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Different gene expression arrangements seem to lead to the extraordinary variety of colors and iridescence observed in bird feathers and flower organs [ 99, 95].
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As in Fig. 6A, Type I patterns (upper left) show a typical protein expression arrangement with marshalin staining throughout the cytoplasm.
We computed correlation co-efficients among each of 6,603 genes and reverse-engineered transcriptional networks using PCIT [24]: In brief, PCIT belongs to the family of weighted network algorithms and works by comparing the co-expression arrangements for triplets of genes, with all triplets being exhaustively explored.
These differential co-expression arrangements are computed system-wide for all regulators (~1000) versus all DE genes (85 in our data).
Because substantial changes to modest co-expression relationships provide such useful re-wiring information, no attempt is made during RIF to assess the significance of the individual (breed level) co-expression arrangements.
Nevertheless, it is true that small differential co-expression arrangements make a smaller contribution to the RIF output than the large co-expression changes, assuming the abundance and differential expression of the target gene remains constant.
The differential co-expression arrangement is simply the difference in co-expression between the two breeds i.e. +0.76 – –0.34 = + 1.1.
The new – now modest to strong - positive co-expression arrangement (+0.76) reflects this change in protein behaviour.
In the wildtype Wagyu breed, across the ten time points, MSTN has a fairly weak negative co-expression arrangement with MYL2 (−0.34).
We have designed a range of AAV type 2-based vectors encoding different configurations of the EOFF expression system to evaluate optimal arrangements for further in vivo studies.
Both were students of Kazimir Malevich, the influential founder of the Suprematist movement whose abstract theories distilled expression into arrangements of squares, circles and crosses.
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