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ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

Halees AS, El-Badrawi R, Khabar KS - Nucleic Acids Res. (2007)

Bottom Line: As a result, we performed quantitative assessment of ARE conservation in human, mouse and rat transcripts.We found that a significant proportion ( approximately 25%) of human genes differ in their ARE patterns from mouse and rat transcripts.ARED-Integrated, another updated and expanded version of ARED, is a compilation of ARED versions 1.0 to 3.0 and updated version 4.0 that is devoted to human mRNAs.

View Article: PubMed Central - PubMed

Affiliation: The Biomolecular Research Program, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.

ABSTRACT
ARED Organism represents the expansion of the adenylate uridylate (AU)-rich element (ARE)-containing human mRNA database into the transcriptomes of mouse and rat. As a result, we performed quantitative assessment of ARE conservation in human, mouse and rat transcripts. We found that a significant proportion ( approximately 25%) of human genes differ in their ARE patterns from mouse and rat transcripts. ARED-Integrated, another updated and expanded version of ARED, is a compilation of ARED versions 1.0 to 3.0 and updated version 4.0 that is devoted to human mRNAs. Thus, ARED-Integrated and ARED-Organism databases, both publicly available at http://brp.kfshrc.edu.sa/ARED, offer scientists a comprehensive view of AREs in the human transcriptome and the ability to study the comparative genomics of AREs in model organisms. This ultimately will help in inferring the biological consequences of ARE variation in these key animal models as opposed to humans, particularly, in relationships to the role of RNA stability in disease.

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AUUUA pentamer count-difference distribution among ARE genes in the orthologs. X-axis denotes score differences in pentamers between orthologs in each organism pair and Y-axis denotes the observed frequency of each difference.
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Figure 1: AUUUA pentamer count-difference distribution among ARE genes in the orthologs. X-axis denotes score differences in pentamers between orthologs in each organism pair and Y-axis denotes the observed frequency of each difference.

Mentions: ARED Organism allowed us to study ARE cluster variations among the organism pairs. Based on strict criteria, we extracted 907 pairs of orthologous human/mouse genes from 23 035 pairs, 394 from 20 715 human/rat pairs and 411 from 26 695 mouse/rat pairs. Due to subtle deviations in ARE clusters, for example, due to non-functional mutations or sequencing errors, numerical score assignment (0–5, depending on the number of pentamers) may deviate slightly from the ‘true’ value. We therefore compared the classes of the gene pairs by examining the distribution of both the signed and absolute difference in the ARE scores between matched gene pairs (Figure 1). We generated randomized pairings by shuffling (a thousand times) the cluster score within each ortholog list and obtained corresponding distributions. We finally compared the information content in the observed versus randomized distributions and found it to be significantly larger in all cases (P < 0.005). Using conventional Chi-squared test, we found that the probability of independence is extremely unlikely (−log P > 30) for all three organism pairs. Thus, both methods support statistical significance of overall ARE conservation among the three organisms.Figure 1.


ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

Halees AS, El-Badrawi R, Khabar KS - Nucleic Acids Res. (2007)

AUUUA pentamer count-difference distribution among ARE genes in the orthologs. X-axis denotes score differences in pentamers between orthologs in each organism pair and Y-axis denotes the observed frequency of each difference.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238997&req=5

Figure 1: AUUUA pentamer count-difference distribution among ARE genes in the orthologs. X-axis denotes score differences in pentamers between orthologs in each organism pair and Y-axis denotes the observed frequency of each difference.
Mentions: ARED Organism allowed us to study ARE cluster variations among the organism pairs. Based on strict criteria, we extracted 907 pairs of orthologous human/mouse genes from 23 035 pairs, 394 from 20 715 human/rat pairs and 411 from 26 695 mouse/rat pairs. Due to subtle deviations in ARE clusters, for example, due to non-functional mutations or sequencing errors, numerical score assignment (0–5, depending on the number of pentamers) may deviate slightly from the ‘true’ value. We therefore compared the classes of the gene pairs by examining the distribution of both the signed and absolute difference in the ARE scores between matched gene pairs (Figure 1). We generated randomized pairings by shuffling (a thousand times) the cluster score within each ortholog list and obtained corresponding distributions. We finally compared the information content in the observed versus randomized distributions and found it to be significantly larger in all cases (P < 0.005). Using conventional Chi-squared test, we found that the probability of independence is extremely unlikely (−log P > 30) for all three organism pairs. Thus, both methods support statistical significance of overall ARE conservation among the three organisms.Figure 1.

Bottom Line: As a result, we performed quantitative assessment of ARE conservation in human, mouse and rat transcripts.We found that a significant proportion ( approximately 25%) of human genes differ in their ARE patterns from mouse and rat transcripts.ARED-Integrated, another updated and expanded version of ARED, is a compilation of ARED versions 1.0 to 3.0 and updated version 4.0 that is devoted to human mRNAs.

View Article: PubMed Central - PubMed

Affiliation: The Biomolecular Research Program, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.

ABSTRACT
ARED Organism represents the expansion of the adenylate uridylate (AU)-rich element (ARE)-containing human mRNA database into the transcriptomes of mouse and rat. As a result, we performed quantitative assessment of ARE conservation in human, mouse and rat transcripts. We found that a significant proportion ( approximately 25%) of human genes differ in their ARE patterns from mouse and rat transcripts. ARED-Integrated, another updated and expanded version of ARED, is a compilation of ARED versions 1.0 to 3.0 and updated version 4.0 that is devoted to human mRNAs. Thus, ARED-Integrated and ARED-Organism databases, both publicly available at http://brp.kfshrc.edu.sa/ARED, offer scientists a comprehensive view of AREs in the human transcriptome and the ability to study the comparative genomics of AREs in model organisms. This ultimately will help in inferring the biological consequences of ARE variation in these key animal models as opposed to humans, particularly, in relationships to the role of RNA stability in disease.

Show MeSH