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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.

Filtering by Tag: DiseaseLand

[Event] Learn|Network|Impact 2017 OmicSoft User Group Meeting

Vivian Zhang

OmicSoft, now a QIAGEN company, would like to invite you to our annual Omicsoft User Group Meeting being held in Cambridge, MA on September 19-20, 2017. 

FREE registration and attendance, limited time only. For registration and more details, please directly go to our UGM page.

In the past ten years, OmicSoft has helped numerous users from major pharma and biotech companies (as well as research institutions) accelerate their bioinformatics and genomics research (who are our customers?). Last year, OmicSoft successfully held our kick-off OmicSoft User Group Meeting. More than 30 leading pharmaceutical and biotech companies, more than 100 experts and scientists in the field of bioinformatics/genomics/genetics attended the meeting.

Last year, our action-packed one-day meeting provided an open platform for our users and industry peers to learn, to network, and to impact the development of OmicSoft products. Click here for 2016 OmicSoft UGM meeting agenda. This year OmicSoft has had several milestones and technology breakthroughs including: our acquisition by QIAGEN, Array Suite 10,0. release, Cloud-Based Lands, Single Cell RNA-Seq support, upcoming integration with QIAGEN's bioinformatics products, Web-based solutions and more. We are expanding the 2017 OmicSoft User Group Meeting into a two-day event with:

  • More product training - Get the most out of Omicsoft products, and QIAGEN's bioinformatics products
  • More user talks and networking opportunities - Learn from others' experiences, industry best practices, and expand professional network
  • More One-On-One meetings - Get problems solved, questions answered and get personalized training from our experienced staff

 

Learn, network, impact. Come join us and leading pharma, biotech companies and research institutions.

  • Learn to Use OmicSoft Products More Efficiently 
  • Impact Future Product Development
  • Network with Peers and Industry Experts
  • Get One-On-One Help from Experts
  • Explore more QIAGEN Bioinformatics products

 

Please contact us for potential presentation and collaboration opportunities. 

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

Vivian Zhang

Last time, we introduced  some of the basic views in DiseaseLand. In this article, we would like to introduce you to some advanced functionality: SampleSets and GeneSets. 

 

The SampleSet is powerful concept/tool that allow users to create custom sample groupings, based on data in the Land or imported tables. This video tutorial demonstrates several ways to build a SampleSet from data using selection and filters, then uses SampleSets in Land Analytics to scan the entire DiseaseLand to discover differential splicing.

Grouping lesional vs non-lesional Psoriasis samples in ImmunoLand (DiseaseLand). 

Grouping lesional vs non-lesional Psoriasis samples in ImmunoLand (DiseaseLand). 

Serpinb7 Transcript Expression grouped by lesional vs. non-lesional samples. 

Serpinb7 Transcript Expression grouped by lesional vs. non-lesional samples. 

With the newly created sampleset, users can visualize isoform differential expression at the transcript level in the Genome Browser:

Differential expression of Serpinb 7 in lesional vs. non-lesional samples.

Differential expression of Serpinb 7 in lesional vs. non-lesional samples.

3. GeneSets

Besides the SampleSet tool, GeneSets are a powerful tool for grouping and comparing genes, including members of a gene family, a pathway, or co-regulated genes. These GeneSets can be used to discover DiseaseLand studies that share "genetic signatures" of common up- or down-regulated genes with your GeneSet.

After adding GeneSet Some_IBD_Genes, the geneset becomes available for search.

After adding GeneSet Some_IBD_Genes, the geneset becomes available for search.

With the created geneset, users can visualize and perform analyses on the set of genes. 

Heatmap of Comparison for GeneSet Some_IBD_Genes.

Heatmap of Comparison for GeneSet Some_IBD_Genes.

 

Stay tuned for a DiseaseLand comparison views tutorial!

[Land Tutorial] DiseaseLand (ImmunoLand And CVMLand) Comparison Views

Vivian Zhang

 DiseaseLand features Comparison Views, allowing users to easily search and visualize statistical contrasts between groups of samples using common queries: Treated vs Control, Disease vs Normal, Responder vs Non-Responder etc. By searching a gene, the user can visualize the association with comparisons across thousands of projects, and narrow down to find interesting projects interactively. (Additional reading: ComparisonLand ). In this article, we will introduce you on how to use comparison views.

Video Tutorial: Comparison

Comparison Distribution by comparison types:

Comparison distribution by comparison type. Statistics from previous Land version. Actually distribution and number of comparison update quarterly. 

Comparison distribution by comparison type. Statistics from previous Land version. Actually distribution and number of comparison update quarterly. 

 

Search gene and view comparisons:

In DiseaseLand, you can search for a gene and view its expression in all samples or a single project, or you can visualize which comparisons detected up- or down-regulation of the gene. This way, you can identify projects of interest, and discover trends in your favorite gene's regulation.

 

Comparison details for Serpinb 7 by treatment vs. control. By selecting the comparisons (dots) of interest, detailed information will pop up.

Comparison details for Serpinb 7 by treatment vs. control. By selecting the comparisons (dots) of interest, detailed information will pop up.

Comparison Details Views:

Omicsoft uses manually curated metadata to generate statistical tests (called comparisons) for each project/study included in DiseaseLand, generally following the comparisons in the original paper. The Comparison collection is useful for finding the common differential expression patterns/signatures between studies, such as between an microarray and NGS study, or to find links between a gene knockout experiment and a compound treatment study.

