Omics Data Analysis
What are Omics
Omics refers to large-scale, high-throughput fields of biology that systematically measure and characterize entire classes of molecules within a biological system.
| Omics field | What is measured | Typical technologies | Stability | Distance from current phenotype | Main question |
|---|---|---|---|---|---|
| Genomics | DNA sequence & variation | Whole-genome sequencing, WES | High | Farther | What genetic variants does a person carry? |
| Transcriptomics | RNA abundance & splicing | RNA-seq, microarrays | Medium | Intermediate | Which genes are being transcribed? |
| Proteomics | Proteins & modifications | Mass spectrometry (LC-MS/MS), TMT/iTRAQ | Medium-low | Closer | Which proteins are expressed or circulating? |
| Metabolomics | Small molecules & metabolites | MS, NMR | Low | Very close | What is the current metabolic state? |
| Epigenomics | Chromatin state & methylation | ATAC-seq, ChIP-seq, bisulfite sequencing |
Common Omics Data Analysis Workflow
- Define biological / clinical question
- Data preprocessing and QC
- Normalization and transformation
- Differential analysis
- Dimensionality reduction and clustering
- Functional interpretation
- Validation and biological interpretation
Common Analysis Methods
Differential analysis
= comparisons between groups (e.g., disease vs control)
metrics
- (log2) fold change = a measure of how much a quantity changes between two conditions (e.g., treated vs control)
- fold change ≥ 2 = upregulated proteins
- fold change ≤ 0.5 = downregulated proteins
- p-values, FDR/adjusted p-values
visualization
- volcano plots
- heatmaps
- PCA/UMAP clustering
Enrichment analysis
See LearningNotes/Enrichment Analysis
Network analysis
PPI (Protein-Protein Interaction) network analysis
= constructs an interaction map using databases like STRING or BioGRID to reveal hubs and regulatory modules
Multi-omics integration
Specific Omics Analysis
- Proteomics Analysis and Modeling
- Transcriptomics Analysis
- Genomics Analysis
- Metabolomics Analysis