hexamers

This approach calculates frequencies for hexamers 1, 2 and 3 as well as

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

Following the link "View Results per microRNA" the user is taken to a page (B) showing miRNAs sorted according to a combinatorial score produced by the values of hexamers 1 and 2.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

We investigated whether it is possible to distinguish between similar miRNAs by using the p-values of flanking hexamers 1 and 3.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

Non-overlapping six nucleotide long motifs (hexamers) are counted on the 3′UTR sequence of protein coding genes provided by Ensembl.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

The option to use hexamers conserved between human and mouse provides a refinement of results for processes and miRNAs that are conserved between the two species.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

After the input gene lists have been determined, we proceed to compare the distributions of all possible hexamers on the 3′UTR sequences between them.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

Briefly, equal concentrations of RNA from each sample was reverse transcribed in the presence of 1X reaction buffer which included dNTPs, random hexamers, oligo (dT), MgCl

PLoS ONE Alerts: New Articles Shaomei Wang et al. 2010

RNA was quantified using a Nanodrop spectrophotometer (Thermo Scientific). 1 µg of RNA was DNase-treated (Promega) and used in reverse transcription reactions primed with random hexamers (Superscript III, Invitrogen). cDNA samples were treated with RNase H and 5 µL of each sample were used for quantitative real-time PCR reactions.

PLoS ONE Alerts: New Articles Morgan A. Sammons et al. 2010

At the top of the page is the histogram of the distribution of - lnp values for all possible hexamers and at the bottom, the sorted list of hexamers that can be mapped on deregulated miRNAs with corresponding p-values.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010

The optimal weights combination for hexamers 1 and 3 were identified as 0.6 and 0 respectively.

PLoS ONE Alerts: New Articles Panagiotis Alexiou et al. 2010