TSS assembly pipeline for Mm_EPDnew_002

Introduction

This document provides a technical description of the transcription start site assembly pipeline that was used to generate EPDnew version 002 for M. musculus.

Source Data

Promoter collection:

Name Genome Assembly Promoters Genes PMID Access data
UCSC Known Genes July 2007 NCBI37/mm9 25221 19378 26590259 SOURCE DOC DATA

Experimental data:

Name Type Samples Tags PMID Access data
FANTOM5 CAGE 340 7,089,874,024 24670764 SOURCE DOC DATA
DBTSS7 CAGE 1 19,840,450 19910371 SOURCE DOC DATA

Assembly pipeline overview

Description of procedures and intermediate data files

1. UCSC Download

Data was downloaded from UCSC table browser the 15th of MAy 2014 Then, transcrips have been filtered according to the following rules:
  1. Transcripts of protein coding genes only
  2. Transcript lies on full chromosomes
  3. Genes must be annotated [Associated Gene Name present]
  4. Gene and transcripts status known
Gene names were taken from the field "Associated Gene Name". Since the EPD format doesn't allow gene names longer than 18 characters, we checked whether the names repsected this limitation.
Transcripts with the same TSS position were merged under a common ID. As a conseguence of this and of the filters, from the 55420 transcrips originally present in the UCSC database, ~30000 were merged, leaving 67440 uniquely mapped promoters in the input list.

2. UCSC TSS collection

The UCSC TSS collection is stored as a tab-deliminated text file conforming to the SGA format under the name:
    ucsc_promoter_list.sga
The six field contain the following kinds of information:
  • NCBI/RefSeq chromosome id
  • "TSS"
  • position
  • strand ("+" or "-")
  • "1"
  • gene name
Note that the second and forth fields are invariant.

3. Data import from DBTSS7

Solexa Tag Data were downloaded from DBTSS ftp-site (see link above). The source files are the following:
  • 3t3_data.tab.gz: Mouse 3T3 Solexa tag mapping data;
According to the readme file included in the ftp archive, the 5' end tags were mapped to the Human genome hg18. The source format is a non-standard tab-delimited format that has been converted to SGA via an ad hoc perl script. All tissues have been merged into a single file.

3. Data import from FANTOM5

BAM files for high quality CAGE samples (hCAGE) were downloaded from FANTOM5 ftp-site (see link above). FIles were then converted into SGA format using in-house software. There are a total number of 339 samples in this collection. Individual SGA files can be downloaded from our ftp website (link above).

5. mRNA 5' tags peak calling

For each individual sample (340), peak calling for the merged file has been carried out using ChIP-Peak on-line tool with the following parameters:
  • Window width = 200
  • Vicinity range = 200
  • Peak refine = Y
  • Count cutoff = 9999999
  • Threshold = 5

6. TSS validation and shifting

Each sample in the collection (mRNA peaks and UCSC TSS) was then separately processed in a pipeline aiming at validating transcription start sites with mRNA peaks. A UCSC TSS was experimentally confirmed if an mRNA peak lied in a window of 500 bp around it. The validated TSS was then shifted to the nearest base with the higher tag density.

7. UCSC not-validated TSS

The total number (summing up all samples) of non experimentally validated TSS was around 3000.

8. Promoter collection for each sample

Each sample in the dataset was used to generate a separate promoter collection. Potentially, the same transcript could be validated by multiple samples and it could have different start sites in different samples. To avoid redundancy, the individual collections were used as input for an additional step in the analysis (Assembly pipeline part B).

9. Merging collections and second TSS selection

The 340 promoter collections were merged into a unique file and further analysed. The promoter of a transcript was mantained in the list only if validated by at least two samples. Transcript validated by multiple samples could potentially have the TSS set on a broader region and not to single position. To avoid such inconsistency, for each transcript we selected the position that was validated by the larger number of samples as the true TSS.

10. Filtering

Transcription Start Sites that mapped closed to other TSS that belonged to the same gene (500 bp window) were merged into a unique promoter following the same rule: the promoter that was validated by the higher number of samples was kept.

10. Final EPDnew collection

The 21201 experimentally validated promoter were stored in the EPDnew database that can be downloaded from our ftp site. Scientist are wellcome to use our other tools ChIP-Seq (for correlation analysis) and SSA (for motifs analysis around promoters) to analyse EPDnew database.

Last update Dec. 2016