Biomaterial Database

MACPET: model-based analysis for ChIA-PET. 2020

Ioannis Vardaxis, and Finn Drabløs, and Morten B Rye, and Bo Henry Lindqvist

Department of Mathematical Sciences, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.

We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared with MACS in terms of motif occurrence and spatial resolution. Furthermore, significant binding sites discovered by MACPET are involved in a higher number of significant three-dimensional interactions than those discovered by MACS. MACPET is freely available on Bioconductor. ChIA-PET; MACPET; Model-based clustering; Paired-end tags; Peak-calling algorithm.

UI	MeSH Term	Description	Entries
D008954	Models, Biological	Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.	Biological Model,Biological Models,Model, Biological,Models, Biologic,Biologic Model,Biologic Models,Model, Biologic
D011485	Protein Binding	The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.	Plasma Protein Binding Capacity,Binding, Protein
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000081204	Chromatin Immunoprecipitation Sequencing	A technique for identifying the BINDING SITES on nucleic acid sequences that are associated with binding proteins.	ATAC-Seq,Assay for Transposase-Accessible Chromatin Using Sequencing,CLIP-Seq,ChIA-PET,ChIP Sequencing,ChIP-Chip,ChIP-Exo,ChIP-Exonuclease,ChIP-PET,ChIP-Seq,Chromatin Immuno-Precipitation Paired-End Tag,Chromatin Immuno-precipitation Sequencing,Chromatin Immunoprecipitation Paired-End Tag,Chromatin Immunoprecipitation Sequencing-Chip,Cross-Linking and Immunoprecipitation Followed by Deep Sequencing,HITS-CLIP,High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation,Assay for Transposase Accessible Chromatin Using Sequencing,ChIP Exonuclease,Chromatin Immuno Precipitation Paired End Tag,Chromatin Immuno precipitation Sequencing,Chromatin Immunoprecipitation Paired End Tag,Chromatin Immunoprecipitation Sequencing Chip,Chromatin Immunoprecipitation Sequencing-Chips,Cross Linking and Immunoprecipitation Followed by Deep Sequencing,High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation,Sequencing, ChIP,Sequencing, Chromatin Immuno-precipitation,Sequencing, Chromatin Immunoprecipitation
D016678	Genome	The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.	Genomes
D017422	Sequence Analysis, DNA	A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.	DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D047369	Chromatin Immunoprecipitation	A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.	Immunoprecipitation, Chromatin
D059014	High-Throughput Nucleotide Sequencing	Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.	High-Throughput Sequencing,Illumina Sequencing,Ion Proton Sequencing,Ion Torrent Sequencing,Next-Generation Sequencing,Deep Sequencing,High-Throughput DNA Sequencing,High-Throughput RNA Sequencing,Massively-Parallel Sequencing,Pyrosequencing,DNA Sequencing, High-Throughput,High Throughput DNA Sequencing,High Throughput Nucleotide Sequencing,High Throughput RNA Sequencing,High Throughput Sequencing,Massively Parallel Sequencing,Next Generation Sequencing,Nucleotide Sequencing, High-Throughput,RNA Sequencing, High-Throughput,Sequencing, Deep,Sequencing, High-Throughput,Sequencing, High-Throughput DNA,Sequencing, High-Throughput Nucleotide,Sequencing, High-Throughput RNA,Sequencing, Illumina,Sequencing, Ion Proton,Sequencing, Ion Torrent,Sequencing, Massively-Parallel,Sequencing, Next-Generation