Update of two important resources for researchers studying gene expression regulation
The Mathelier Group at NCMM has recently been involved in the update of the JASPAR and ReMap databases, two key resources for the scientific community
Successful computational biology research relies on high quality data, and both of these databases - JASPAR and ReMap - provide vital information for researchers studying gene expression regulation.
Building a better understanding of how and where transcription factors interact with DNA
With the growing field of personalised medicine, it is becoming more and more important to understand how mutations specific to an individual can trigger a disease, such as cancer.
Transcription Factors (TFs) are key proteins regulating when and where genes are expressed through their interaction with the DNA at specific binding sites. It is known that mutations within these binding sites can alter gene expression, thereby causing human diseases like cancer.
The JASPAR and ReMap resources are critical to build a ‘map’ showing where TFs bind in the human genome, and are thus a fundamental resource for researchers.
JASPAR: A collection of transcription factor DNA-binding preferences
The first publication describes the seventh release of JASPAR, a high quality open-access and widely used database that stores TF binding profiles (modelling how TFs interact with the DNA).
JASPAR is a database allowing researchers to study how TFs bind to the DNA to control gene expression. The TF binding preferences are principally modelled as matrices, which can be converted into Position Weight Matrices (PWMs or PSSMs), and then used for scanning genomic sequences.
The JASPAR database is amongst the most popular and longest maintained database for TF- binding profiles, and is a standard resource in the field. As of today, manuscripts describing JASPAR have been cited about 4,000 times, showing the importance of such a resource for the community. Data is open source, meaning it can be used with no restrictions.
The 2018 release of the database has been led by the Mathelier lab, in collaboration with six other laboratories from Canada, France, UK, Denmark, and Belgium. JASPAR was first published in 2004, and the resource is constantly updating and evolving.
This new update represents a critical expansion of the database and comes with a range of new functionalities and a redesigned web-interface.
ReMap: The presentation of a unique collection of regulatory regions in human bound by transcriptional regulators
The second Nucleic Acids Research publication from the Benoît Ballester lab and the Mathelier Group details a significant update of the ReMap database.
The ReMap resource effectively acts as an atlas that defines the regulatory regions bound by transcriptional regulators (TRs, which are specific proteins that regulate when and where genes are transcribed) in humans.
In this second release of ReMap, 2,829 ChIP-seq datasets from public sources have been uniformly processed to predict where 485 TRs bind on the DNA.
ReMap was first introduced in 2015 by Dr. Benoît Ballester's laboratory at the French Institute of Health and Medical Research, France. This most recent update has been made in close collaboration between Dr Ballester’s lab and the Mathelier lab.
ReMap 2018 provides a significant resource to the research community for an in-depth view of the complexity of the regulatory landscape in human.
Read the papers in full:
- JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework Khan et al, https://doi.org/10.1093/nar/gkx1126
- ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments, Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoit Ballester, https://doi.org/10.1093/nar/gkx1092
Open access resources
Both of the databases are open access, with multiple ways to download the data. See more at:
JASPAR 2018: http://jaspar.genereg.net/
ReMap: 2018: http://remap.cisreg.eu