Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
Constructing library of tissue-specific genes johannes.helmuth RNA Sequencing 0 10-20-2011 03:20 AM
ChIP-Seq: GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experi Newsbot! Literature Watch 0 11-18-2010 03:20 AM
RNA-Seq: Computational identification of tissue-specific alternative splicing element Newsbot! Literature Watch 0 08-06-2010 03:00 AM
PubMed: ChIP-seq accurately predicts tissue-specific activity of enhancers. Newsbot! Epigenetics 0 02-13-2009 06:00 AM

Thread Tools
Old 07-05-2011, 04:00 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default ChIP-Seq: Tissue-specific prediction of directly regulated genes.

Syndicated from PubMed RSS Feeds

Tissue-specific prediction of directly regulated genes.

Bioinformatics. 2011 Jun 30;

Authors: McLeay RC, Leat CJ, Bailey TL

Direct binding by a transcription factor (TF) to the proximal promoter of a gene is strong evidence that the TF regulates the gene. Assaying the genome-wide binding of every TF in every cell type and condition is currently impractical. Histone modifications correlate with tissue/cell/condition-specific ("tissue-specific") TF binding, so histone ChIP-seq data can be combined with traditional position-weight matrix (PWM) methods to make tissue-specific predictions of TF-promoter interactions. RESULTS: We use supervised learning to train a na´ve Bayes predictor of TF-promoter binding. The predictor's features are the histone modification levels and a PWM-based score for the promoter. Training and testing uses sets of promoters labeled using TF ChIP-seq data, and we use cross-validation on 23 such datasets to measure accuracy. A PWM+histone na´ve Bayes predictor using a single histone modification (H3K4me3) is substantially more accurate than a PWM score or a conservation-based score (phylogenetic motif model). The na´ve Bayes predictor is more accurate (on average) at all sensitivity levels, and makes only half as many false positive predictions at sensitivity levels from 10% to 80%. On average, it correctly predicts 80% of bound promoters at a false positive rate of 20%. Accuracy does not diminish when we test the predictor in a different cell type (and species) from training. Accuracy is barely diminished even when we train the predictor without using TF ChIP-seq data. AVAILABILITY: Our tissue-specific predictor of promoters bound by a TF is called Dr Gene and is available at CONTACT:

PMID: 21724591 [PubMed - as supplied by publisher]

Newsbot! is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 12:58 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO