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Overview

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

Exciting Updates and Latest News

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.

[Land Tutorial] Getting Started With DiseaseLand (ImmunoLand And CVMLand)

Vivian Zhang

 

Starting with the Q2 2016 release, Omicsoft replaced ImmunoLand and CVMLand with DiseaseLand in its Land user interface.  DiseaseLand focuses on datasets of common genetic disease including but not limited to immunological diseases, neurological disorders, metabolic diseases and cardiovascular diseases. 

Relatively new to customers, DiseaseLand has been gaining popularity among our prestigious client companies. For a quick review of DiseaseLand content, please check out our wiki article Introduction to DiseaseLand Content. Today, we would like to introduce to you our ImmunoLand video tutorials to help you quickly get started with DiseaseLand.

 

 

DiseaseLand is similar to OncoLand at large. If you are already an OncoLand user, DiseaseLand has most of the advanced analytics functions as covered in OncoLand trainings. 

Besides sample, gene and variable views, DiseaseLand features comparison views. It allows users to easily search and visualize data using common queries: Treated vs Control, Disease vs Normal, Responder vs Non-Responder etc. Comparison statistics are also available when taking a first look at DiseaseLand:

Comparison Distribution View. Comparison Details and Project Details are available once the users select a group of samples. For examples, Comparison Details include information on comparison test method and comparison category as highlighted in the figure.   

Comparison Distribution View. Comparison Details and Project Details are available once the users select a group of samples. For examples, Comparison Details include information on comparison test method and comparison category as highlighted in the figure. 

 

 

At present, DiseaseLand data is primarily focused on gene expression from microarrays and NGS studies. The user can search for a gene of interest and narrow down to find interesting projects interactively. The default view for DiseaseLand is Disease vs Normal Comparison. By selecting the comparison of interest, sample details of the comparison will be displayed in the Details Window. More details on gene, probe and project level are also available. 

 

 

Experimental designs in projects within DiseaseLand are quite different, and batch effects in microarray projects are difficult to remove. Omicsoft created project-specific views to display expression values based on experimental design within each project. Expression Intensity Project View provides log 2 expression intensity values. The users can easily filter their project of interest, or any other filters like disease, clinical details, or even project contributors.

Expression Intensity Project View of Project GSE14580.

Expression Intensity Project View of Project GSE14580.

 

 

To maximize inter-study comparisons of RNA-seq data in Diseaseland, Omicsoft processes data from each study, starting from fastq files, through a commmon pipeline. Expression values from RNA-Seq studies are expressed as FPKM values, with upper quantile normalization. DiseaseLand offer project-specific views and also a merged view from all samples. Views display log transformed FPKM values. Samples and projects can be filtered interactively to allow exploration of data.

Gene FPKM View of all psoriasis samples in DiseaseLand HumanDisease. Samples can be categorized by project name (Change Symbol Properties) and clicking each project name selects the samples from the project to display the details in Detailed Window.

Gene FPKM View of all psoriasis samples in DiseaseLand HumanDisease. Samples can be categorized by project name (Change Symbol Properties) and clicking each project name selects the samples from the project to display the details in Detailed Window.

 

Stay tuned for more DiseaseLand tutorials!