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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.

The x-axis indicates the Rich factor of each pathway, and the y-axis indicates the name for each pathway.

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 %).

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).

We sought mammalian orthologs of CRAM-1, based on hierarchical identification of sequences most conserved between species with a common ancestor; TreeFam (www.treefam.org) identified HYPK as the most likely human ortholog of CRAM1, whereas Inparanoid7 (inparanoid.sbc.su.se) identified SERF2 (small EDRK-rich factor-2).

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.