Using Hierarchical Cluster and Factor Analysis to Classify and Built a phylogenetic Tree Species of ND1 Mitochondria

The research amied to classify and characterize 11 different organisms according to amino acid sequencing of ND1 mitochondria gene by using the two analysis methods of factor analysis and cluster analysis, in order to achieve this goal, we collected amino acid sequencing from Database of national center biotechnology information (NCBI) for eleven organisms (human, chimpanzee, monkeys, cow, horse, mouse, rat, fish, frog, chicken and rabbit) and this was one of the most important of the results which was as follows: A: By using factor analysis the organisms was classified into six groups. B: By using cluster analysis the organisms was classified into four groups. Each group did included similar number of organism, they were identical with each other. This was a result of a similar chain peptide multiple for ND1. Results of the two methods (cluster and factor analysis) were cluster organisms (human and chimpanzee and monkey) in one group and was the lowest value between humans and chimpanzees, with distance equal to 0.09, the great affinity between the human and chimpanzee and monkey and clustering of chicken as a single group and reached the highest value between human and chicken with distance equal to 0.642012 and to move away genetic traits to humans from chicken. The conclusion factor analysis method was able to give more precise details of the method from cluster analysis through the. identification and clustering of new groups with genetic dimension for the other group. Introduction Mitochondria DNA as a genetic material has its own replication system separate from that of the nuclear genome, it is also only inherited from the mother [1]. Mitochondria are about 0.5–1 mm in diameter and up to 7 mm long [2]. The genes found within the mitochondria contain the information that codes for the production of many of the important enzymes that drive the biochemical reactions to produce the body’s source of energy: a chemical called ATP (Adenosine Triphosphate) that is used by the body to drive the various reactions essential for the body to function, grow and develop [3]. The cells in the body, especially in organs such as the brain, heart, muscle, kidneys and liver, cannot function normally unless they are receiving a constant supply of energy [4]. Four of these five complexes contain mtDNA-encoded subunits; complex II, the succinate-ubiquinone oxidoreductase complex, is the exception. The ND1, ND2, ND3, ND4, ND4L, ND5, and ND6 subunits of complex I (NADH-ubiquinone oxidoreductase) are all core subunits localized in the membrane arm of the enzyme. The ND1 subunit is implicated in ubiquinone binding [5]. Changes in any of these mitochondrial genes that make them faulty can result in biochemical problems due to absence of enzymes involved in the respiratory chain, or enzymes that are impaired and do not work properly. This leads to a reduction in the supply of ATP, and may result in problems with the body’s functions. Mitochondria play a pivotal role in cellular metabolism. About 1% of patients with diabetes mellitus had the 3243 mutation, a typical mutation of MELAS, facilitated a search for patients with common diseases caused by mtDNA mutations [6]. MtDNA mutations have also been found in patients with other common diseases such as cardiomyopathy, migraine, cluster headache, and deafness [7]. Similarities and divergence among related biological sequences revealed by sequence alignment often have to be rationalized and visualized in the context of phylogenetic tree. Thus, molecular phylogenetics is a fundamental aspect of bioinformatics .