Hibernation Omics Analysis Workflows

Interactive visualization pipelines for seasonal metabolic reprogramming research.
From sequence alignment to multi-omics integration, specialized for torpor-arousal cycles.

BLAST & Sequence Annotation

Sequence alignment, functional annotation & phylogenetic analysis

Hibernation Focus: Seasonal gene family expansion (UCP, PPAR, HSP), ortholog identification across hibernators, conserved domain architecture in torpor-associated proteins
1
Data Preparation
Clean FASTA Build DB QC Stats
2
BLAST & Filtering
BLASTn/p/x E-value Top Hits
3
Annotation
GO/KEGG InterProScan Enrichment
4
MSA & Phylogeny
MAFFT IQ-TREE ggtree
Recommended Tools
Alignment Heatmap Ortholog Venn Circos Synteny Phylo Tree JBrowse

Bulk RNA-seq

Seasonal transcriptional reprogramming & metabolic switching

Hibernation Focus: Time-series DEG analysis across torpor-arousal cycles, circadian rhythm disruption, cold-inducible RNA binding proteins
1
Batch Correction & QC
ComBat-seq RIN > 7 Seasonal Factor
2
Time-series DEG Analysis
MASTS/Limma 5 Stages Trend Clustering
3
Rhythmicity & Pathway
Cosinor GSEA OXPHOS Score
4
Cross-tissue Integration
Circos Liver-Brain Axis Ketone Metabolism
Recommended Tools
ComplexHeatmap GSEA Plot Circos Boxplot Volcano Plot Venn Diagram

Single-cell RNA-seq

Cell-type specific metabolic quiescence & reactivation

Hibernation Focus: Cell cycle arrest (G0/G1), adipocyte browning trajectory, hypoxia-inducible states
1
Cross-season Integration
Harmony/SCVI Batch Correction Active vs Torpor
2
Cell Cycle & Metabolic Scoring
Seurat G0 Arrest OXPHOS/Glycolysis
3
Trajectory Inference
Monocle3 Adipocyte Browing RNA Velocity
4
Cell-Cell Communication
CellChat Leptin/Adiponectin Seasonal LR Pairs
Recommended Tools
UMAP/PCA Violin Plot Chord Diagram RNA Velocity Heatmap

Spatial Transcriptomics

Tissue microenvironment & metabolic zonation

Hibernation Focus: Intestinal villus atrophy zones, BAT activation regions, hypothalamic nucleus metabolic gradients
1
Histology Alignment
H&E Overlay Villus/Crypt ID BayesSpace
2
Spatial Domain Identification
SVG Analysis SPARK Metabolic Gradients
3
Niche Interactions
Cell2location Mucus Layer Microbiome Host
4
Multi-modal Integration
MALDI-MSI Metabolite-Gene Liver Zonation
Recommended Tools
Spatial Heatmap Spatial Plot Niche Matrix Dual Overlay

Genomics / WGS

Adaptive evolution & hibernation-associated variants

Hibernation Focus: Positive selection on metabolic genes (PPAR, CPT1), convergent evolution across species, SV in lipid metabolism clusters
1
Selection Pressure Analysis
dN/dS PAML Hibernation Genes
2
Convergent Evolution
Cross-species Bear vs Squirrel Fatty Acid Oxidation
3
Structural Variation
CNV CPT1A Cluster SV Impact
4
Phenotype Association
TMB Serum β-HB Metabolic Traits
Recommended Tools
Manhattan Plot Lollipop Plot Phylo-Heatmap Circos SV Venn

Epigenomics (ChIP/ATAC/DNAme)

Metabolic switch memory & reversible chromatin states

Hibernation Focus: PPARα promoter methylation dynamics, H3K27me3 bivalent states, chromatin accessibility at lipid metabolism genes during entrance vs arousal
1
Peak/DMR Calling
MACS2 DiffBind methylKit
2
TF Footprinting
HINT-ATAC PPAR/FOXO HIF1A
3
Epigenetic-Transcriptome Link
Chrom Switch ATAC vs RNA Pdk4 Locus
4
Seasonal Memory
DNAme Trajectory Reversible Marks Next Season
Recommended Tools
IGV Browser TF Heatmap Chrom Switch Methylation Venn

Proteomics & Metabolomics

Energy currency & metabolic flux quantification

Hibernation Focus: ATP/AMP ratios, NAD+/NADH redox state, β-hydroxybutyrate dynamics, 13C-flux tracing from fatty acids to ketone bodies
1
Quantification & QC
LFQ/DIA MaxQuant QC-RSC
2
Pathway Activity
sPTM/MEA OXPHOS Down Ketogenesis Up
3
Metabolic Flux Analysis
13C-Tracing Palmitate TCA Cycle
4
Energy Status Radar
ATP/ADP NAD+/NADH Acetyl-CoA
Recommended Tools
Volcano Plot Radar Chart Network Bar-Dot Correlation

Microbiome

Gut microbiota seasonal succession & host-metabolite axis

Hibernation Focus: Mucin-degrading Akkermansia bloom during fasting, SCFA (butyrate) decline, bile acid transformation, fecal transplant validation
1
Diversity Dynamics
α/β Diversity Entrance Crash QIIME2
2
Community Succession
Firmicutes↓ Bacteroidetes↑ SourceTracker
3
Functional Prediction
PICRUSt2 SCFA Synthesis Bile Acid 7α-DH
4
Gut-Liver-Brain Axis
Procrustes Butyrate-FFAR3 Sankey Flow
Recommended Tools
PCoA Plot Bar-Dot Co-occurrence Sankey Heatmap

Multi-omics Integration

Epigenome-Microbiome-Metabolome-Transcriptome causal networks

System-level Understanding: MOFA+ latent factor extraction, Bayesian causal inference (microbiome→SCFA→host gene), dynamic ODE modeling of entrance kinetics
1
Data Harmonization
MOFA+ Latent Factors Seasonal Variance
2
Cross-omics Correlation
sPLS Sparse PLS Multi-block
3
Causal Inference
Bayesian Net Microbiome→Host Mediation Analysis
4
Dynamic Modeling
ODE Models Entrance Kinetics Predictive Sim
5
System Map Visualization
Circos Pathway Map Ketone Flux
Integration Stack
MOFA+ Factor Correlation Circle Bayesian DAG Trajectory Pathway Map