Sadovsky, M. G. | Search bioRxiv

bioRxiv2020

COMPARATIVE ANALYSIS OF TRIPLET COMPOSITION OF COMMON MITOCHONDRIAL AND CHLOROPLAST GENES OF THE SAME SPECIES

We studied the relation between the genes encoding the same protein (ATP synthase) in mitochondria and chloroplasts, of the same species. 85 species are studied. The relation is revealed through the unsupervised clustering via elastic map implementation of the points in 64-dimensional space of the triplet frequencies of the genes. The triplet composition was counted with a nucleotide shift of the reading frame along a gene. Three types of clustering have been analyzed: for mitochondria genes solely, for chloroplast genes solely, and for the merged set of the genes from the genomes of both organellae. It was found that the encoded function is the feature in clustering: all the clusters in all three versions of clustering patterns clearly exhibit distinct separation of the genes encoding the same subunit into a separate cluster. This behaviour was found for all three types of cluster patterns.

genomics↗

bioRxiv2019

Patients with different cancer types are stratified by CBC data

Searching for informative indices indicating cancer type and cause of the disease is of great importance. Here we tried to identify those indices from the data of complete blood analysis, only. We studied the inhomogeneity in the mutual distribution of a number of oncology patients with various types of tumors in the space of qualitative data provided by the complete blood count. The patients with oncology in hematology system were excluded. Ultimate goal is to reveal the relation between such inhomogeneity issues and the cause of a disease. We used the database on complete blood count comprising oncology patients with various causes of tumor development. The analysis has been carried out both by linear (K-means) and non-linear (elastic map technique) methods. No linear clustering has been found. On the contrary, elastic map technique yields stable clustering identifying not less than three clusters, in the set of patients. No relation of those clusters to sex or age of patients has been found. Four indices (namely, BAS, EOS, WBC and IG) exhibit no relation to the cluster structure, while all others do it. Thus, the patients are stratified according to their respond on the stress caused by cancer tumor. The data on complete blood count may be used for preliminary diagnostics of a tumor and its cause, for oncology patients. This type of analysis is cheap, standard and available at any medical organization.

cancer biology↗