Transcriptomic Analysis Results

Complete expression profiling of 4 independent samples (NPFM1-4). Download annotated expression tables, pairwise comparisons, and view multivariate clustering visualizations.

Access Raw Data on Google Drive

Data Deliverables

Annotated Expression Table

.xlsx

The main expression profiling table for all 4 samples. Contains Gene IDs, Chromosomal coordinates, Gene Names, and Functional Descriptions.

Generation Process: Raw reads were filtered for rRNA, mapped via Bowtie2, quantified with featureCounts, and merged with GTF annotations using Python pandas. Includes Average Expression, StdDev, and Z-scores across all 4 independent samples.
Download Table

Pairwise Fold-Changes

.xlsx

Calculated pairwise Log2 Fold-Changes between all combinations of the 4 independent samples (e.g., NPFM1 vs NPFM2) to observe relative changes without statistical group testing.

Generation Process: Since biological replicates and control/treatment groups are absent, standard DESeq2 statistical testing was bypassed. Instead, Log2FC was calculated directly between each sample pair on FPKM-normalized values.
Download Comparisons

FPKM Normalized Counts

.csv

Raw gene counts normalized for sequencing depth and gene length using Fragments Per Kilobase of transcript per Million mapped reads (FPKM).

Generation Process: Using the DESeq2 R package, size factors were estimated treating all samples as independent (design = ~1). FPKM was calculated using the fpkm() function factoring in gene lengths from the GTF.
Download FPKM

Visualizations

Principal Component Analysis Plot

PCA Plot

Principal Component Analysis based on Variance Stabilized Transformation (rlog) of the read counts. Demonstrates how the individual samples cluster along the two axes of highest variance.

Sample Distance Matrix

Sample Distance Matrix

Euclidean distance clustering of the 4 samples based on rlog-transformed counts. Darker colors represent greater similarity between samples.

Top 50 Variable Genes Heatmap

Top 50 Variable Genes

A heatmap illustrating the expression patterns of the 50 genes with the highest variance across the 4 independent samples, highlighting specific expression signatures.

GO Classification (With Labels)

GO Classification

Gene Ontology (GO) classification bar chart, displaying the percentage and count of all unigenes versus Differentially Expressed Genes (DEGs).