Analysis of changes in transcription start site distribution by a classification approach

Article ID	Journal	Published Year	Pages	File Type
5906064	Gene	2014	12 Pages	PDF

Abstract

Change in transcription start site (TSS) usage is an important mechanism for the control of transcription process, and has a significant effect on the isoforms being transcribed. One of the goals in the study of TSS is the understanding of how and why their usage differs in different tissues or under different conditions. In light of recent efforts in the mapping of transcription start site landscape using high-throughput sequencing approaches, a quantitative and automated method is needed to process all the data that are being produced. In this work we propose a statistical approach that will classify changes in TSS distribution between different samples into several categories of changes that may have biological significance. Genes selected by the classifiers can then be analyzed together with additional supporting data to determine their biological significance. We use a set of time-course TSS data from mouse dendritic cells stimulated with lipopolysaccharide (LPS) to demonstrate the usefulness of our method.

Keywords

TAK1 LSAMP TLR4 SOCS1 IL6 IFIT1 IRF USP18 TBK1 ISG15 TRAF family member-associated NF-κB activator NF-κB Mouse dendritic cells TRAF IKZF1 NRXN1 Fibroblast growth factor 14 STAT5A RIP1 Ubiquitin-like modifier FGF14 MYD88 TTR TSS inhibitor of kappa B kinase interleukin receptor-associated kinase ubiquitin specific peptidase 18 TSC AP-1 Gadd45g LPS IKK GM-CSF cDNA DNA complementary to RNA JAK/STAT MAPK TRIF chromatin immunoprecipitation Interleukin 27 interleukin 6 cap analysis of gene expression TTR, Transthyretin tumor necrosis factor alpha TANK-binding kinase 1 transcription start site Statistical approach suppressor of cytokine signaling 1 IRAK TNF-α nuclear factor kappa B cage lipopolysaccharide Alternative promoters granulocyte macrophage colony-stimulating factor tank myeloid differentiation primary response gene 88 Limbic system-associated membrane protein mitogen-activated protein kinase CHiP janus kinase/signal transducers and activators of transcription Jun proto-oncogene Voltage-gated potassium channel Toll-like receptor 4