mugdata.json

{"nodes":
 [{"name":"MNase-seq","description":"Information about the position of Nucleosomes along the genome, generally obtained using MNase-seq method, but also using other related techniques."},
  {"name":"RNA-seq","description":"Data on the relative expression of genes of a particular cell population, obtained by sequencing RNA transcripts extracted from cells."},
  {"name":"Histone marks","description":"Data on epigenetic histone modifications (in particular methylation of their N-terminal tails), typically obtained using ChIP-seq."},
  {"name":"Hi-C","description":"Matrices encoding contact probabilities between loci along a portion of a genome, obtained using techniques derived from chromosome conformation capture, such as Hi-C."},
  {"name":"Physical models (bp)","description":"Physical models of chromatin at the base-pair resolution, encoding the elastic properties and interactions of naked DNA and nucleosomes, to describe the behaviour of several thousand bps."},
  {"name":"Chromatin structure","description":"Three-dimensional structures of chromatin, generally predicted on the basis of contact matrices."},
  {"name":"ChIP-seq","description":"Information on the genome sequences to which a DNA-binding protein is bound in the cell."},
  {"name":"Physical models (kbp)","description":"Physical models of chromatin at the kilo-base-pair resolution, used to describe the epigenetic-dependent mechanics and interactions of chromatin segments of several million bps."},
  {"name":"FISH","description":"Microscopy imaging data obtained by marking with fluorescent probes specific regions of the genome, used to identify the (relative) location of genome segments in the cell."},
  {"name":"Atomistic MD","description":"Time-dependent behaviour of DNA and protein-DNA complexes at the atomic scale, obtained using Molecular Dynamics with an underlying physical model, giving access to space- and time-resolved information on the complex."}
 ],
 "links":
 [{"source":"MNase-seq","target":"RNA-seq","flow":0,"description":"Relate nucleosome dynamics with gene expression","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/26818620","text":"Deniz et al., 2016"}],"notes":"Through sequence","tools":[],"type":"1","links":[],"pilot":2},
  {"source":"MNase-seq","target":"Histone marks","flow":0,"description":"Effect of histone marks on the arrangement of nucleosomes at genes","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/25480300","text":"Rhee et al., 2014"}],"notes":"Through sequence","tools":[],"type":"1","links":[],"pilot":2},
  {"source":"MNase-seq","target":"Hi-C","flow":1,"description":"Identify quantitative representations of MNase data that can be integrated into 3D modeling of chromatin","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"1","links":[],"pilot":2},
  {"source":"MNase-seq","target":"Physical models (bp)","flow":1,"description":"Guide the positioning of nucleosomes in polynuclesome models","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"2","links":[],"pilot":3},
  {"source":"Chromatin structure","target":"ChIP-seq","flow":0,"description":"Relate the 3D proximity of loci with information on protein binding","reference":[{"link":"arxiv.org/abs/1512.00268","text":"Pancaldi et al., 2016"}],"notes":"Using network theory","tools":[],"type":"1","links":[],"pilot":3},
  {"source":"Hi-C","target":"Histone marks","flow":0,"description":"Drosophila chromatin colors","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/20888037","text":"Filion et al., 2010"}],"notes":"Through sequence","tools":[],"type":"1","links":[],"pilot":1},
  {"source":"Chromatin structure","target":"Histone marks","flow":0,"description":"Structural features of chromatin colors","reference":[{"link":"biorxiv.org/content/early/2016/01/15/036764","text":"Serra et al., 2016"}],"notes":"","tools":[{"text":"TADbit"}],"type":"0","links":[],"pilot":1},
  {"source":"Histone marks","target":"Chromatin structure","flow":1,"description":"Identify quantitative representations of histone mark data that can be integrated in 3D modelling of chromatin","reference":[{"link":"www.ncbi.nlm.nih.gov/pmc/3799458","text":"Peng et al., 2013"}],"notes":"","tools":[],"type":"1","links":[],"pilot":3},
  {"source":"Chromatin structure","target":"Physical models (kbp)","flow":1,"description":"Provide (initial) coordinates for chromatin models","reference":[{"link":"github.com/3DGenomes/TADbit","text":""}],"notes":"","tools":[{"text":"TADbit"}],"type":"0","links":[],"pilot":3},
  {"source":"Hi-C","target":"ChIP-seq","flow":0,"description":"Effect of protein binding on TAD formation","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/25497547","text":"Rao et al., 2014"}],"notes":"","tools":[],"type":"1","links":[],"pilot":7},
  {"source":"Hi-C","target":"Chromatin structure","flow":1,"description":"3D modelling of chromatin structure","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/25980604","text":"Serra et al., 2015"}],"notes":"","tools":[{"text":"TADbit"}],"type":"0","links":[],"pilot":7},
