## Description

This track shows 5' cap analysis gene expression (CAGE) tags and clusters from FANTOM Consortium and the Riken Omics Science Center in RNA extracts from different timepoints during the differentiations of human cell line THP-1. A CAGE cluster is a region of overlapping tags with an assigned value that represents the expression level.

## Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected views, uncheck the boxes next to the ones that you wish to hide. This track contains the following views:

Plus and Minus Clusters
  These views display clusters of overlapping read mappings on the forward and reverse genomic strands.
Reads
  The alignments view shows the individual tags (read mappings). Each tag is named with the timepoint that it was discovered during. Different timepoints can be excluded or highlighted using the filters. For example typing "H04" in the box and selecting "include" will only display tags from the hour 4 timepoint.

## Methods

The Clusters track was generated to help visualize the raw read data. The goal was to assign each region of the genome a score to indicate the likelihood of being a promoter based on CAGE data. As noted in the Fantom Consortium et al. paper below the distribution of reads for a particular region tends to follow a power law. For each CAGE read the number of total reads within a 45 bp window were counted and the number of regions of the genome with that score were determined. Fitting a power law to that data resulted in an alpha coefficient of 1.197 which was used to calculate the posterior probability of a particular region of the genome. This posterior probability is then plotted.

The Reads track was generated from the alignments done by the FANTOM Consortium. For visualization in the browser the score for the beds is the number of reads seen multiplied by 100.

## Credits

These data were generated and analyzed by The FANTOM Consortium and the Riken Omics Science Center. The data files were downloaded from the Fantom Functional Annotation of the Mammalian Genome download area.

## References

Faontom Consortium and the Riken Omics Science Center. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genetics. 2009 May; 41(5):553-62.

Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biology. 2009 Apr; 10(4):R40.