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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.

[IMMUNOLOGICAL RESEARCH] Research an Immunological Genome Study in ImmunoLand

Vivian Zhang

Traditionally immunology studies are focused on a particular protein or pathway. However, immunological activity is a system-level response, which is well suited for large-scale integrative approaches and requires an overall perspective on the immune system(s). With advanced technologies enabling large-scale, genome-level approaches, immunology studies are embracing the era of immunogenomics (Related Readings: Beyond the transcriptome: completion of act one of the Immunological Genome Project. ).

ImmunoLand is Omicsoft's most recently developed Land database. It is an immune-related genomics database and visualization software that helps users explore public and private immune-focused genomics datasets. In ImmunoLand, researchers can search a gene, multiple genes, a pathway, a project or multiple projects across more than 22,000 samples from public projects, including GEO (Gene Expression Omnibus), SRA (Sequence Read Archive), ArrayExpress, dbGAP (The Database of Genotypes and Phenotypes), and other large data repositories like BluePrint, GTEx, and ImmGen (The Immunological Genome Project). 

Here is how:

Immunological genomics studies are currently conducted based on many different diseases, immune cells, activation responses, treatments, tissues, states of cell differentiation and so forth. In ImmunoLand, each study in the database is carefully reviewed by Omicsoft’s curators, with meta data clean-up occurring, outliers removal, and then statistically-driven comparisons generated for each study. ImmunoLand allows the users to be able to search across projects, or search directly for a project of interest. For example, let's search for the project GSE37448 from the Immunological Genome Project:

Figure: Gene Expression Intensity Heatmap categorized by disease category

Figure: Gene Expression Intensity Heatmap categorized by disease category

By default, the view is displaying a heatmap of the expression intensity of samples, categorized by disease category. It is interesting to look at the heatmap of the genes with highest differential expression across cell types: 

Figure: Gene Expression Intensity Heatmap of genes with Gene Rank Expression Intensity <100

Figure: Gene Expression Intensity Heatmap of genes with Gene Rank Expression Intensity <100

Figure: Expression Per-Gene View showing gene CD3G

Figure: Expression Per-Gene View showing gene CD3G

Next, the user can search for their gene(s) of interest across projects to compare different comparisons (diseases, immune cells, activation responses, treatments, tissues, states of cell differentiation). The GSE37448 study was done in mouse. It might, for instance, be interesting to check out the gene expression in human organs in ImmunoLand2015 instead of ImmunoMouse2015.