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Deciphering transcription regulation: from individual sites to cell type specific expression
Published on Oct 23, 20122846 Views
Understanding how transcription regulation is encoded in the genomes of complex multicellular organisms has been a big challenge, not least due to the large non-coding space where relevant interac
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Chapter list
Transcription Regulation: From Sites to Cell-type Specificity00:00
The impact of deep sequencing00:18
The ENCODE project01:06
Computational Biology of Gene Regulation05:22
A schematic view of cis-regulatory DNA regions06:09
Regulation of transcription08:39
Motif representations09:21
Experimental mapping: “Footprinting”10:17
Common problems/tasks12:22
The challenges13:06
The cis-regulatory code15:50
Mapping of open chromatin17:10
The setup18:31
DHS across 19 least related cell lines19:34
Specificity of open chromatin21:56
Defining expression patterns23:25
Models to distinguish expression patterns25:56
Classifier Performance29:49
Looking inside the models33:37
Example application: sex determination34:41
The Network in Supporting Cells37:31
Building a TF network in Supporting Cells38:05
A fine-time series transcriptome38:46
Cascades of dimorphic expression39:05
A Hidden Markov Model to identify dimorphic expression39:57
Different paths to dimorphic expression40:54
Activation and Repression in the Gonad41:17
New candidate regulators41:51
RNAi to validate predictions42:10
DNase-seq on E13.5 XY identifies known testis specific enhancers42:36
Identify Enhancers in DNase-seq data44:15
Future directions44:38
The need and challenges for machine learning46:53
Acknowledgements49:30