box plot

par(mai=c(2,1.5,1.5,.5))
par(mgp=c(5, 0.5, 0))

b = boxplot(log2(mat.sel$HL)~mat.sel$type, xlab = "pA_type", ylab = "HL (hr)", las = 3, cex.axis=0.7, varwidth=T)
boxplot(log2(mat.sel$HL)~mat.sel$type, xlab = "pA_type", ylab = "HL (hr)", las = 3, cex.axis=0.7, varwidth=T, names=paste(b$names, "(n=", b$n, ")"))

mRNA degradation

After export to the cytoplasm, mRNA is protected from degradation by a 5’ cap structure and a 3’ poly adenine tail. In the deadenylation dependent mRNA decay pathway, the polyA tail is gradually shortened by exonucleases. This ultimately attracts the degradation machinery that rapidly degrades the mRNA in both in the 5’ to 3’ direction and in the 3’ to 5’ direction. Additional mechanisms, including the nonsense mediated decay pathway, bypass the need for deadenylation and can remove the mRNA from the transcriptional pool independently



Inside eukaryotic cells, there is a balance between the processes of translation and mRNA decay. Messages that are being actively translated are bound by ribosomes, the eukaryotic initiation factors eIF-4E and eIF-4G, and poly(A)-binding protein. eIF-4E and eIF-4G block the decapping enzyme (DCP2), and poly(A)-binding protein blocks the exosome complex, protecting the ends of the message. The balance between translation and decay is reflected in the size and abundance of cytoplasmic structures known as P-bodies

The presence of AU-rich elements in some mammalian mRNAs tends to destabilize those transcripts through the action of cellular proteins that bind these sequences and stimulate poly(A) tail removal.

Binding of a miRNA to a message can repress translation of that message and accelerate poly(A) tail removal, thereby hastening mRNA degradation.

Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons.

T-test and F-test for goodness of fit

• The F test compares the variances of the Y values to the variances of the fitted Y values.
• 
  
• The T test compares the means of the differences between the Y values and the fitted Y values to the 
• corresponding mean standard deviations.
• 
  
• Both the F and T tests judge goodness of fit depending on how close the results of the calculations are to 1.
• 
  
• The T test compares the means of the differences between the Y values and the fitted Y values to the corresponding mean standard deviations. 

• Both the F and T tests judge goodness of fit depending on how close the results of the calculations are to 1.

http://books.google.com/books?id=tIsjh56pI0IC&pg=PA159&lpg=PA159&dq=nonlinear+regression%22+t+test%22&source=bl&ots=dPZAyra-P3&sig=g-GIgmlz2SA8LmBy-xfaaTrPZO8&hl=en&sa=X&ei=PJBlUZd2kajgA-2fgMgB&ved=0CEwQ6AEwAw#v=onepage&q=nonlinear%20regression%22%20t%20test%22&f=false

mRNA degradation

• PUF-binding motifs and AU-rich elements (AREs) in 3'-untranslated region (UTR) and CG di-nucleotides in the 5′-UTR accelerated mRNA decay
• Using microarrays we compiled a database of mRNA degradation rates in mouse ES cells (19977 genes).
• Unstable mRNA species are enriched in regulatory genes (transcription factors, signal transduction, cell cycle), and stable mRNA species are enriched in structural genes and genes associated with metabolism
• Number of exons per ORF length was the strongest predictor of mRNA degradation rate, indicating that exon junctions increase mRNA stability.
• ARE (AU-rich elements) in 3′UTR negatively affected mRNA stability; sequence non-specific AREs had a stronger effect than sequence-specific AREs
• CG elements in 5′UTR negatively affected mRNA stability
• Differentiation of ES cells after LIF withdrawal decreased average mRNA stability, whereas differentiation induced by RA resulted in increased average stability
• There was no global relation between changes in mRNA stability and gene expression in ES cells upon differentiation 

1. Different mRNAs within the same cell have distinct lifetimes (stabilities). In bacterial cells, individual mRNAs can survive from seconds to more than an hour; in mammalian cells, mRNA lifetimes range from several minutes to days. The greater the stability of an mRNA the more protein may be produced from that mRNA
2. Inside eukaryotic cells, there is a balance between the processes of translation and mRNA decay
3. eIF-4E and eIF-4G block the decapping enzyme (DCP2), and poly(A)-binding protein blocks the exosome complex, protecting the ends of the message
4. The presence of AU-rich elements in some mammalian mRNAs tends to destabilize those transcripts through the action of cellular proteins that bind these sequences and stimulate poly(A) tail removal
5. Binding of a miRNA to a message can repress translation of that message and accelerate poly(A) tail removal, thereby hastening mRNA degradation

nohup perl 0001.compare_2sets.v5.pl > v5.out &

nohup perl 0001.compare_2sets.v5.pl > v5.out &

RNA polymerase

Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA. All are structurally and mechanistically related to each other and to bacterial RNAP:

• RNA polymerase I synthesizes a pre-rRNA 45S (35S in yeast), which matures into 28S, 18S and 5.8S rRNAs which will form the major RNA sections of the ribosome.^[6]
• RNA polymerase II synthesizes precursors of mRNAs and most snRNA and microRNAs.^[7] This is the most studied type, and, due to the high level of control required over transcription, a range of transcription factors are required for its binding to promoters.
• RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.^[8]
• RNA polymerase IV synthesizes siRNA in plants.^[9]
• RNA polymerase V synthesizes RNAs involved in siRNA-directed heterochromatin formation in plants.^[10]

How to use CPAN as a non-root user

wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib
eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`
echo 'eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`' >> ~/.profile

cpanm Module::name

e.g. cpanm List::Permutor