DNA microarrays are a powerful tool in functional genomics to mine ‘big data’. From the beginning, microarrays were used for cluster analysis, i.e., finding genes that are active together. Read the PNAS paper from 1998 by Michael Eisen et al. (Links to an external site.)Links to an external site. about cluster analysis to discover patterns of gene expression in yeast and human tissues. Genes of similar function cluster together, and cluster analysis is now used to infer the function of novel genes by ‘association’ if they show the same activity as genes within a cluster of genes with known function. Discuss this cluster analysis tool using DNA microarrays and include the idea of normalization of data (Links to an external site.)Links to an external site. needed for comparing data from different studies and across different samples and organisms. Read the abstract, introduction and discussion parts, and try to understand one or two figures included. You do not need to read through all the technical details, but ‘listen’ to the authors’ interpretation of their own findings.
Bio Peer response: 4/27/19 100 words min
A DNA microarray is a collection of small DNA spots attached to a solid surface and is used for genotyping and gene expression studies. Microarray allows monitoring the expression levels of tens of thousands of genes simultaneously. There are various tools used for microarray data analysis and since microarray data sets are extremely large, it is useful to reduce the dataset in groups distinguished by classes. One of the common methods for in depth microarray data analysis is clustering. Clustering simply classifies data into groups of genes with similar patterns that are characteristic to the group. I am assuming that because no two genomes are going to be identical, so to make any interpretation, we need to group (cluster) genomes with others which share some similarity.
Now measurements on microarrays may sometimes be systematically biased by diverse effects (such as efficiency of RNA extraction, label incorporation, exposure, scaling, etc.) that can affect the measured gene expression levels. There also may be systematic effects due to characteristics of the array (such as effects of using different probes, spotting effects, region effects, etc.). To compensate for such effects, an essential procedure in the analysis of DNA microarrays called normalization is applied that can minimize the systematic variations in the measured gene expression levels. There are several methods used for normalization (which i won’t discuss, because it is too technical for me). Usually one of these methods is used for normalization and the others are used to validate the result for optimal results.
Today, microarray technology are generally used in clinical diagnostic tests for some diseases as well as to determine which drugs might be best prescribed for a particular patient (pharmacogenomics). It is also one of the most recent advances being used for cancer research.
Bio questions: 4/25/19
1. Making human proteins to treat diseases in animal and plant hosts offers several advantages over extracting those proteins from human and animal sources. What are some of those advantages?
2. What is the difference between pluripotent and multipotent stem cells?
3. What are ‘Bt crops’? What potential risks are associated with this technology?
4. STRs are
a) used for DNA profiles
b) repeat sequences present in the human genome
c) highly variable in copy number
d) all of these
e) none of these
Bio questions: 4/26/19
1. Hemophilia and colorblindness are both recessive conditions caused by gene on the X chromosome. To calculate the recombination frequency between the two genes, you draw a large number of pedigrees that include grandfathers with both hemophilia and color blindness, their daughters (who presumably have one chromosome with the normal alleles and one chromosome with two mutant alleles), and the daughter’s sons. Analyzing all the pedigrees together shows that 25 grandsons have both color blindness and hemophilia, 24 have neither of the traits, 1 has colorblindness only, and one has hemophilia only. How many centimorgans (map units) separate the hemophilia locus from the locus for color blindness? Show your analysis or calculation, not just the final number.
2. Which of the following is not and activity carried out in the field of bioinformatics?
a) collecting and storing DNA sequence information produced by various genome sequencing projects
b) analyzing genome sequences to determine the location of genes
c) determining the three-dimensional structure of proteins
d) comparing genomes of different species
e) none of these
3. When the human genome sequence was finally completed, scientists were surprised to discover that the genome contains far fewer genes than expected. How many genes are present in the human genome? Scientists have also found that there are many more different kinds of proteins in the human cells that there are different genes in the genome. How can this be explained?
4. How does proteomics differ from genomics? What kinds of information can proteomics provide that is not available from genomics studies?