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Introduction

Expression visualisation for genes of the CAGE macrophage activation and M.tb infection experiment based on CAGE-seq PMID:25678556.

Short description

A gene can have several promoter regions. Here we show expression for individual promoters and summed expression over all promoters as gene expression. To derive a single expression value for a gene, the expression (normalised tags-per-million counts) of each promoter of the gene was averaged over replicates and sub-sequently the expression of all promtoers for a gene summed. The gene to promoter association was done by proximity (500bp) of CAGE-promoters to ENSEMBL transcripts.

Enhancers were derived by identfying closely located divergent bidirectional expression clusters. Exression was derieved by speciying a window of 200bp around the mid-point of the divergent clusters and counting the CAGE-tags within this window.

Contents

The database currently contains 9278 enhancers and 24494 promoters for 10773 genes.

Cite

If you use this data in your research please consider citing the following publication(s):

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJL, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Bajic VB, Guler R, Brombacher F, Suzuki H. Nucleic Acids Research, 2015, doi: 10.1093/nar/gkv646


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