  {"source":"Hi-C","target":"Physical models (kbp)","flow":1,"description":"Use (selected) chromatin contacts to guide physical simulations of chromatin models","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/26729303","text":"Pichugina et al., 2016"}],"notes":"","tools":[],"type":"1","links":[],"pilot":2},
  {"source":"Physical models (kbp)","target":"Hi-C","flow":1,"description":"Validate contact data using physical simulation ensembles","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"1","links":[],"pilot":2},
  {"source":"Physical models (bp)","target":"Atomistic MD","flow":1,"description":"Determine bp-resolution, biologically relevant information on the topological strain on DNA","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"2","links":[],"pilot":6},
  {"source":"Atomistic MD","target":"Physical models (bp)","flow":1,"description":"Parameterisation of DNA flexibility","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/25228467","text":"Petkeviciute et al., 2014"}],"notes":"","tools":[{"text":"cgDNA"}],"type":"0","links":[],"pilot":6},
  {"source":"ChIP-seq","target":"Physical models (bp)","flow":1,"description":"Effect of proteins on the shape and flexibility of DNA, and on its interactions with other proteins","reference":[{"link":"","text":""}],"notes":"Through MD of Protein-DNA complexes","tools":[],"type":"2","links":[],"pilot":7},
  {"source":"FISH","target":"Physical models (kbp)","flow":1,"description":"Identify quantitative representations of FISH data that can be integrated into physical simulations of chromatin","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/26729303","text":"Pichugina et al., 2016"}],"notes":"","tools":[],"type":"1","links":[],"pilot":1},
  {"source":"FISH","target":"Chromatin structure","flow":1,"description":"Validate 3D models using quantitative information extracted from microscopy images","reference":[{"link":"www.ncbi.nlm.nih.gov/pmc/4681004","text":"Belton et al., 2015"},{"link":"www.ncbi.nlm.nih.gov/pubmed/25274727","text":" Le Dily et al., 2014"},{"link":"www.ncbi.nlm.nih.gov/pubmed/26760202","text":" Boettiger et al., 2016"}],"notes":"","tools":[],"type":"1","links":[],"pilot":1},
  {"source":"FISH","target":"Hi-C","flow":1,"description":"Identify quantitative representations of FISH data that can be integrated into 3D modeling of chromatin","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/15839726","text":"Bolzer et al., 2005"}],"notes":"","tools":[],"type":"1","links":[],"pilot":1},
  {"source":"FISH","target":"Histone marks","flow":0,"description":"Effect of histone marks on chromatin folding","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/26760202","text":"Boettiger et al., 2016"}],"notes":"","tools":[],"type":"1","links":[],"pilot":1},
  {"source":"RNA-seq","target":"FISH","flow":0,"description":"Spatial localisation of RNAs (MERFISH)","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/25858977","text":"Chen et al., 2015"}],"notes":"","tools":[],"type":"1","links":[],"pilot":1},
  {"source":"RNA-seq","target":"Physical models (kbp)","flow":0,"description":"Relation between active transcription of genes and nucleosome rearrangement on those genes","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"2","links":[],"pilot":6},
  {"source":"Histone marks","target":"Physical models (bp)","flow":1,"description":"Provide information on the chromatin-type-dependent, coarse-grain charge distribution on nucleosomes","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"2","links":[],"pilot":6},
  {"source":"Histone marks","target":"Physical models (kbp)","flow":1,"description":"Parameterise the physical interactions between the 'beads' on the basis of chromatin type","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/25092923","text":"Jost et al., 2014"}],"notes":"","tools":[],"type":"1","links":[],"pilot":3},
  {"source":"Physical models (bp)","target":"Physical models (kbp)","flow":1,"description":"Parameterisation of interactions & flexibility","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"2","links":[],"pilot":6},
  {"source":"Physical models (kbp)","target":"Physical models (bp)","flow":1,"description":"Back-map bp-resolution coordinates from kbp-resolution coordinates","reference":[{"link":"","text":""}],"notes":"","tools":[],"type":"2","links":[],"pilot":6},
  {"source":"ChIP-seq","target":"Atomistic MD","flow":1,"description":"Provide information on the in-vivo consensus sequence of a DNA-binding protein","reference":[{"link":"xxx.com","text":"Bouvier et al., 2009"}],"notes":"","tools":[{"text":"Various (omictools.com)", "link":"http://omictools.com/motif-discovery-category"}],"type":"0","links":[{"link":"http://jaspar.genereg.net/"}],"pilot":6},
  {"source":"Histone marks","target":"Atomistic MD","flow":1,"description":"Effect of histone marks on chromatin folding","reference":[{"link":"www.ncbi.nlm.nih.gov/pubmed/26192632","text":"Colleparo-Guevara et al., 2015"}],"notes":"","tools":[],"type":"1","links":[],"pilot":6}
 ]}