Dataset Information


CENTDIST: Discovery of Co-associated Factors by Motif Distribution

ABSTRACT: Transcription factors (TFs) do not function alone but work together with other TFs (called co-TFs) in a combinatorial fashion to precisely control the transcription of target genes. Mining co-TFs is thus important to understand the mechanism of transcriptional regulation. Although existing methods can identify co-TFs, their accuracy depends heavily on the chosen background model and other parameters such as the enrichment window size and the PWM score cut-off. In this study, we have developed a novel web-based co-motif scanning program called CENTDIST ( In comparison to current co-motif scanning programs, CENTDIST does not require the input of any user-specific parameters and background information. Instead, CENTDIST automatically determines the best set of parameters and ranks co-TF motifs based on their distribution around ChIP-seq peaks. We tested CENTDIST on 14 ChIP-seq datasets and found CENTDIST is more accurate than existing methods. In particular, we applied CENTDIST on an Androgen Receptor (AR) ChIP-seq dataset from a prostate cancer cell line and correctly predicted all known co-TFs (8 TFs) of AR in the top 20 hits as well as discovering AP4 as a novel co-TF of AR (which was missed by existing methods). Taken together, CENTDIST, which exploits the imbalanced nature of co-TF binding, is a user-friendly, parameter-less, and powerful predictive web-based program for understanding the mechanism of transcriptional co-regulation. Genome-wide binding analyses of AP4 in LNCaP with DHT (5alpha-dihydrotestosterone) stimulation using ChIP-Seq.

ORGANISM(S): Homo sapiens  

SUBMITTER: Cheng W Chang   Edwin Cheung  Wan L Goh  Cheng Wei Chang  Zhizhuo Zhang  Wing-Kin Sung 

PROVIDER: E-GEOD-28857 | ArrayExpress | 2012-04-25



Similar Datasets

2012-04-26 | E-GEOD-28950 | ArrayExpress
2011-11-16 | E-GEOD-28264 | ArrayExpress
2015-05-28 | E-GEOD-68195 | ArrayExpress
2011-06-03 | E-GEOD-23852 | ArrayExpress
2013-07-05 | E-GEOD-42348 | ArrayExpress
2015-01-23 | PXD001212 | Pride
2013-09-25 | E-GEOD-51142 | ArrayExpress
2013-08-15 | E-GEOD-49402 | ArrayExpress
2013-10-01 | E-GEOD-51290 | ArrayExpress
2016-04-07 | E-GEOD-77576 | ExpressionAtlas