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References: Transcriptomics and Gene Regulatory Networks

  1. RNA-Seq - Wikipedia - Comprehensive overview of RNA sequencing technology, covering library preparation, read mapping, transcript quantification, differential expression analysis, and comparison with microarray approaches.

  2. Gene Regulatory Network - Wikipedia - Describes networks of transcription factors, enhancers, and target genes that control gene expression, covering Boolean and continuous modeling approaches for regulatory circuit analysis.

  3. Weighted Correlation Network Analysis - Wikipedia - Explains the WGCNA method for constructing co-expression networks from transcriptomic data, including soft-thresholding, module detection, and hub gene identification for systems biology.

  4. RNA-Seq Data Analysis: A Practical Approach - Eija Korpelainen - CRC Press - Step-by-step guide to RNA-seq analysis covering experimental design, quality control, alignment, quantification, differential expression, and downstream pathway enrichment analysis.

  5. Gene Regulation and Expression - David Latchman - Taylor and Francis - Textbook covering transcriptional and post-transcriptional regulation mechanisms, providing biological context for understanding gene regulatory network inference from expression data.

  6. DESeq2 Vignette - Bioconductor - Official tutorial for the DESeq2 differential expression analysis package, explaining normalization, statistical modeling, shrinkage estimation, and result visualization for RNA-seq data.

  7. WGCNA Package Tutorial - Steve Horvath Lab - Step-by-step tutorial for weighted gene co-expression network analysis in R, covering network construction, module detection, module-trait relationships, and hub gene identification.

  8. Galaxy Training: Transcriptomics - Galaxy Project - Collection of hands-on tutorials for RNA-seq analysis in Galaxy, covering read mapping, transcript quantification, differential expression, and visualization of results.

  9. ENCODE Project - ENCODE Consortium - Guide to accessing ENCODE regulatory element data including transcription factor binding sites, histone modifications, and chromatin accessibility essential for regulatory network construction.

  10. GenePattern Notebook: RNA-seq Analysis - GenePattern/Broad Institute - Interactive notebook environment for RNA-seq analysis workflows, demonstrating differential expression, gene set enrichment, and network visualization in reproducible notebooks.