Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations.
Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway e.g.lund@medisin.uio.no.
Eivind
E
Lund
Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway.
Anja R
AR
Oldenburg
Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway e.g.lund@medisin.uio.no.
Philippe
P
Collas
D000465:Algorithms; D002478:Cells, Cultured; D002843:Chromatin / Q000737:chemistry*; D047369:Chromatin Immunoprecipitation; D015894:Genome, Human; D006801:Humans; D034904:Lamin Type A / Q000032:analysis; D034921:Lamin Type B / Q000032:analysis; D020411:Oligonucleotide Array Sequence Analysis; D014158:Transcription, Genetic
D002843:Chromatin; D034904:Lamin Type A; D034921:Lamin Type B