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Journal articles on the topic 'EGene identification'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

An, Yeeun, and Chaeyoung Lee. "Identification and Interpretation of eQTL and eGenes for Hodgkin Lymphoma Susceptibility." Genes 14, no. 6 (2023): 1142. http://dx.doi.org/10.3390/genes14061142.

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Genome-wide association studies (GWAS) have revealed approximately 100 genomic signals associated with Hodgkin lymphoma (HL); however, their target genes and underlying mechanisms causing HL susceptibility remain unclear. In this study, transcriptome-wide analysis of expression quantitative trait loci (eQTL) was conducted to identify target genes associated with HL GWAS signals. A mixed model, which explains polygenic regulatory effects by the genomic covariance among individuals, was implemented to discover expression genes (eGenes) using genotype data from 462 European/African individuals. O

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2

Ge, Mei, Chenyu Li, and Zhiyan Zhang. "SNP-Based and Kmer-Based eQTL Analysis Using Transcriptome Data." Animals 14, no. 20 (2024): 2941. http://dx.doi.org/10.3390/ani14202941.

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Traditional expression quantitative trait locus (eQTL) mapping associates single nucleotide polymorphisms (SNPs) with gene expression, where the SNPs are derived from large-scale whole-genome sequencing (WGS) data or transcriptome data. While WGS provides a high SNP density, it also incurs substantial sequencing costs. In contrast, RNA-seq data, which are more accessible and less expensive, can simultaneously yield gene expressions and SNPs. Thus, eQTL analysis based on RNA-seq offers significant potential applications. Two primary strategies were employed for eQTL in this study. The first inv

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3

Song, Xiya, Han Jin, Xiangyu Li, et al. "Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort." PLOS Genetics 21, no. 7 (2025): e1011770. https://doi.org/10.1371/journal.pgen.1011770.

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Background Clear cell renal carcinoma (ccRCC) is the predominant form of kidney cancer, but the prognostic value of expression quantitative trait loci (eQTLs) remains underexplored, particularly in Asian populations. Objective We analyzed whole-exome sequencing and RNA sequencing data from 100 Japanese ccRCC patients to identify eQTLs. Multiple Cox proportional hazard models assessed survival associations, with validation in the Cancer Genome Atlas ccRCC cohort (n = 287). Results We identified 805 eGenes and 4,558 cis-eQTLs in the Japanese cohort. Survival analysis revealed a total of 9 eGenes

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4

Tleppaeva, Aizhan M. "First record of Sphenoptera (Chilostetha) egena Mannerheim, 1852 (Coleoptera: Buprestidae) from Kazakhstan with notes on its bionomics and distribution." Acta Biologica Sibirica 11 (March 17, 2025): 269–78. https://doi.org/10.5281/zenodo.15030272.

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During the fieldwork conducted between 2021 and 2023 in the territory adjacent to the Tarbagatai Natural Park, a new species of jewel beetle (Coleoptera, Buprestidae), <em>Sphenoptera </em>(<em>Chilostetha</em>) <em>egena </em>Mannerheim, 1852, was discovered, marking a noteworthy addition to the fauna of Kazakhstan. Specimens of this species were collected in June from arid shrub-steppe slopes in the western part of the Tarbagatai Range, specifically near the village of Taskesken in the Karakol River floodplain. Prior to this discovery, <em>Sphenoptera egena</em> had only been reported from r

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Zhou, Meng, Chenjin Ling, Hui Xiao, and Zhiyan Zhang. "Identification of Gene Expression and Splicing QTLs in Porcine Muscle Associated with Meat Quality Traits." Animals 15, no. 9 (2025): 1209. https://doi.org/10.3390/ani15091209.

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Understanding the genetic regulation of gene expression and splicing in muscle tissues is critical for elucidating the molecular mechanisms of meat quality traits. In this study, we integrated large-scale whole-genome sequencing and strand-specific RNA-seq data from 582 F2 hybrid pigs (White Duroc × Erhualian) to characterize the expression and splicing quantitative trait loci (eQTLs/sQTL) in longissimus dorsi muscle. We identified 11,058 cis-eQTL-associated genes (eGenes) and 5139 cis-sQTL-associated genes (sGenes), of which 29% of eGenes and 80% of sGenes were previously unreported in the Pi

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6

Cox, Nicholas J. "Speaking Stata: Identifying Spells." Stata Journal: Promoting communications on statistics and Stata 7, no. 2 (2007): 249–65. http://dx.doi.org/10.1177/1536867x0700700209.

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Spells in time series (and more generally in any kind of one-dimensional series) may be defined as sequences of observations that are homogeneous in some sense. For example, a categorical variable may remain in the same state, or values of a measured variable may satisfy the same true–false condition. Devices for working with spells in Stata include marking the start of each spell with indicator variables and tagging spells with integer codes. Panel data are easy to handle with the by: prefix. Some kinds of spell identification require two passes through the data, as when only spells of some m

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7

Tishechkin, Alexey, Alexander Konstantinov, Sanjay Bista, Robert Pemberton, and Ted Center. "Review of the continental Oriental species of Lilioceris Reitter (Coleoptera, Chrysomelidae, Criocerinae) closely related to Lilioceris impressa (F.)." ZooKeys 103 (June 10, 2011): 63–83. https://doi.org/10.3897/zookeys.103.983.

