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UID:7048@i2m.univ-amu.fr
DTSTART;TZID=Europe/Paris:20190513T110000
DTEND;TZID=Europe/Paris:20190513T120000
DTSTAMP:20241120T202656Z
URL:https://www.i2m.univ-amu.fr/evenements/correlating-trbs-chip-seq-peaks
 -from-multiple-datasets-in-remap-using-deep-convolutional-autoencoders-que
 ntin-ferre/
SUMMARY:Quentin Ferré (TAGC\, Aix-Marseille Université): Correlating TRBS
  ChIP-seq peaks from multiple datasets in ReMap using deep convolutional a
 utoencoders - Quentin Ferré
DESCRIPTION:Quentin Ferré: Cis-regulatory elements (CREs) are genomic regi
 ons regulating gene expression by binding proteins called Transcriptional 
 Regulators (TRs). TR binding is mostly studied experimentally\, via ChIP-S
 eq\, but these experiments have false positives\, and there is no method t
 o discern them. However\, TRs are known to be co-occurent\, and many repli
 ca datasets exist. As such\, we use common TR and/or datasets combinations
  to identify “atypical” peaks. We use the ReMap database to learn such
  correlations.\nCREs are represented as 3D tensors of peak presence (namel
 y ‘position’\, ‘TR’\, and ‘dataset’). We use an autoencoder to
  perform a lossy compression of each\, to keep common patterns and discard
  rare elements (atypical peaks). The regions are viewed by the model throu
 gh convolutional filters to focus on the correlations. Each peak gets an a
 nomaly score corresponding to the autoencoder reconstruction error.\nWe us
 e artificial data to confirm the model’s ability to discover correlation
  groups of TR/datasets and label lonely/anomalous peaks. Application to Re
 Map is in progress\, currently on a curated subset of data. To our knowled
 ge\, our research shows the first use of a large-scale meta-analysis to co
 rroborate different ChIP-Seq datasets\, using deep learning to integrate t
 hem in complex combinations and eliminate atypical peaks.\n\nhttp://colleg
 e-doctoral.univ-amu.fr/fr/inscrit/10183
ATTACH;FMTTYPE=image/jpeg:https://www.i2m.univ-amu.fr/wp-content/uploads/2
 019/05/Quentin_Ferre.jpg
CATEGORIES:Séminaire,MABioS
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