Temporal Transcription Factor Identification

A workflow for characterizing stage-specific transcription factor expression patterns during control/endogenous differentiation using bulk time-series RNA-seq data.

View the Analysis

The full analysis is available as a GitHub Pages site: https://zohebkhan1.github.io/temporal-transcription-factor-identification/

Data Source

This workflow uses publicly available data from:

Martinez JL et al. Transcriptional consequences of trisomy 21 on neural induction. Front Cell Neurosci. 2024;18:1341141. doi:10.3389/fncel.2024.1341141

Generated Figures

Temporal TF Expression Heatmap

Stage-specific transcription factor expression modules identified via hierarchical clustering, sorted by peak expression timing.

TF Expression Trends by Cluster

Mean expression trends with confidence intervals for each TF cluster across differentiation timepoints.

TF Cluster Expression Patterns

Overlay of all cluster expression trajectories showing the temporal wave pattern.

D21 vs T21 Comparison

Comparison of TF cluster expression between control (D21) and experimental (T21) samples.

Dependencies

The following R packages are required:

• DESeq2
• AnnotationDbi
• org.Hs.eg.db
• edgeR
• dplyr
• tidyr
• tibble
• ggplot2
• pheatmap
• RColorBrewer
• viridis
• patchwork

Install Bioconductor packages:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("DESeq2", "AnnotationDbi", "org.Hs.eg.db", "edgeR"))

Install CRAN packages:

install.packages(c("dplyr", "tidyr", "tibble", "ggplot2", "pheatmap", "RColorBrewer", "viridis", "patchwork"))