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The correct OPTION is (d) It doesn’t filter out linker sequences from experimentally obtained SAGE tags

Explanation: It has a filtering FUNCTION that filters out linker sequences from experimentally obtained SAGE tags and allows expression pattern comparison between normal and diseased human tissues. The data OUTPUT can be presented using subprograms such as the Anatomic Viewer, Digital Northern, and Digital Gene Expression DISPLAY.

The correct choice is (d) The overlapping EST SEQUENCES are computationally PROCESSED to represent a set of expressed genes

The best I can explain: The database is constructed based on combined information from dbEST, GenBank mRNA database, and “electronically spliced” genomic DNA. Only ESTS with 3’poly-A ends are clustered to minimize the problem of chimerism. The RESULTING 3’EST sequences provide more unique representation of the transcripts.

The correct answer is (a) PROTEINS do not operate as a complex

For explanation I WOULD SAY: The logic behind the co-occurrence approach is that proteins normally operate as a complex. If one of the COMPONENTS of the complex is lost, it results in the failure of the ENTIRE complex. Under the selective pressure, the rest of the nonfunctional interacting partners in the complex are also lost during evolution because they have become functionally unnecessary.

The correct OPTION is (b) It doesn’t INVOLVE neural networks

Explanation: This pattern recognition algorithm employs neural networks. The distance between the input data POINTS and the centroids are calculated. The data points are successively adjusted among the nodes, and their distances to the centroids are recalculated. After many iterations, a stabilized CLUSTERING pattern are reached with the minimum distances of the data points to the centroids. The DIFFERENCES between SOM and k-means are that, in SOM, the nodes are not treated as isolated entities, but as connected to other nodes.

Correct choice is (b) False

Best explanation: SAGE measures “absolute” mRNA EXPRESSION levels without arbitrary reference standards, whereas DNA microarrays indicate the relative expression levels. THEREFORE, SAGE expression data are more comparable across experimental conditions and platforms. This makes PUBLIC SAGE databases more informative by allowing comparison of data from reference conditions with VARIOUS experimental treatments.

The CORRECT option is (a) True

The EXPLANATION is: It is an example of posttranslational modification. Even in prokaryotes, PROTEINS can be targeted to the inner or outer MEMBRANES, the periplasmic space between these membranes, or the extracellular space. The sorting of these proteins is similar to that in eukaryotes and relies on the presence of signal peptides.

Right option is (a) True

For explanation I would say: Find Mod is a SUBPROGRAM that USES experimentally determined PEPTIDE fingerprint information to compare the MASSES of the peptide fragments with those of theoretical peptides. If a difference is found, it predicts a particular type of modification basedona set of predefined rules. It can predict twenty-eight types of modifications, INCLUDING methylation, phosphorylation, lipidation, and sulfation.

The correct answer is (b) False

Easiest explanation: Is a web server that predicts the disulfide BONDING states of cysteine residues in a protein SEQUENCE by BUILDING profiles based on multiple sequence alignment information. A RECURSIVE neural network ranks the candidate residues for disulfide formation.

Right option is (B) Collecting a SAGE library is quite economical

The best I can EXPLAIN: The Gene identification from SAGE data is ALSO more cumbersome because the mRNA tags have to be extracted, compiled, and identified computationally, whereas in DNA microarrays, the identities of the probes are already known. In SAGE, comparison of gene expression profiles to discover differentially expressed GENES and co-expressed genes is PERFORMED manually, whereas for microarrays, there are a large number of software algorithms to automate the process.

Correct ANSWER is (b) It is not similar to the DISTANCE phylogenetic tree-building method

Explanation: A hierarchical clustering method is in PRINCIPLE similar to the distance phylogenetic tree-building method. When genes with similar expression profiles are grouped in such a way, functions for unknown genes can often be inferred. Hierarchical clustering uses the agglomerative approach that works in MUCH the same way as the UPGMA method, in which the most similar data pairs are joined FIRST to form a cluster.

The correct option is (d) The oligonucleotides don’t react with cDNA samples

Easy explanation: The oligonucleotides are CALLED probes that hybridize to labeled cDNA samples. Shorter oligo probes tend to be more specific in hybridization because they are better at discriminating perfect complementary sequences fromsequences containing MISMATCHES. However, longer oligos can be more sensitive in BINDING cDNAs.

The correct answer is (B) Functional associations INCLUDE only the direct protein-protein interactions

For explanation: Functional associations include both direct and indirect protein-protein interactions.

Indirect interactions can MEAN enzymes in the same PATHWAY sharing a common substrate or proteins REGULATING each other in the genetic pathway.