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For instance, the protein TERA08399 belongs to the superfamily of secreted cysteine rich factors and its N-terminal domain sequence exhibits the idiosyncratic features of the IGFBP (Insulin-Like Growth Factor Binding Protein) family reported to be vertebrate-specific [ 59].
(TIFF 2076 kb) Additional file 3: The rich factors and number of genes involved in each pathway derived from a comparison of gene expression in TBvsTL, OTBvsOTL, TBvsOTB and TL2vsOTL2.
The estimated rich factors (number of DEGs mapped to a certain pathway/total number of genes mapped to this pathway) of secondary metabolism were 0.4 0.7 in TBvsOTB and TLvsOTL (Fig. 3a and b), whereas they were 0.1 0.3 in TBvsTL and OTBvsOTL (Fig. 3c and d).
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(doc 114 KB) Additional file 7: The enriched pathways by DEGs and rich factor in comparisons.
For this purpose, we have compared the distribution of GC rich factor Sp1 with GATA-3 distribution.
To verify whether the slope is caused by the GC rich content of the human promoters, we have analyzed the distribution of hits for GC rich factor.
A lower rich factor between two stages for either of two species implies that steady metabolism occurs during this period (Additional file 3).
The top-five enriched pathways and corresponding rich factor in the comparison R3 were as follows: photosynthesis-antenna proteins (38.46 %), carotenoid biosynthesis (34.78 %), glycerolipid metabolism (20.59 %), galactose metabolism (20.63 %) and photosynthesis (20.75 %).
To identify cofactors that modulate intracellular amyloid formation, a genetic screen was performed and led to the discovery of MOAG-4/SERF (Modifier of aggregation-4/Small EDRK rich factor) as an evolutionary conserved class of amyloid-regulating proteins (van Ham et al., 2010).
In our present study, it was found that galactose metabolism was identified as enriched pathways in the R3 comparison with the rich factor reached 34.78 %, but just 3.17%% in the S3 comparison, suggesting that galactose metabolism plays essential roles in conferring plant improved tolerance to cold stress.
The slope in the z-score distribution of the AT-rich factors like GATA-3, Ets-1 and TCF-1 is the manifestation of the under-representation of their binding sites around the functional window.
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