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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 OncoLand

Vivian Zhang

OncoLand is an Oncology database and visualization software that helps users explore public and private cancer genomics datasets. It contains tens of thousands of carefully processed and curated oncology -Omic data samples. OmicSoft uses the Land framework to deliver an increasing number of large datasets, including data types such as RNA-Seq, DNA-Seq, miRNA-Seq, Copy Number Variation, Gene Expression Chip, Protein Expression, Methylation and hundreds of clinical measurements. 

Omicsoft contains data from more than 10 large public dataset, including TCGA, CCLE, CGCI, ICGC, TARGET, Multiple Myeloma, GTEx, Blueprint and more. In this blog, we will introduce our data content based on our video tutorials: Getting Started With OncoLand

For more details about Land content, please refer to our NEW wiki pages: Introduction to TCGA Land Content and Introduction to CCLE Land Content

A first look at OncoLand

Most our OncoLand users are likely to be familiar with our Land interface. After selecting Land, you are likely to see the graphical interface similar to the following:

Example TCGA_B37 default view, displaying Sample Distribution view. 

Example TCGA_B37 default view, displaying Sample Distribution view. 

 

TCGALand Introduction and Overview

TCGA, The Cancer Genome Atlas, is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of genome analysis technologies. TCGALand is OncoLand's signature Land, it contains RNA-Seq, Expression Array, DNA-Seq, CNV, Methylation, and Protein data from more than 30 tumor types. 

TCGALand Sample Distribution across Tumor Type.

TCGALand Sample Distribution across Tumor Type.

TCGALand provides table and figure views on the sample, gene and clinical data level. We will introduce genomic data views in the following article, or you can refer to our video tutorials: Getting Started With OncoLand. Here, we would like to highlight clinical data views, which is introduced in the TCGALand Introduction and Overview video clip.

Clinical Significance - Group Association is a dynamic view showing the association of all clinical variables with the selected grouping variable. It quickly provides insights on which clinical variables are potentially associated with the selected grouping variable. 

Clinical Association for TCGALand Tumor Type.

Clinical Association for TCGALand Tumor Type.

Another useful view is Survival View. It plots survival rate over time for selected grouping variables

TCGALand Survival Plot by Tumor Type.

TCGALand Survival Plot by Tumor Type.

 

CCLELand Introduction and Overview

The Cancer Cell Line Encyclopedia (CCLE) project is an effort to conduct a detailed genetic characterization of a large panel of human cancer cell lines. CCLE provides public access analysis and visualization of DNA copy number, mRNA expression, mutation data and more, for 1000 cancer cell lines. CCLELand groups data according to Primary Site (Tissue), with histology as the secondary grouping.

CCLELand Primary Grouping by Primary Site, instead of Tumor Type.

CCLELand Primary Grouping by Primary Site, instead of Tumor Type.

 

Stay tuned for more on OncoLand!