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Register a new userA Comparative Study of CpG Islands Detected by Different Tools: Newcpgreport and CpGCluster
دراسة مقارنة لخصائص جزر الCpG المكتشفة باستخدام أداتي newCpGReport و CpGCluster
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Damascus University ورقة بحثية
Publication date
2012
fields
Medical Device Engineering
and research's language is
العربية
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Shamra Editor
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تؤدي جزر الCpG دوراً مهماً في تنظيم عملية نسخ الجينات. و يعود ذلك لتراكب عدد كبير من هذه الجزر مع محفزات نسخ الجينات. إِذ إن مْثيلة الجزر الموجودة في منطقة المحفزات يمكن أن يعطل عملية نسخ الجين المسؤول عنه هذا المحفز. و من أهم هذه الحالات تعطل الجينات المثبطة لتطور الأورام السرطانية, فقد بينت العديد من الدراسات أن مثيلة جزر الCpG هو من العلامات المهمة على وجود السرطان أو إمكانية تطوره. وانطلاقاً من أهمية جزر CpG, فقد طُورت عدة خوارزميات للكشف عنها في سلاسل النكليوتيدات. و تقسم هذه الخوارزميات بشكل عام إلى نوعين رئيسين و هما: الخوارزميات التي تعتمد على المسافة, و من أهمها خوارزمية (CpGCluster), و الخوارزميات التي تعتمد على النافذة المنزلقة و منها (newCpGReport).إلا أن هناك بعض الاختلافات في نتائج تطبيق كل من هاتين الخوارزميتين، لذلك فإن هدف هذه الدراسة هو مقارنة أداء كل من الخوارزميتين السابقتين. كُشف عن جزر الCpG الموجودة على الصبغي 22 عند الإنسان من خلال تطبيق كلتا الخوارزميتين على هذا الصبغي. و قد أظهرت النتائج وجود اختلاف واضح بين عدد الجزر المكتشفة في كلتا الخوارزميتين، فضلاً عن وجود تباين في طول الجزر المكتشفة. كما أظهرت النتائج وجود تقاطع بين نحو 60 % من الجزر المكتشفة في كلتا الطريقتين.درِس في هذا البحث تأثير قيم بارامترات جزر الCpG و هي الطول و محتوى C+G content) C+G) و نسبة الملاحظ/المتوقع في عدد الجزر المكتشفة. و تبين أن لعتبة الطول تأثيراً كبيراً في عدد الجزر المكتشفة باستخدام newCpGReport, على عكس خوارزمية CpGCluster التي لا يتأثر أداؤها بعتبة الطول. كما درِس تأثير جعل الجزر المكتشفة باستخدام newCpGReport تبدأ و تنتهي بزوج النكليوتيدات CpG, و كانت النتيجة زيادة قيم كل من بارامتري المحتوى و نسبة الملاحظ/المتوقع لنسبة كبيرة من الجزر، مع الأخذ بالحسبان انخفاض طول نحو 25 % من الجزر إلى ما دون 200 نكليوتيد.
CpG islands play an important role in genes transcription regulation, due to the fact that these islands overlap with the genes’ promoter regions, and the methylation of those CpG islands may repress the transcription of the associated genes. Previous studies reported that methylation of CpG islands is an important indicator of the presence and possibility of developing cancers. There are mainly two types of algorithms to identify CpG islands in the nucleotides sequences: distance-based and sliding-window algorithms. The outputs of these algorithms are different for the same nucleotide sequence. The aim of this study is to compare the performance of the above mentioned algorithms by using two web tools named CpGCluster and newCpGReport. CpG islands in human chromosome 22 were identified by applying the two algorithms on this chromosome, and the variation in the number and length of the identified islands was clear. The results also show that about 60% of both tools’ output is crossed. Moreover, the effect of the traditional parameters of CpG islands (length, C+G content and Observed/expected ratio) on the number of the identified islands was studied. The results show that the length parameter has a great effect on the number of islands identified by newCpGReport, while it does not affect CpGCluster’s performance. The effect of making CpG islands identified by newCpGReport start and end with CpG was also studied, due to this operation C+G content and Observed/expected ratio increased for most islands, taking into account that 25% of the islands became shorter than 200 nucleotides.
References used
Illingworth R.S., Bird A.P., (2009), “CpG islands – ‘A rough guide’”, FEBS letters, Vol. 583, p.p. 1713-1720
Hou P., Ji M., Liu Z., Shen J., Cheng L., He N., Lu Z., (2003), “A microarray to analyze methylation patterns of p16Ink4a gene 5’-CpG islands”, Clinical Biochemistry, Vol. 36, p.p. 197-202
Bastian P.J., Yegnasubramanian S., Palapattu G.S., Rogers C.G., Lin X., De Marzoa A.M., Nelson W.G., (2004), “Molecular Biomarker in Prostate Cancer: The Role of CpG Island Hypermethylation”, European Urology, Vol. 46, p.p. 698-708
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