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We compared the fragility of transcriptional regulatory program with other determinants of expression variability, and showed that the fragility is an important source of expression variability.
While exon size, intron length, CAI and d N are stronger determinants of expression levels, CpG O/E of promoter is a better indicator of expression breadths.
Even in 22q11.2 deletion syndrome (22q11.2DS), where the recurrent 22q11.2 deletion imparts a 25% risk of developing schizophrenia (Fung et al. 2010; Schneider et al. 2014), there remain undiscovered determinants of expression.
While genetic factors are important in determining the risk of development of asthma, environmental factors are still likely to be the primary determinants of expression of atopic diseases [ 3].
In particular, our study indicates that a target gene's transcription rate and onset of activation are major determinants of expression range, revealing previously unrecognized layers in the interpretation of morphogen gradients.
To ensure the robustness of our findings to the presence of unknown hidden factors, we utilized the probabilistic estimation of expression residuals (PEER) framework [ 55], which infers hidden determinants of expression levels and generates a residual expression profile.
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Here we have shown that sequences beyond the translational initiation region are critical and that codon usage is a key determinant of expression yield.
Copy number can be a major determinant of expression levels for some genes.
However, this assumes that gene dose is the only determinant of expression level, which is unlikely [ 31, 32].
We have demonstrated that key proteins are differentially expressed in bone invasive meningiomas and that the anatomical location of bone invasion is a key determinant of expression pattern of MMP1, OPN, and ITGB1.
ChIP-chip has revealed the tissue-specific pattern of binding of transcription factors to human chromosome 21, and – when this whole chromosome is transplanted into a mouse nucleus – this pattern remains essentially unchanged; clearly, DNA sequence is a major determinant of expression [ 23 ].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com