A Quantum-Inspired Genetic K-Means Algorithm for Gene Clustering

2020 ◽  
pp. 13-24
Author(s):  
Chun Hua ◽  
Narengerile Liu
Keyword(s):  
Gene Clustering

scholarly journals Gene clustering by using query-based self-organizing maps

2010 ◽  
Vol 37 (9) ◽  
pp. 6689-6694 ◽  
Author(s):  
Ray-I Chang ◽  
Chih-Chun Chu ◽  
Yu-Ying Wu ◽  
Yen-Liang Chen
Keyword(s):  
Gene Clustering ◽  
Self Organizing Maps ◽  
Self Organizing

scholarly journals Gene Clustering Based on RNAi Phenotypes of Ovary-Enriched Genes in C. elegans

2002 ◽  
Vol 12 (22) ◽  
pp. 1959-1964 ◽  
Author(s):  
Fabio Piano ◽  
Aaron J. Schetter ◽  
Diane G. Morton ◽  
Kristin C. Gunsalus ◽  
Valerie Reinke ◽  
...  
Keyword(s):  
Gene Clustering ◽  
C Elegans

scholarly journals Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 163
Author(s):  
Natalia Petrova ◽  
Natalia Mokshina
Keyword(s):  
Gene Expression ◽  
Fusarium Oxysporum ◽  
Essential Role ◽  
Protein Biosynthesis ◽  
Plant Immunity ◽  
Gene Clustering ◽  
Root Tips ◽  
Lectin Gene ◽  
Depth Analysis ◽  
Lectin Genes

Plant proteins with lectin domains play an essential role in plant immunity modulation, but among a plurality of lectins recruited by plants, only a few members have been functionally characterized. For the analysis of flax lectin gene expression, we used FIBexDB, which includes an efficient algorithm for flax gene expression analysis combining gene clustering and coexpression network analysis. We analyzed the lectin gene expression in various flax tissues, including root tips infected with Fusarium oxysporum. Two pools of lectin genes were revealed: downregulated and upregulated during the infection. Lectins with suppressed gene expression are associated with protein biosynthesis (Calreticulin family), cell wall biosynthesis (galactose-binding lectin family) and cytoskeleton functioning (Malectin family). Among the upregulated lectin genes were those encoding lectins from the Hevein, Nictaba, and GNA families. The main participants from each group are discussed. A list of lectin genes, the expression of which can determine the resistance of flax, is proposed, for example, the genes encoding amaranthins. We demonstrate that FIBexDB is an efficient tool both for the visualization of data, and for searching for the general patterns of lectin genes that may play an essential role in normal plant development and defense.

scholarly journals Genetic Variability in Molecular Pathways Implicated in Alzheimer's Disease: A Comprehensive Review

2021 ◽  
Vol 13 ◽  
Author(s):  
David Vogrinc ◽  
Katja Goričar ◽  
Vita Dolžan
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Age Of Onset ◽  
Association Studies ◽  
The Elderly ◽  
Gene Clustering ◽  
Molecular Pathways ◽  
Genome Wide Association Studies ◽  
Cellular Processes ◽  
Increased Risk

Alzheimer's disease (AD) is a complex neurodegenerative disease, affecting a significant part of the population. The majority of AD cases occur in the elderly with a typical age of onset of the disease above 65 years. AD presents a major burden for the healthcare system and since population is rapidly aging, the burden of the disease will increase in the future. However, no effective drug treatment for a full-blown disease has been developed to date. The genetic background of AD is extensively studied; numerous genome-wide association studies (GWAS) identified significant genes associated with increased risk of AD development. This review summarizes more than 100 risk loci. Many of them may serve as biomarkers of AD progression, even in the preclinical stage of the disease. Furthermore, we used GWAS data to identify key pathways of AD pathogenesis: cellular processes, metabolic processes, biological regulation, localization, transport, regulation of cellular processes, and neurological system processes. Gene clustering into molecular pathways can provide background for identification of novel molecular targets and may support the development of tailored and personalized treatment of AD.

scholarly journals Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference

2021 ◽  
Author(s):  
Yan-Ting Jin ◽  
Cong Ma ◽  
Xin Wang ◽  
Shu-Xuan Wang ◽  
Kai-Yue Zhang ◽  
...  
Keyword(s):  
Protein Function ◽  
Codon Position ◽  
Systematic Investigation ◽  
Functional Category ◽  
Gene Clustering ◽  
Base Frequency ◽  
Significant Difference ◽  
Prokaryotic Genomes ◽  
Functional Classes ◽  
Clustering Pattern

AbstractIn 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2–T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence. Graphical abstract

Proximal cis-acting elements cooperate to set Hoxb-7 (Hox-2.3) expression boundaries in transgenic mice

Development ◽  
1993 ◽  
Vol 118 (1) ◽  
pp. 71-82 ◽  
Author(s):  
R. Vogels ◽  
J. Charite ◽  
W. de Graaff ◽  
J. Deschamps
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Hox Genes ◽  
Gene Clustering ◽  
Lacz Gene ◽  
Dependent Manner ◽  
Endogenous Gene ◽  
Cis Acting ◽  
Gene Map ◽  
Partial Overlap

The Hox genes have been proved to be instrumental in establishing the positional identity of cells along the embryonic anteroposterior (A-P) axis. Studying the regulation of these genes is a first step toward elucidating the molecular basis of regionalization during embryogenesis. We report here on the identification of cis-acting elements controlling the expression of Hoxb-7 (Hox-2.3). We show that elements driving A-P restricted gene expression are located within the 3.5 kb proximal upstream sequences of the Hoxb-7 gene. A deletion analysis provides evidence for at least three cis-acting control elements upstream from Hoxb-7, and for cooperative interactions between some of these elements in generating the A-P restricted transgenic pattern. One element, conferring by itself Hox-like expression boundaries to the transgene, has been studied in more detail and found to act in an orientation-and promoter-dependent manner. Together the 3.5 kb sequences proximal to Hoxb-7 mediate A-P restricted Hoxb-7/lacZ gene expression in a domain showing rostral boundaries more posterior than those of Hoxb-7. The evolution throughout embryogenesis of the expression pattern of a transgene carrying these sequences has been analysed and shown to mimick that of the endogenous gene, except for a slight delay in the initial expression. We conclude that the transgenes that we tested, spanning a total of 27 kb genomic sequences, do not reproduce all the features of the Hoxb-7 expression pattern. The differences in expression between Hoxb-7 and the transgenes may reveal an aspect of the Hox regulation for which either remote cis-acting control elements and/or gene clustering is required. Additional features that may have favoured maintenance of clustered organisation during evolution are partial overlap of transcription units with the regulatory regions of the neighbouring genes, and cis-regulatory interactions between multiple Hox genes: not only do cis-acting control elements of the Hoxb-7 gene map in the 3′ untranslated sequences of the Hoxb-8 (Hox-2.4) gene, but our experiments suggest that Hoxb-7 control sequences modulate expression of the Hoxb-8 gene as well.

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