🧬 Cell Fate Analyzer BETA

TPM-Normalized RNA-seq Exploratory Analysis Subsystem • Dataset: GSE290316_hypo_TPM.csv.gz

TOTAL GENES

Validated Gene Symbols

TOTAL SAMPLES

RNA-seq Replicates

NORMALIZATION

log2(TPM + 1)

TPM Pre-Normalized

EXPRESSION MEAN

Global Average

EXPRESSION VARIANCE

Overall Spread

📍 2D Principal Component Analysis (PCA)

Variance Explained

Sample coordinates projected onto PC1 & PC2 space showing sample relationships.

🔥 Sample Correlation Heatmap

Pairwise Pearson correlation matrix ($r$) across RNA-seq replicates.

📊 Expression Level Distribution

Histogram distribution of $\log_2(\text{TPM}+1)$ expression levels.

⭐ Top Variable Genes (Bar Plot)

Top 20 genes ranked by expression variance across samples.

⚡ Differential Gene Expression & Pathway Analysis

Comparative Statistical Contrast (Group A vs Group B) • Welch's t-test with Benjamini-Hochberg FDR Adjustment

⚠️

Scientific & Methodological Scope Notice: This analysis is exploratory and is based on log-transformed TPM values with three biological replicates per group. Welch’s t-test is used as an approximate statistical comparison. For confirmatory RNA-seq differential expression, raw counts and dedicated count-based models such as DESeq2 or edgeR are recommended.

👥 Biological Group Summary

GROUP A (hypoTOs)

3 Replicates

Samples: hypoTOs-1, hypoTOs-2, hypoTOs-3

GROUP B (hypo)

3 Replicates

Samples: hypo-2, hypo-2.1, hypo-2.2

DE SIGNIFICANCE STATISTICS

↑ Upregulated (log2FC ≥ 0.5, p_adj ≤ 0.05): --

↓ Downregulated (log2FC ≤ -0.5, p_adj ≤ 0.05): --

🌋 Volcano Plot (log2FC vs -log10 p_adj)

🔥 Differential Expression Heatmap

🔴 Top Upregulated Genes (log2FC ↑)

🔵 Top Downregulated Genes (log2FC ↓)

🗺️ Functional Pathway & Gene Ontology Over-Representation Analysis

Fisher's Exact Test ORA

Database	Term / Pathway	Overlap	Gene Ratio	Raw p-value	FDR p_adj	Associated DE Genes
Loading functional pathway enrichment...

🤖 Machine Learning Preview (Unsupervised Discovery)

2D UMAP Manifold Projection & K-Means Unsupervised Clustering (K=2) on Top 500 Variable Genes

ℹ️

Exploratory ML Notice: This is an exploratory unsupervised visualization based on six samples. It is not a validated cell fate prediction model. Supervised machine learning requires a substantially larger labeled dataset.

🗺️ 2D UMAP Manifold Projection

UMAP + K-Means

Non-linear 2D manifold reduction displaying unsupervised sample partitioning.

🧩 K-Means Cluster Membership Summary (K=2)

Sample Name	Cluster ID	Known Biological Group	Alignment Status
Loading K-Means cluster assignments...

Group Alignment Summary: --

🧬 Biological Interpretation & Top Variable Genes

Enriched Annotations

Rank	Gene Symbol	Gene Name	Mean Expr	Variance	Biological Function	Associated Pathway	Biological Role	External Links	Action
Loading top variable gene annotations...