PMID- 23577217
OWN - NLM
STAT- MEDLINE
DCOM- 20131022
LR  - 20240319
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 8
IP  - 4
DP  - 2013
TI  - IMACULAT - an open access package for the quantitative analysis of chromosome 
      localization in the nucleus.
PG  - e61386
LID - 10.1371/journal.pone.0061386 [doi]
LID - e61386
AB  - The alteration in the location of the chromosomes within the nucleus upon action 
      of internal or external stimuli has been implicated in altering genome function. 
      The effect of stimuli at a whole genome level is studied by using two-dimensional 
      fluorescence in situ hybridization (FISH) to delineate whole chromosome 
      territories within a cell nucleus, followed by a quantitative analysis of the 
      spatial distribution of the chromosome. However, to the best of our knowledge, 
      open access software capable of quantifying spatial distribution of whole 
      chromosomes within cell nucleus is not available. In the current work, we present 
      a software package that computes localization of whole chromosomes - Image 
      Analysis of Chromosomes for computing localization (IMACULAT). We partition the 
      nucleus into concentric elliptical compartments of equal area and the variance in 
      the quantity of any chromosome in these shells is used to determine its 
      localization in the nucleus. The images are pre-processed to remove the smudges 
      outside the cell boundary. Automation allows high throughput analysis for 
      deriving statistics. Proliferating normal human dermal fibroblasts were subjected 
      to standard a two-dimensional FISH to delineate territories for all human 
      chromosomes. Approximately 100 images from each chromosome were analyzed using 
      IMACULAT. The analysis corroborated that these chromosome territories have 
      non-random gene density based organization within the interphase nuclei of human 
      fibroblasts. The ImageMagick Perl API has been used for pre-processing the 
      images. The source code is made available at www.sanchak.com/imaculat.html.
FAU - Mehta, Ishita
AU  - Mehta I
AD  - Department of Biological Sciences, Tata Institute of Fundamental Research, 
      Mumbai, India.
FAU - Chakraborty, Sandeep
AU  - Chakraborty S
FAU - Rao, Basuthkar J
AU  - Rao BJ
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20130408
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - Cell Nucleus/*genetics
MH  - Cell Proliferation
MH  - Chromosomes, Human/*metabolism
MH  - Fibroblasts/cytology
MH  - Humans
MH  - Image Processing, Computer-Assisted/*methods
MH  - Molecular Imaging
MH  - Reproducibility of Results
MH  - *Software
PMC - PMC3620108
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2013/04/12 06:00
MHDA- 2013/10/23 06:00
PMCR- 2013/04/08
CRDT- 2013/04/12 06:00
PHST- 2012/11/12 00:00 [received]
PHST- 2013/03/07 00:00 [accepted]
PHST- 2013/04/12 06:00 [entrez]
PHST- 2013/04/12 06:00 [pubmed]
PHST- 2013/10/23 06:00 [medline]
PHST- 2013/04/08 00:00 [pmc-release]
AID - PONE-D-12-35390 [pii]
AID - 10.1371/journal.pone.0061386 [doi]
PST - ppublish
SO  - PLoS One. 2013;8(4):e61386. doi: 10.1371/journal.pone.0061386. Epub 2013 Apr 8.