparisons in the Lands as well as customer gene sets for on-premises customers. Recently, Omicsoft officially released our new GeneSet Analysis function. For more details, check out our webinar recording Announcing GeneSet Analysis Functionality, integrated with Omicsoft’s Land databases presented by Matt Newman, VP of Business Development at Omicsoft on September 28th, 2016. 

Previously, Omicsoft's Land system offered a simplified GeneSet Enrichment Analysis. It allowed users to compare their own gene sets with those contained in the Lands: 

Although this was powerful enough to identify comparisons with similar gene sets:

1. it was restricted within a specific Land of choice and not shared across Lands

2. it did not take directionality into account

3. it was not able to include other genesets beyond Land data as target gene sets 

4. it required the user to be familiar with the Land system, and not just the analysis sub-system of Array Suite.

Even though Omicsoft's Array Studio also provides a Molecular Signature module that allows users to compare to Broad's molecular signature database, the Molecular Signature module also does not take directionality into account and requires user to add straight lists to Array Studio Projects, with no ability to incorporate inference reports, nor any of the important data stored within the Lands or easily incorporate customer Gene Sets.


In order to more fully leverage Omicsoft's data assets, we have officially released our new GeneSet Analysis module. The new GeneSet Analysis allows the users to query across OncoLand, DiseaseLand, Molecular Signatures, and more. 

GeneSet Analysis Wizard

GeneSet Analysis Wizard

In addition to the geneset databases included, the new GeneSet Analysis also provides directional results -- up and down p-values and directions.

GeneSet Analysis result

GeneSet Analysis result

We are still in active development of the GeneSet Analysis module, constantly improving our content, functions and visualizations. Here are a couple examples we are working on:

1. Multi-species data support in addition to human and mouse data

2. Additional visualizations based on table results

If you have any comments or suggests, please let us know. 


Want to give it a try? Please check out our latest webinar Announcing GeneSet Analysis Functionality, integrated with Omicsoft’s Land databases and our GeneSet Analysis wiki for detailed illustration.