- Title
- MARS Motif: Assessment and Ranking Suite for transcription factor binding motifs
- Creator
- Kibet, Cabel K, Machanick, Philip
- Subject
- To be catalogued
- Date
- 2016
- Type
- text
- Type
- article
- Identifier
- http://hdl.handle.net/10962/439339
- Identifier
- vital:73568
- Identifier
- https://doi.org/10.1101/065615
- Description
- We describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs. The increased number of learned motif models that are spread across databases and in different PWM formats, leading to a choice dilemma among the users, is our motivation. This increase has been driven by the difficulty of modelling transcription factor binding sites and the advance in high-throughput sequencing technologies at a continually reducing cost. Therefore, several experimental techniques have been developed resulting in diverse motif-finding algorithms and databases. We collate a wide variety of available motifs into a benchmark database, including the corresponding experimental ChIP-seq and PBM data obtained from ENCODE and UniPROBE databases, respectively. The implemented tools include: a data-independent consistency-based motif assessment and ranking (CB-MAR), which is based on the idea that ‘correct motifs’ are more similar to each other while incorrect motifs will differ from each other; and a scoring and classification-based algorithms, which rank binding models by their ability to discriminate sequences known to contain binding sites from those without. The CB-MAR and scoring techniques have a 0.86 and 0.73 median rank correlation using ChIP-seq and PBM respectively. Best motifs selected by CB-MAR achieve a mean AUC of 0.75, comparable to those ranked by held out data at 0.76 – this is based on ChIP-seq motif discovery using five algorithms on 110 transcription factors. We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif discovery.
- Format
- 20 pages, pdf
- Language
- English
- Relation
- bioRxiv, Kibet, C.K. and Machanick, P., 2016. MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs. bioRxiv, p.065615, bioRxiv volume 2016 number 1 1 20 2016
- Rights
- Publisher
- Rights
- Use of this resource is governed by the terms and conditions of the bioRxiv Statement (https://www.biorxiv.org/about-biorxiv)
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Collections
Machanick, Philip (Assoc Prof)
RU Department of Computer Science
RU Research Unit in Bioinformatics (RUBi)
SDG 09. Industry, Innovation and Infrastructure
RU Department of Biochemistry, Microbiology and Bioinformatics
| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | SOURCE1 | MARS.pdf | 1 MB | Adobe Acrobat PDF | View Details Download |