CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Jonathan
J
Cairns
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Paula
P
Freire-Pritchett
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.|Bioinformatics Group, Babraham Institute, Cambridge, UK.
Steven W
SW
Wingett
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Csilla
C
Várnai
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Andrew
A
Dimond
UCL Genetics Institute, London, UK.
Vincent
V
Plagnol
European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
Daniel
D
Zerbino
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Stefan
S
Schoenfelder
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Biola-Maria
BM
Javierre
Department of Medical and Molecular Genetics, King's College, London, UK.
Cameron
C
Osborne
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
Peter
P
Fraser
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK. mikhail.spivakov@babraham.ac.uk.
Mikhail
M
Spivakov
D000465:Algorithms; D002843:Chromatin / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D023281:Genomics; D006801:Humans; D020407:Internet; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software
D002843:Chromatin
Capture Hi-C; Convolution background model; Gene regulation; Nuclear organisation; P value weighting; Promoter-enhancer interactions