Gene Set Analysis Categories

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Categories for OmicSoft Gene Sets

Source

Generally, the source Land (e.g. TCGA_B7, MouseDisease_B38, LINCS_B37, etc.) but can also limit to "Molecular Signatures" (from MSigDB).

Type

Analysis to the Land Comparison Category, a general descriptor of the difference between the case and control samples used to make the Gene Set.

Details for how individual Land datasets were processed can be found here.

  • ARCHIVED: From MSigDB
  • Cancer specific copy number: Derived from TCGA copy number data
  • Cancer specific gene expression: Cancer-specific genes, From CCLE and TCGA
  • Cell type specific gene expression: Cell type-specific genes, from Blueprint
  • CellType1 vs. CellType2: Land comparisons between cell types, from DiseaseLand and OncoGEO
  • Computational gene sets: From MSigDB category C4
  • Condition Specific Gene Expression: Condition-specific (including tissue or cell type-specific) expression, from single cell Lands
  • Curated gene sets: From MSigDB category C2
  • Disease vs. Normal: Land comparisons between disease vs. normal tissue, from DiseaseLand and OncoGEO
  • Disease1 vs. Disease2: Land comparisons between tissue from two disease states, from DiseaseLand and OncoGEO
  • GO gene sets: From MSigDB category C5
  • Hallmark gene sets: From MSigDB category H
  • Immunologic signatures: From MSigDB category C7
  • Motif gene sets: From MSigDB category C3
  • Oncogenic signatures: From MSigDB category C6
  • Other Comparisons: Specialized Land comparisons, from DiseaseLand and OncoGEO
  • Positional gene sets: From MSigDB category C1
  • Resistant vs. Sensitive: Land comparisons between samples that were resistant vs sensitive to a treatment, from DiseaseLand and OncoGEO
  • Responder vs. Non-Responder: Land comparisons between samples that responded to a treatment vs non-responders, from DiseaseLand and OncoGEO
  • Tissue Specific Gene Expression: Cell type-specific genes, from GTEx
  • Tissue1 vs. Tissue2: Land comparisons between samples from two tissues, from DiseaseLand and OncoGEO
  • Treatment vs. Control: Land comparisons between treated and untreated samples, from DiseaseLand and OncoGEO, as well as LINCS
  • Treatment1 vs. Treatment2: Land comparisons between samples that were subjected to either of two treatments, from DiseaseLand and OncoGEO