Barcode genes and temporal response of super-critical genes on chromosomes.

<p>A) Genes of critical phases are mapped into a human chromosome (UCSC hg19), corrected for the multiplicity of probes (mRNA expression) such as multiple probes of a gene due to an mRNA variant; the <i>x</i>- and <i>y</i>-axes show the chromosome position and chromosome number including X and Y chromosomes, respectively. Based on the distinct physical properties of the critical states, genes on a chromosome are clustered to form barcode genes (yellow: super-critical (<i>N</i> = 1262); red: near-critical (<i>N</i> = 3072); blue: sub-critical (<i>N</i> = 2952); gray: the unknown chromosome region), where the boundary of a barcode is defined as when two neighboring genes belong to different critical states; for instance, a sequence of.. S-S-S-T-T-S.. has two barcode genes, S-S-S and T-T; D: dynamic domain: super-critical; T: transit domain: near-critical; S: static domain: sub-critical (the plot was provided by I. E. Motoike). B) Frequency distribution of the correlation length of barcode genes for critical phases (the colors are the same as those in the barcode) shows the size of barcode genes within the range from kbp to Mbp for all states. The correlation length is estimated as the base length from the start codon of the initial gene to the end codon of the last gene within a barcode; the <i>x</i>- and <i>y</i>-axes show the common logarithm of a base pair and the number of barcodes (bin size: one-tenth of a unit length). C) Pearson correlation, <i>P</i>(<i>t</i>₀;<i>t</i>_j) of super-critical genes on chromosomes, which shows temporally four most responsive chromosomes (chromosome 2: black, 14: blue, 16: red, 19: green) with the singular like responses at 15–30 min (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128565#pone.0128565.g004" target="_blank">Fig 4A</a>). The x-axis represents log₁₀(<i>t</i>_j[min]).