Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Agilent]

ABSTRACT: High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-level expression estimation with a method to control for variability across replicate samples. Cuffdiff robustly identifies differentially regulated isoforms and genes and reveals differential splicing or 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 and uncover a critical role for this gene in the maintenance of adult cells. We show that HOXA1 is requi

ORGANISM(S): Homo sapiens

SUBMITTER: Cole Trapnell 

PROVIDER: E-GEOD-37690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress