مصفوفة دنا صغيرة
مصفوفة دنا صغيرة إنگليزية: DNA Microarray هي تقنية جزيئية يتم استخدامها في الأبحاث العلمية لعدة أغراض كدراسة التعبير الجيني، أو دراسة تأثير دواء ما على المرضى و غيرها العديد من التطبيقات. يتم عرض نتائج الفحص على شكل مصفوفات دقيقة مضاءة بألوان مختلفة حسب التهجين.
مبدأ هذه التقنية يعتمد على عملية التهجين بين المادة (الدنا) المراد دراستها مع آلاف الجينات الموجودة على رقاقة زجاجية أو بلاستيكية صغيرة تسمى برقاقة الدنا. تحوي هذه الرقاقة على العديد من قطع الدنا تعرف باسم مسابر الدنا. هذه المسابر ماهي إلا عبارة عن تسلسل معروف و معين من النيوكليوتيدات و يمثل جزء من مورثة معينة.
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الاستخدامات والأنواع
Applications include:
| Technology or Application | Synopsis |
|---|---|
| Gene expression profiling | In an mRNA or gene expression profiling experiment the expression levels of thousands of genes are simultaneously monitored to study the effects of certain treatments, diseases, and developmental stages on gene expression. For example, microarray-based gene expression profiling can be used to identify genes whose expression is changed in response to pathogens or other organisms by comparing gene expression in infected to that in uninfected cells or tissues. [1] |
| Comparative genomic hybridization | Assessing genome content in different cells or closely related organisms. [2] [3] |
| Chromatin immunoprecipitation on Chip | DNA sequences bound to a particular protein can be isolated by immunoprecipitating that protein (ChIP), these fragments can be then hybridized to a microarray (such as a tiling array) allowing the determination of protein binding site occupancy throughout the genome. Example protein to immunoprecipitate are histone modifications (H3K27me3, H3K4me2, H3K9me3, etc), Polycomb-group protein (PRC2:Suz12, PRC1:YY1) and trithorax-group protein (Ash1) to study the epigenetic landscape or RNA Polymerase II to study the transcription lanscape. |
| SNP detection | Identifying single nucleotide polymorphism among alleles within or between populations.[4] Several applications of microarrays make use of SNP detection, including Genotyping, forensic analysis, measuring predisposition to disease, identifying drug-candidates, evaluating germline mutations in individuals or somatic mutations in cancers, assessing loss of heterozygosity, or genetic linkage analysis. |
| Alternative splicing detection | An 'exon junction array design uses probes specific to the expected or potential splice sites of predicted exons for a gene. It is of intermediate density, or coverage, to a typical gene expression array (with 1-3 probes per gene) and a genomic tiling array (with hundreds or thousands of probes per gene). It is used to assay the expression of alternative splice forms of a gene. |
| Tiling array | Genome tiling arrays consist of overlapping probes designed to densely represent a genomic region of interest, sometimes as large as an entire human chromosome. The purpose is to empirically detect expression of transcripts or alternatively splice forms which may not have been previously known or predicted. |
Microarrays and bioinformatics
Gene expression values from microarray experiments can be represented as heat maps to visualize the result of data analysis.
انظر أيضاً
- Microfluidics or lab-on-chip
- Cyanine dyes, such as Cy3 and Cy5, are commonly used fluorophores with microarrays
- Serial analysis of gene expression
- Significance analysis of microarrays
المصادر
- ^ Adomas A, Heller G, Olson A, Osborne J, Karlsson M, Nahalkova J, Van Zyl L, Sederoff R, Stenlid J, Finlay R, Asiegbu FO (2008). "Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus". Tree Physiol. 28: 885–897. PMID 18381269.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO (1999). "Genome-wide analysis of DNA copy-number changes using cDNA microarrays". Nat Genet. 23: 41–46. doi:10.1038/14385. PMID 10471496.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology. 150: 3363–3382. doi:10.1099/mic.0.27221-0. PMID 15470115.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Hacia JG, Fan JB, Ryder O, Jin L, Edgemon K, Ghandour G, Mayer RA, Sun B, Hsie L, Robbins CM, Brody LC, Wang D, Lander ES, Lipshutz R, Fodor SP, Collins FS (1999). "Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays". Nat Genet. 22: 164–167. doi:10.1038/9674. PMID 10369258.
{{cite journal}}: CS1 maint: multiple names: authors list (link)
المعجم
- An Array or slide is a collection of features spatially arranged in a two dimensional grid, arranged in columns and rows.
- Block or subarray: a group of spots, typically made in one print round; several subarrays/blocks form an array.
- Case/control: an experimental design paradigm especially suited to the two-colour array system, in which a condition chosen as control (such as healthy tissue or state) is compared to an altered condition (such as a diseased tissue or state).
- Channel: the fluorescence output recorded in the scanner for an individual fluorophore and can even be ultraviolet.
- Dye flip or Dye swap or Fluor reversal: reciprocal labelling of DNA targets with the two dyes to account for dye bias in experiments.
- Scanner: an instrument used to detect and quantify the intensity of fluorescence of spots on a microarray slide, by selectively exciting fluorophores with a laser and measuring the fluorescence with a filter (optics) photomultiplier system.
- Spot or feature: a small area on an array slide that contains picomoles of specific DNA samples.
- For other relevant terms see:
وصلات خارجية
- Many important links can be found at the Open Directory Project
- PLoS Biology Primer: Microarray Analysis
- Rundown of microarray technology
- CLASSIFI - Gene Ontology-based gene cluster classification resource
- Microarray data processing using Self-Organizing Maps tutorial: Part 1 Part 2