DNA Microarray Basics Quiz

Functional Genomics

• Functional genomics aims to understand the roles of genetic sequences (DNA and RNA) within a species.
• Researchers study genes in large groups to analyze their interactions in metabolic pathways.
• This research describes how gene products interact for cellular processes.

Proteomics

• Proteomics is the study of the entire protein collection (proteome) of a cell or organism.
• Scientists aim to understand the functions and interactions of proteins.
• The goal is to determine the traits of a species.
• Proteomics involves experimental and computational approaches.

Bioinformatics

• Bioinformatics uses computers, mathematical tools, and statistics to analyze biological information.
• This field examines genetic data (e.g., DNA sequences) and other biological information.
• Bioinformatics plays a crucial role in functional genomics and proteomics.

DNA Microarrays

• DNA microarrays, also called gene chips, quantify gene expression in thousands of genes concurrently.
• A small slide holds thousands of DNA sequences corresponding to different genes.
• Using fluorescently labeled cDNA, the amount of a gene's transcription can be measured.
• High fluorescence intensity signifies a large mRNA presence linked to that specific DNA spot.

RNA Sequencing (RNA-Seq)

• RNA-Seq is a newer transcriptome analysis method using next-generation sequencing.
• It sequences cDNA produced from RNA to identify specific RNAs and their concentrations.
• RNA-Seq compares transcriptomes across different cell types, disease states, or environmental conditions.

Gene Knockout Collections

• Gene knockout collections are useful in determining gene functions.
• Researchers inactivate individual genes one at a time to observe the resulting phenotypes.
• This approach aids in understanding cellular pathways and complex traits associated with genes.
• Transposable elements and CRISPR-Cas technology are used for gene knockout collections.

Two-Dimensional Gel Electrophoresis (2-DE)

• 2-DE is a protein separation technique.
• Separates proteins in a gel based on isoelectric point (charge) and molecular mass.
• Identifies and isolates thousands of different proteins within a single sample.

Mass Spectrometry

• Mass spectrometry precisely determines molecule masses, including fragments of proteins.
• Tandem mass spectrometry sequences peptides to identify whole proteins.
• Used to identify proteins from 2-DE spots and further study protein covalent modifications.

Protein Microarrays

• Protein microarrays provide a platform for examining protein expression and function.
• Using tiny spots of purified proteins from a cell, researchers can analyze protein-ligand interactions (e.g., drug interactions).
• Antibody microarrays and functional protein arrays are two types.

Bioinformatics I: Overview of Computer Analyses and Gene Prediction

• Bioinformatics integrates computer science, mathematics and statistics to analyze biological data (e.g. sequences).
• Sequences are stored in computer data files which are then analyzed by computer programs.
• Sequence recognition, pattern recognition and sequence element (motif) identification are computational strategies used in sequence analysis.
• Gene prediction identifies protein-coding DNA segments.
• Computational tools identify sequences of particular meaning or function.

Bioinformatics II: Databases

• Databases are organized collections of biological data like DNA, RNA and protein sequences.
• These databases store genetic sequences, additional information (annotations) and references.
• Examples include GenBank, EMBL and DDBJ (nucleotide sequences), UniProt, SwissProt, and PIR (amino acid sequences).
• Clinical databases, such as OMIM and ClinVar provide crucial genetic information related to human diseases.

Bioinformatics III: Homology

• Homology refers to similarities in organisms or molecules due to shared ancestry.
• Homologous genes are derivates of a common ancestral gene.
• Orthologs serve the same function in different species, whereas paralogs carry out different functions in the same species.
• Computer programs, such as BLAST, identify similar sequences from a database search which can help predict gene function.
• Multiple sequence alignment compares homologous sequences to find conserved sites which may be functionally important.