When searching for project(s), a few views are available:

Here are a couple example views:

Example Volcano Plot of project GSE38713.

Example Volcano Plot of project GSE38713.

Example Venn Diagram of project GSE14905.

Example Venn Diagram of project GSE14905.

Example Significant Genes of project GSE58121, GSE63980 and GSE63980.

Example Significant Genes of project GSE58121, GSE63980 and GSE63980.

[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!

[New Feature] Manage Land Sample Clinical Data

Vivian Zhang

Omicsoft has been working diligently over the past few months to both strengthen our ability to incorporate clinical data, as well as  growing our list of curated clinical measurements from public datasets. Currently, there are more than 1000 different clinical measurement variables in total, including sample demographics, survival data, symptoms, treatments and more in OncoLand and DiseaseLand. Moreover, users often have their sets of internal clinical data they wish to add to the system. If you have not started leveraging the power of our clinical data subsystem, please take a look at OncoLand Case Study - Clinical Variables for a 10 mins quick video tutorial on how to utilize clinical data to identify novel associations.

To help users better manage Land clinical data, we recently implemented Manage Sample Clinical Data function in Land. This function can be accessed through:

 

 

This function allows users to add clinical data, manage clinical variable meta data, remove samples and remove clinical vatiables: 

Add Clinical Data

Add Clinical Data

Adding clinical data is straightforward. In addition, "Metadata" for clinical data columns can be controlled by adding a second table. For example, clinical data column grouping can be controlled by a table where the first column contains Clinical Data column names, and the second column contains category:

Add Clinical Variable Metadata

Add Clinical Variable Metadata

 

The function is easy-to-use and straightforward, allowing users to manage their clinical data efficiently and effectively. For more details on the function, please refer to our wiki page

Stay tuned for additional functionality coming at the end of this year, including support for CDISC formatted files, to include time-series measurement data.

[Land Update] Omicsoft Quarterly Land Update Summary

Vivian Zhang

Omicsoft is excited to announce it’s latest Land updates, including OncoLand and DiseaseLand.

Highlights include:

OncoLand:

  • Official release of the B38 Human Lands, including TCGA, CCLE, GTEx, Blueprint, and Sanger
  • Additional samples in the TARGET and Blueprint Lands
  • 5700 new Somatic Mutation samples in the TumorMutation Land
  • 350 new samples and 80 new comparisons in the OncoGeo Land
  • 1750 new expression samples in the ClinicalOutcome Land
  • Updated clinical data and CNVCall data in TCGA
  • New Comparison data (Tumor vs Normal) for 24 tumor types in TCGA




DiseaseLand:

  • 3916 single cell samples from 5 projects to the Single Cell Human Land, including seven new cell types
  • 5466 single cell samples from 10 projects to the Single Cell Human Land, including seven new mouse cell types
  • 840 new RNA-Seq samples in Human DiseaseLand, along with additional comparisons
  • 2402 new RNA-Seq samples in Mouse DiseaseLand, along with additional comparisons
  • DiseaseLand now includes over 67,000 human samples, with 3239 comparison from 1000+ projects and almost 21,000 mouse samples, with 2,248 comparisons from over 650 projects. 


Incorporation with the recently introduced Gene Set Analysis module provides extra value to the release, as we now allow users to query against all of the new Land data as well. 
 

 

Matt Newman, VP of Business Development, will spend 45 minutes on December 12th, at 11:00 am EST, to give an overview of all the new datasets and visualizations that are included with this latest release. Please register here. We will contact users about this release update shortly after our webinar. Please stay tuned. 

[Important Land Update] Land Filter Now Carries Over Across Multiple Searches

Vivian Zhang

Omicsoft's Lands are known for being comprehensive, powerful and integrated, allowing users to navigate across samples, genes, data types, datasets and platforms. As comprehensive and flexible as it can be, the system may appear to be complex for some users, with growing numbers of samples, datasets and data types. To help user apply filters more easily and efficiently, Omicsoft recently improved its filtering logic in the Lands. 

Previously, filters applied to one search do not carry over from the main Land tab, requiring users to apply filters all over again for any new search.

For example, if the user wants to compare gene expression FPKM for EGFR in KIRC (Kidney Renal Clear Cell Carcinoma) and KIRP (Kidney Renal Papillary Cell Carcinoma), the first step might be to filter the tumor types in the TCGA_B37 main tab (to see sample numbers and understand the overall distribution of samples). Next, the user can search for EGFR and go to Gene FPKM view (Step 2). If the user wants to see the gene expression of TP53, previously the Land doesn't carry over the filter and the user needs to redo the filter again (Step 3).

Step 1  filter for Tumor Type KIRC and KIRP, and check sample statistics (data availability in this example search):

Step 2 search for Gene EGFR and view Gene FPKM view:

Step 3 search for Gene TP53, the sample filter does not carry over and the user has to redo the filter all over again:

 

Now with the new version, the filter carries  over without any additional steps:

 

Imagine when one has already filtered many steps and navigated to a group of samples/genes that appear intriguing, how easy and time-saving it becomes to directly have all the filter steps applied to the new search. 

This filter logic applies to all left-hand side filter tabs including Sample, Comparison and all data type filter tabs. 

If the user does not want to apply the filters, simply click Clear All Filters button to reset everything: