.. _intro:

1. Introduction
==================

**Primary Usage:** Identification of cis-regulatory elements initially identified by matrix scoring and then additionally scored on 7 other relevant contextual datapoints.  Based on analysis of protein-coding transcripts in the Ensembl database.

.. image:: https://raw.githubusercontent.com/thirtysix/TFBS_footprinting/master/tfbs_logo.png
	:alt: logo

- This work is a derivative of `"Transcription factors" <https://commons.wikimedia.org/wiki/File:Transcription_Factors.svg>`_ by `kelvin13 <https://commons.wikimedia.org/wiki/User:Kelvin13>`_, used under `CC BY 3.0 <https://creativecommons.org/licenses/by/3.0/>`_.


.. note::
	TFBS_footprinting is now available in a `Docker image <https://hub.docker.com/r/thirtysix/tfbs_footprinting/>`_.


Predict TFBSs in the promoters any of 1-80,000 human protein coding transcripts in the Ensembl database.  TFBS predictions can also be made for 87 unique non-human species (including model organisms such as mouse and zebrafish), present in the following groups:

- 70 Eutherian mammals
- 24 Primates
- 11 Fish
- 7 Sauropsids

The TFBS footprinting method computationally predicts transcription factor binding sites (TFBSs) in a target species (e.g. homo sapiens) using 575 position weight matrices (PWMs) based on binding data from the JASPAR database.  Additional experimental data from a variety of sources is used to support or detract from these predictions:

* DNA sequence conservation in homologous mammal species sequences
* proximity to CAGE-supported transcription start sites (TSSs)
* correlation of expression between target gene and predicted transcription factor (TF) across 1800+ samples
* proximity to ChIP-Seq determined TFBSs (GTRD project)
* proximity to qualitative trait loci (eQTLs) affecting expression of the target gene (GTEX project)
* proximity to CpGs
* proximity to ATAC-Seq peaks (ENCODE project)