The key difference between sequence-based and gene expression based methods is that the latter provides quantitative information, not just qualitative sequence identities.
The defect of least square based methods is that they create a delay in estimation process but Kalman filter based methods provide instantaneous estimation.
The main limitation of composition based methods is that the length of fragments may significantly influence their performance.
Further, a known limitation of bisulfite sequencing based methods is that the protocol is unable to distinguish difference between 5-methylcytosine and 5-hydroxymethylcytosine.
A major limitation of this method, as with all 2D SDS-PAGE based methods, is that it cannot reliably visualize or produce analytical quantities of low abundance proteins that are present in less than 1000 copies per cell.
The main advantage of such methods over single gene based methods is that they directly link the ranked gene list with biological knowledge and therefore provide better functional insight into the cause of the phenotypic differences under study.
It has often been considered that one of the advantages of ML over parsimony based methods is that it allows for the use of different models of evolution depending on the dataset being examined.
The disadvantage of TV based methods is that in the presence of noise they can lead to the staircase effect, i.e., smooth regions appear as piecewise constant regions [ 18].
As shown in Figure 1C, the common hypothesis underlying these gene expression based methods is that every biological state can be described through a proper gene signature, which can be defined as a set of genes combined with a specific pattern of expression.
The rationale for the homology-based method is that two proteins with a similar sequence or structure could evolve from a common ancestor and thus have similar functions.
The basic idea of alignment-graph-based method is that false positive protein interactions are rare possible to duplicate in other species and merging two PPI networks being compared according homologous mappings between proteins can filter false positive protein interactions.
