This set of Tricky Bioinformatics Questions and Answers focuses on “Prediction of Gene Function Based on a Composite Analysis”.
1. When two proteins share a considerable degree of sequence identity throughout the sequence alignment, they are least likely to share the same function.
a) True
b) False
View Answer
Explanation: In the mentioned case they are more likely to share the same function. A considerable fraction of a genome may encode proteins whose function may not be identified in this manner because the proteins are not related to another of known function.
2. Other types of evidence for a relationship between two genes are also given that are not dependent in sequence similarity. Which of the following is a wrong statement?
a) genes are closely linked on the same chromosomes
b) genes are transcribed from the same DNA strand
c) gene fusions are observed between otherwise separate genes
d) phylogenetic profiles show the genes are not that commonly present in organisms
View Answer
Explanation: Phylogenetic profiles reveal the genes are both commonly present in many organisms implying they have interdependent metabolic functions. Option a and b imply coordinated regulation in an operon-like structure. Option c suggests the encoded proteins are physically associated in a common complex.
3. In Genome-wide prediction of protein functions by a combinatorial method– Each point represents a protein, and branches between proteins indicate a relationship by one of several criteria indicated in the legend.
a) True
b) False
View Answer
Explanation: Branch lengths are shorter for closely related proteins and thicker when two or more prediction methods indicate a relationship. The links are based on experimental data, proteins whose homologs are known to operate sequentially in metabolic pathways, proteins that evolved in a correlated fashion as evidenced by presence in fully sequenced genomes, proteins whose homologs are fused into a single protein in another organism, and proteins whose mRNA expression profiles are similar under a range of cellular and environmental conditions.
4. Which of the given statement is untrue about functional genomics?
a) Known functions are derived from experimental evidence in molecular biology and genetic studies with model organisms
b) Non-Orthologous genes between biologically distinct species can be identified, and it is strong evidence for a related function
c) Sequence-based methods of gene prediction can be augmented by the types of genome comparisons that are designed to identify related genes based on common patterns of expression, evolutionary profiles, chromosomal locations, and other features
d) Genome analysis depends to a large extent on sequence analysis methods that identify gene function based on similarity between proteins of unknown function and proteins of known function
View Answer
Explanation: Orthologous genes between biologically distinct species (for example, yeast and fruit flies) can be identified, and the high sequence similarity between them is strong evidence for a related function. Given the more complex multicellular biology of flies, the fly gene could have an additional function that is not predictable by the yeast model. In other cases, the occurrence of families of paralogous genes that share common domains can make a precise guess of function of one of these proteins more difficult because all match a model protein to some degree.
5. In case of functional genomics– Two general types of approaches are used—one in which a genetic construct is made that interferes with the expression of a particular gene (and sometimes a set of related genes) and a second in which a large number of random mutations are generated in a population of organisms.
a) True
b) False
View Answer
Explanation: The individual with a mutation in a particular gene is then identified. Once mutants are obtained, the effect of the mutant genes on phenotype is determined. The gene function may then be predicted on the basis of the observed alterations. Because such extreme genetic experiments cannot be performed with humans, the mouse model for the human genome serves the same purpose.
6. A genome database may also be interfaced with other types of data, such as clinical data.
a) True
b) False
View Answer
Explanation: These types of organization, termed data warehousing, can facilitate the search for novel relationships among the data by data-mining methods. These methods include genetic algorithms, neuronetworks, and others.
7. The ultimate step in genome analysis is to collect the information found on gene and protein sequences, alignments, gene function and location, protein families and domains, relationships of genes to those in other organisms, chromosomal rearrangements, and so on, into a comprehensive database.
a) True
b) False
View Answer
Explanation: This database should be logically organized so that all types of information are readily accessible and easily retrievable by users who have widely divergent knowledge of the organism. This goal is best achieved by using controlled vocabularies that can identify the same genetic or biochemical function in different organisms without ambiguity.
8. In addition to the care needed in organizing genome databases, a great deal of human input is needed to annotate the genome manually with information.
a) True
b) False
View Answer
Explanation: This information can be about individual genes and proteins, effects of mutations in these genes, and other types of genome variations that cannot be readily incorporated into the database by automated methods. For the human genome, this activity will occupy the time of many scientists for many years to come.
9. In Reverse-genetics analysis of gene function– Even though a particular gene may be _____ ortholog of a gene of known function in another organism, that gene may be acquired by a _____ function.
a) a highly predicted, similar
b) a highly predicted, same
c) a highly predicted, novel
d) less predicted, novel
View Answer
Explanation: For example, a defect in a plant or animal gene that is a homolog of a yeast gene may have an effect on a developmental process or other biologically unique function of multicellular organisms. Information on knockout mutants in model organisms is available through the genome Web sites.
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