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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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Get started with ImmunoLand

Gary Ge

Get started with ImmunoLand

As the name implies, ImmunoLand is an immune-focused public database containing data from multiple data types (RNA-Seq, Expression Array, more) with a focus on immune-related diseases: asthma/respiratory diseases, arthritis, allergies, COPD, IBD, psoriasis, SLE (systemic lupus erythematosus), multiple sclerosis, and infectious diseases. We create these short videos to walk though the basic use of ImmunoLand.

1. The first look at ImmunoLand [top]

User can first check number and distribution of samples/comparisons in the current ImmunoLand. ImmunoLand is an on-going projects with quarterly updates.

  1. Open Immunoland [00:33]
  2. Sample distribution view [00:48]
  3. Change view grouping [01:27]
  4. View controller in the task tab [01:41]
  5. Filter samples using metadata [02:00]
  6. Comparison distribution view [03:00]

2. Gene search and comparison view [top]

User can search a gene and narrow down to find interesting projects interactively.

  1. Search gene (example: serpinb7) [00:08]
  2. Default comparison view: Disease vs Normal [00:25]
  3. Details on demand for each comparison [00:55]
  4. Filter compairsons (example: NGS projects) [01:30]

3. ImmunoLand microarray projects [top]

The experiment designs in different project are quite different and the batch effects in microarray projects are dfficult to remove. Omicsoft created project specific views to display expression values based on experiment design in each project.

  1. Microarray project view [00:21]
  2. Filter by project meta data [00:46]
  3. Customize view using options in task tab [00:58]
  4. Filter projects by disease areas [01:08]

4. ImmunoLand RNA-Seq Projects [top]

Omicsoft quantified expression values from RNA-Seq studies in FPKM fashion and further conducted upper quantile normalization. ImmunoLand offer project specific views and also a merged view from all samples. Views display log transformed FPKM values where samples/projects can be filtered interactively.

  1. Open RNA-Seq quantification project view [00:05]
  2. Filter projects [00:28]
  3. Open RNA-Seq quantification view arocss projects [00:58]
  4. Filter NGS samples to skin tissue[01:00]
  5. Change view grouping/profile to sample pathology [01:16]
  6. Filter by projects to psoriasis [02:00]
  7. Details on demand for samples [02:30]
  8. Change view symbol properties [02:45]

5. How to create and use sampleset [top]

Sampleset is powerful comcept/tool which allow users to create new sample groups, based on data in land or imported tables. The video below demonstrated building sampleset from data using selection and filter, then using the sampleset in land analytics to scan whole land for target identification.

  1. Create sampleset from view selection [00:30]
  2. Create sampleset set from filter [01:00]
  3. Re-search gene to load with sampleset [01:42]
  4. Group sampleset set from selection [02:16]
  5. Use sampleset in Land analytics: sample grouping to splice [04:00]
  6. Open result set from Land analytics [05:30]
  7. Verification of alternative splicing variants in land [05:50]
  8. Manage sampleset [06:45]

6. Example of checking isoform differential expression [top]

ImmunoLand provides base pair resolution results for RNA-Seq data. User can further drill down and check isoform differential expression at transcirpt, exon and exon junction level.

  1. RNA-Seq gene RPKM/FPKM view [00:35]
  2. Chnage grouping [01:08]
  3. View selected samples in genome browser [01:15]
  4. Check BAS (BAM summary) files in omicsoft genome browser [01:41]
  5. View exon junctions in genome browser showing difference between isoforms [02:10]
  6. RNA-Seq transcript view [02:50]
  7. RNA-Seq exon detail view [03:30]

7. Comparison [top]

Omicsoft manually curated the statistical testing (called comparison) in each project/study. The compairson collection is very useful to finding the common differential expression patterns/signatures between studies, such as between an microarray and NGS study, or find linkage between a knock out experiment and compound treatment study.

  1. Distribution of compairsons in ImmunoLand [00:30]
  2. Search gene and view comparisons [01:20]
  3. Search a comparison and view details for all genes [03:30]
  4. Filter and then view selected comparisons in volcano plot, PCA, Venn diagram, etc. [04:45]
  5. Create and then search a gene set [07:25]
  6. Immunoland views for multiple genes [08:30]

8. Related articles [top]
  1. Get started with Oncoland