Differential analysis of gene regulation at transcript resolution with RNA-seq

By Cole Trapnell, David G Hendrickson, Martin Sauvageau, L. Goff, Johannes Rinn, Lior S. Pachter. Nature Biotechnology, 2012

3,547 citations recorded by the source corpus.

Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses numerous statistical challenges. We present Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. Cuffdiff 2 robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1, which we show is required for lung fibroblast and HeLa cell cycle progression. Loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/55507aba54a92b31a200e8112f088f5c356ed7bc

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Citations in the corpus

Enterochromaffin Cells Are Gut Chemosensors that Couple to Sensory Neural Pathways. (2017, neutral): “7 Kim et al., 2013 http://ccb.jhu.edu/software/tophat/ index.shtml Cufflinks Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ papers/ Cuffdiff Trapnell et al., 2013 http://cole-trapnell-lab.github.io/cufflinks/ papers/ DAVID Bioinformatics Resources 6.8 Huang et al., 2009 https://”
Comparison of software packages for detecting differential expression in RNA-seq studies (2013, methodology): “None of these comparisons included the very recently introduced Cuffdiff 2, which has been proposed to outperform the previous approaches [10].”
Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis (2017, neutral): “D50ss This paper N/A UTR vector This paper N/A pIRES2-EGFP plasmid Clontech N/A pLuc-EMCV-IRES This paper N/A UTR+In. bGlob vector This paper N/A UTR+In.-ZNF vector This paper N/A UTR+In.HPRT vector This paper N/A MCS+In.b Glob vector This paper N/A Software and Algorithms Trimmomatic Bolger et al. ”
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma (2018, methodology): “…and Algorithms ConsensusClusterPlus Wilkerson and Hayes, 2010 http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html Cufflinks Trapnell et al., 2013 https://cole-trapnell-lab.github.io/cufflinks/ Cell Rep. Author manuscript; available in PMC 2018 August 03.”
A census of human RNA-binding proteins (2014, methodology): “mRNA –seq were calculated using cufflinks2 (Trapnell et al., 2012a) and HTSeq (Anders et al.”
A survey of best practices for RNA-seq data analysis (2016, background): “Additional factors that interfere with intra-sample comparisons include changes in transcript length across samples or conditions [50], positional biases in coverage along the transcript (which are accounted for in Cufflinks), average fragment size [43], and the GC contents of genes (corrected in…”
Computational solutions for omics data (2013, methodology): “As with short-read DNA sequence analysis, short reads are either mapped to reference genomes and transcriptomes 54 or assembled de novo 55 , before transcript counting and data normalization.”
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown (2016, methodology): “Finally, multiple tools for computing differential expression have been developed 20–22 , and these could be used as alternatives to Ballgown.”
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization (2017, positive): “Differential expression analysis was analyzed using Cuffdiff (Trapnell et al., 2013) with default parameters within BaseSpace.”