Feature prioritisation on big genomic data for analysing gene-gene interactions

Abstract Gene regulatory networks (GRNs) have been widely used as a fundamental tool to reveal the genomic mechanisms that underlie the individual’s response to environmental and developmental cues. Standard approaches infer GRNs as holistic graphs of gene co-expression, but such graphs cannot quantify how gene–gene interactions vary among individuals and how they alter structurally across spatiotemporal gradients. Here, we develop a general framework for inferring informative, dynamic, omnidirectional, and personalized networks (idopNetworks) from routine transcriptional experiments. This framework is constructed by a system of quasi-dynamic ordinary differential equations (qdODEs) derived from the combination of ecological and evolutionary theories. We reconstruct idopNetworks using genomic data from a surgical experiment and illustrate how network structure is associated with surgical response to infrainguinal vein bypass grafting and the outcome of grafting. idopNetworks may shed light on genotype–phenotype relationships and provide valuable information for personalized medicine.

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Feature prioritisation on big genomic data for analysing gene-gene interactions

International Journal of Bioinformatics Research and Applications ◽

10.1504/ijbra.2021.114420 ◽

2021 ◽

Vol 17 (2) ◽

pp. 158

Author(s):

Ahmad A. Aloqaily ◽

Siamak Tafavogh ◽

Bronwyn L. Harvey ◽

Daniel R. Catchpoole ◽

Paul J. Kennedy

Keyword(s):

Genomic Data ◽

Gene Interactions

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Discovery of gene interactions in regulatory networks using genomic data mining and computational intelligence methods

10.12681/eadd/26361 ◽

2006 ◽

Author(s):

Andrei Dragomir

Keyword(s):

Data Mining ◽

Computational Intelligence ◽

Regulatory Networks ◽

Genomic Data ◽

Gene Interactions ◽

Genomic Data Mining ◽

Computational Intelligence Methods

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Genetic Variation: Impact on Folate (and Choline) Bioefficacy

International Journal for Vitamin and Nutrition Research ◽

10.1024/0300-9831/a000040 ◽

2010 ◽

Vol 80 (45) ◽

pp. 319-329 ◽

Cited By ~ 9

Author(s):

Allyson A. West ◽

Marie A. Caudill

Keyword(s):

Carbon Metabolism ◽

Genetic Variants ◽

Plasma Homocysteine ◽

Water Soluble ◽

Gene Interactions ◽

Dietary Folate ◽

Methyl Donors ◽

Common Genetic Variants ◽

One Carbon Metabolism ◽

The Impact

Folate and choline are water-soluble micronutrients that serve as methyl donors in the conversion of homocysteine to methionine. Inadequacy of these nutrients can disturb one-carbon metabolism as evidenced by alterations in circulating folate and/or plasma homocysteine. Among common genetic variants that reside in genes regulating folate absorptive and metabolic processes, homozygosity for the MTHFR 677C > T variant has consistently been shown to have robust effects on status markers. This paper will review the impact of genetic variants in folate-metabolizing genes on folate and choline bioefficacy. Nutrient-gene and gene-gene interactions will be considered along with the need to account for these genetic variants when updating dietary folate and choline recommendations.

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Within- and Inter- gene interactions in FKBP5 and GR genes and its association with early response

Pharmacopsychiatry ◽

10.1055/s-2005-918825 ◽

2005 ◽

Vol 38 (05) ◽

Author(s):

D Salyakina ◽

EB Binder ◽

M Ising ◽

M Uhr ◽

S Lucae ◽

...

Keyword(s):

Early Response ◽

Gene Interactions

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Non-allelic gene interactions in a population of maize derived from a cross of two inbred lines

10.31274/rtd-180814-3845 ◽

1960 ◽

Author(s):

Angus Hillyard Hyer

Keyword(s):

Inbred Lines ◽

Gene Interactions ◽

Allelic Gene

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Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79s.1.20 ◽

2019 ◽

Vol 79 (01S) ◽

Author(s):

Pawan Kumar Jayaswal ◽

Asheesh Shanker ◽

Nagendra Kumar Singh

Keyword(s):

Evolutionary Relationship ◽

Genomic Data ◽

Gene Clusters ◽

Species Trees ◽

Model Species ◽

Tubulin Gene ◽

Tubulin Genes ◽

Eukaryotic Species ◽

Relationship Of ◽

Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

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