Alzheimer's+Disease+Data

**Figure 1: Protein ClustalW Alignment** This figure shows a multiple alignment of protein sequences from different species listed in Figure 4. Almost the entire alignment does not have any gaps, which indicates that all the sequences are closely related. **Figure 2: MEGA Protein UPGMA Phylogenetic Tree** This phylogenetic tree shows the phenotypic (physical characteristic) similarities between the protein sequences for each of the species that are included in the ClustalW alignment. Because the bootstrap values shown in this tree are not under 60, it indicates that some the species have similar phenotypic characteristics, so their ApoE proteins might function in a similar way. **Figure 3: MEGA Protein Maximum Parsimony Phylogenetic Tree** This phylogenetic tree represents the similarity in the function of the ApoE protein for all the protein sequences in the ClustalW alignment. None of the bootstrap values in the phylogenetic tree are less than 60, which means that each species’ ApoE protein has somewhat similar pathway functions. **Figure 4: Gene ClustalW Alignment** This figure shows that all the gene sequences in this multiple alignment do not have very similar sequences due to the large amount of gaps that are present throughout the alignment. This phylogenetic tree is a result of all possible relationships between each species that is represented in the gene ClustalW alignment. Because there is a bootstrap value under 60, it indicates that these species are not closely related enough to each other to be significant in helping with the research questions being addressed. This phylogenetic tree shows a more simplified version of the minimum evolution phylogenetic tree shown in figure 3. Because this figure represents similar relationship data as the minimum evolution tree, it also resulted in a bootstrap value that is under 60, which means that this tree is also not helpful with the research questions that are being investigated. This phylogenetic tree shows how much of the gene sequence is similar between all the gene sequences in the ClustalW alignment. Because there is a bootstrap value below 60, this tree is not helpful with the research questions that are being investigated. This phylogenetic tree shows the phenotypic (physical characteristic) similarities between the gene sequences for each of the species that are included in the ClustalW alignment. Because there is a bootstrap value in this tree that is under 60, it indicates that some of the species do not have closely related phenotypic characteristics; so their ApoE genes might not be the same and therefore function differently. This phylogenetic tree represents the similarity in the function of the ApoE gene for all the gene sequences in the ClustalW alignment. There is one bootstrap value in this phylogenetic tree that is less than 60, which means the species’ whose ApoE genes are connected to that point are not the related in function. Other species however, have high bootstrap values, which indicates that the ApoE gene and its pathway have a similar function in the species that are connected at those points.
 * Data and Results **
 * Figure 5: MEGA Gene Maximum Likelihood Phylogenetic Tree**
 * Figure 6: MEGA Gene Neighbor-Joining Phylogenetic Tree**
 * Figure 7: MEGA Gene Minimum Evolution Phylogenetic Tree**
 * Figure 8: MEGA Gene UPGMA Phylogenetic Tree**
 * Figure 9: MEGA Gene Maximum Parsimony Phylogenetic Tree**

Because the Gene ClustalW Alignment has a lot of gaps in the sequences, it is not a good alignment to use for making phylogenetic trees to compare the species that are included in the alignment and therefore, would not make good phylogenetic trees (no bootstrap values above 60). Because all of the bootstrap values are not above 60, it means that the phylogenetic trees do not show enough relation between each species' ApoE gene sequence. PREVIOUS: Methods Used Alzheimer's Disease Home Page NEXT: Data Analysis