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استخراج رابطه علّی- معلولی ترانسکریپتومی در بافت غدد پستانی گاو شیری با استفاده از شبکه بیزی | ||
| علوم دامی | ||
| مقاله 15، دوره 32، شماره 123، شهریور 1398، صفحه 197-216 اصل مقاله (2.86 M) | ||
| نوع مقاله: مقاله پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22092/asj.2018.121024.1656 | ||
| نویسندگان | ||
| امین مرتضوی1؛ امیر رشیدی* 2؛ مصطفی قادری زفره‌ای3؛ پرهام مرادی4؛ محمد رزم کبیر5 | ||
| 1دانشجوی دکتری، ژنتیک و اصلاح دام، گروه علوم دامی، دانشگاه کردستان، سنندج، ایران | ||
| 2استاد ژنتیک و اصلاح دام، گروه علوم دامی، دانشگاه کردستان، سنندج، ایران. | ||
| 3استادیار زیست سامانه‌های محاسباتی، گروه علوم دامی دانشگاه یاسوج، یاسوج، ایران | ||
| 4دانشیار رایانه، گروه مهندسی کامپیوتر، دانشگاه کردستان، سنندج، کردستان، ایران | ||
| 5استادیار ژنتیک و اصلاح دام، گروه علوم دامی، دانشگاه کردستان، سنندج، ایران | ||
| چکیده | ||
| هدف از این مطالعه، شناسایی ژن‌های تنظیمی مؤثر در بروز بیماری ورم پستان در گاو شیری با استفاده از داده-های ریزآرایهDNA بود. بدین منظور فایل بیان ژنی با بیشترین تعداد آرایه و متعلق به پلت‌فرم افی‌متریکس GPL1221 با شماره دسترسی GSE24560از پایگاه GEO استخراج شد. برای آزمون کنترل کیفیت داده از بسته‌یArrayQualityMetrics و برای پیش‌پردازش داده‌ها از تابع Threestep بسته‌ی AffyPLM در محیط R استفاده شد. پس از شناسایی ژن‌های متفاوت بیان‌شده، الگوریتم جستجوی تابو در بسته bnlearn برای شناسایی ژن‌های تنظیمی مورداستفاده قرار گرفت. نتایج حاصل از این پژوهش بیانگر نقش علّی و تنظیمی ژن‌های BCL2A، CCL2، S100A12، AOX1 و MGP بر بیان سایر ژن‌ها در بافت پستانی گاو شیری بود. بررسی هستی‌شناسی ژن‌ها، تفاوت معنی‌داری را در 7 گروه عملکردی مولکولی، 48 گروه فرآیندهای زیستی و 11 گروه اجزای سلولی در شرایط بروز بیماری ورم پستان در بافت غدد پستانی نشان داد. همچنین نتایج غنی-سازی مجموعه دادههای بیان ژنی نشان داد بیشتر ژن‌های متفاوت بیان‌شده در این پژوهش به طور معنی داری(p < 0.05) در مسیرهای متابولیکی (GO:0009605، GO:0002376 و GO:0006954) فعال بوده و در فرآیندهای پاسخ به بروز عوامل بیماری‌زا، پاسخ ایمنی و پاسخ به التهاب در بافت پستانی گاو شیری نقش دارند. | ||
| کلیدواژه‌ها | ||
| ریزآرایهDNA؛ ورم پستان؛ ژن‌های تنظیمی؛ هستی‌شناسی | ||
| عنوان مقاله [English] | ||
| Extraction of cause-and-effect transcriptomic relationship in mammary gland tissue of dairy cattle using Bayesian network | ||
| نویسندگان [English] | ||
| Amin Mortazavi1؛ Amir Rashidi2؛ Mostafa Ghaderi-Zefrehei Ghaderi-Zefrehei3؛ Parham Moradi4؛ Mohammad Razm Razm Kabir5 | ||
| 1Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran | ||
| 2Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran | ||
| 3Department of Animal Science, ّFaculty of Agriculture and Natural Resources, Yasouj university, Yasouj, Iran | ||
| 4Department of Computer Engineering, Faculty of Engineering, University of Kurdistan, Sanandaj, Iran | ||
| 5Department of Animal Science, ّFaculty of Agriculture, University of Kurdistan, Sanandaj, Iran | ||
| چکیده [English] | ||
| The aim of this study was to identify regulatory genes affecting mastitis in dairy cattle using DNA microarray data. To reach this goal, the gene expression data with the largest number of arrays pertained to GPL1221 Platform with accession number GSE24560 was extracted from the GEO database. For quality control of data, ArrayQualityMetrics package and for preprocessing of data, three step function in AffyPLM, an add-in package in R environment were used. After identifying differentially expressed genes, a Tabu search algorithm was used to determine regulatory genes using bnlearn package in R environment. The results of this study revealed the causative and regulatory role for BCL2A, CCL2, S100A12, AOX1 and MGP genes on expression of other genes in mastitis of dairy cattle. Gene anthology analysis, revealed significant differences in 7 groups of molecular function, 48 groups of biological process and 11 groups of cellular components. Also, the results of the enrichment of the gene expression data set showed that most of the differentially genes expressed in this study that were significantly (p < 0.05) active in metabolic pathways (GO: 0009605, GO: 0002376 and GO: 0006954) involved in response to pathogens, immune response and response to inflammation in the mammary tissue of dairy cattle. | ||
| کلیدواژه‌ها [English] | ||
| DNA Microarray, Mastitis, Regulatory Genes, Anthology | ||
| مراجع | ||
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