ComparisonLand

From Array Suite Wiki

Jump to: navigation, search

Contents

Overview

A ComparisonLand is a type of ArrayLand, customized to store, integrate, and display both expression and comparison data from Omic projects. It is built upon OmicSoft File System (OFS), which stores data in database files, such as ALV sample data and TLV comparison data vector files, and different layers of indexes to link gene/markers, samples, and comparisons of genes between samples.

Background

ComparisonLand Data

Land Data stored in ArrayLand consists of three parts:

  1. Data: it is a gene/marker * sample matrix.
  2. Design: these are sample specific meta data, including sample, subject or project level data.
  3. Annotation: these are gene/marker specific information.
    ComparisonLands contain additional layers, which allows for linking of sample-level expression data with statistical inferences:
  4. Comparison Data: For any comparison between a group of samples, measuring differences in expression of genes, the Fold-change and significance calculation
  5. Comparison Metadata: Information about case and control groups (derived from sample metadata), as well as information about the comparison, which is stored independently to sample-level metadata

Each part is stored as database files and indexed by ArrayLand. Land data are hosted in ArrayServer. Based on the ArrayLand technology, the user can quickly extract Omic data for a certain gene or a list of genes across all or subset of samples. Once the user generates new data, he/she can append these data to Land data incrementally.

Land Visualization

In addition to the Views available for ArrayLands, ComparisonLands provide a set of predefined Views to visualize and interact with comparison data, including:

  1. Comparison-level Views of all measured genes between case and control
  2. Gene-level Views of which comparisons contained a difference
  3. Integration Analysis to find similarly-affected Comparisons and Genes

OmicSoft's DiseaseLand collection makes extensive use of ComparisonLand functions, summarizing comparisons between treatment and control, disease and normal, and between cell types.

For a tour of DiseaseLand, please see the latest Tutorials, or the videos on Getting Started with DiseaseLand.

Build Your Own ComparisonLand

Users can generate ComparisonLands from their raw expression data, or can also incorporate comparison/inference data.

ArrayLand Collection