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Criocerine leaf beetles found in Nepal feeding on <i>Dioscorea bulbifera</i> (L.), an exotic, invasive weed of Asian origin, were identified as <i>Lilioceris cheni</i> Gressitt and Kimoto based on a synopsis of the Oriental <i>Lilioceris</i> species and review of the <i>Lilioceris impressa</i> species group. All the continental, Oriental species included in the group are diagnosed and illustrated, and a key for their identification is provided. Species status of <i>Lilioceris thibetana</i> Pic, 1916 is resurrected. The following new synonyms are proposed: <i>L. coomani</i> (Pic, 1928) = <i>L.

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8

Costa, Wilson J. E. M. "Seven new species of the killifish genus Rivulus (Cyprinodontiformes: Rivulidae) from the Paraná, Paraguay and upperAraguaia river basins, central Brazil." Neotropical Ichthyology 3, no. 1 (2005): 69–82. http://dx.doi.org/10.1590/s1679-62252005000100003.

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Seven new species of the Rivulus punctatus group collected during recent field studies in central Brazil are described. Rivulus dapazi n. sp., from the upper rio Correntes drainage, rio Paraguay basin, is diagnosed by a unique color pattern of the anal and caudal fins in males; R. cyanopterus n. sp., from the upper rio São Lourenço drainage, rio Paraguay basin, is diagnosed by a unique color pattern of the anal fin in both sexes; R. rossoi n. sp., from the rio Inhanduí drainage, rio Paraná basin, is diagnosed by a unique color pattern of the caudal fin in males and a reduced number of gill rak

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9

Shukla, Anupama. "Species of Laboulbeniales fungi parasitic on some common Indian insects: Isolation, visualization and characterization by Scanning Electron Micrographs (SEM)." Journal of Applied and Natural Science 16, no. 1 (2024): 110–17. http://dx.doi.org/10.31018/jans.v16i1.5347.

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The Laboulbeniales are a group of lesser-known fungi. They occur as ectoparasites on the exoskeleton of various arthropod species, mainly beetles, cockroaches, ants, dipterans and a few millipede genera appearing as hairs/bristles coming out of their cuticle. They are small, non-mycelial fungi forming compact multicellular thalli, starting from a two-celled sheathed ascospore which continues to envelop the mature thallus. The fungi, being obligate, spend their entire life cycle on their insect hosts. The present study attempted to locate the Laboulbeniales fungi in the common insects of India,

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10

Zhang, Shuo, Zhou Jiang, and Ping Zeng. "Incorporating genetic similarity of auxiliary samples into eGene identification under the transfer learning framework." Journal of Translational Medicine 22, no. 1 (2024). http://dx.doi.org/10.1186/s12967-024-05053-6.

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Abstract Background The term eGene has been applied to define a gene whose expression level is affected by at least one independent expression quantitative trait locus (eQTL). It is both theoretically and empirically important to identify eQTLs and eGenes in genomic studies. However, standard eGene detection methods generally focus on individual cis-variants and cannot efficiently leverage useful knowledge acquired from auxiliary samples into target studies. Methods We propose a multilocus-based eGene identification method called TLegene by integrating shared genetic similarity information ava

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11

Zhou, Heather J., Xinzhou Ge, and Jingyi Jessica Li. "ClipperQTL: ultrafast and powerful eGene identification method." May 21, 2025. https://doi.org/10.5281/zenodo.15485883.

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12

Zhou, Heather J., Xinzhou Ge, and Jingyi Jessica Li. "ClipperQTL: ultrafast and powerful eGene identification method." Genome Biology 26, no. 1 (2025). https://doi.org/10.1186/s13059-025-03662-y.

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Abstract A central task in expression quantitative trait locus analysis is to identify cis-eGenes, i.e., genes whose expression levels are regulated by at least one local genetic variant. Existing cis-eGene identification methods are either computationally expensive, requiring thousands of permutations per gene (FastQTL), or statistically underpowered (eigenMT and TreeQTL). We propose ClipperQTL, which requires only one permutation for data sets with large sample sizes (>450; ClipperQTL works on smaller data sets too). We show that ClipperQTL performs as well as FastQTL and runs up to 500 t

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13

Ruiz-Arenas, Carlos, Carles Hernandez-Ferrer, Marta Vives-Usano, et al. "Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children’s blood." eLife 11 (March 18, 2022). http://dx.doi.org/10.7554/elife.65310.

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Background:The identification of expression quantitative trait methylation (eQTMs), defined as associations between DNA methylation levels and gene expression, might help the biological interpretation of epigenome-wide association studies (EWAS). We aimed to identify autosomal cis eQTMs in children’s blood, using data from 832 children of the Human Early Life Exposome (HELIX) project.Methods:Blood DNA methylation and gene expression were measured with the Illumina 450K and the Affymetrix HTA v2 arrays, respectively. The relationship between methylation levels and expression of nearby genes (1

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14

Kim, Dong Jun, Ji Eun Lim, Hae-Un Jung, et al. "Identification of asthma-related genes using asthmatic blood eQTLs of Korean patients." BMC Medical Genomics 16, no. 1 (2023). http://dx.doi.org/10.1186/s12920-023-01677-7.

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Abstract Background More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are obtained from normal healthy subjects. Methods We performed a blood eQTL analysis using transcriptomic and genotypic data from 433 Korean asthma patients. To identify asthma-related genes, we carried out colocalization, Summary-based Mendelian Randomization

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15

Bon-Baret, Valentin, Arnaud Chignon, Marie-Chloé Boulanger, et al. "System Genetics Including Causal Inference Identify Immune Targets for Coronary Artery Disease and the Lifespan." Circulation: Genomic and Precision Medicine 14, no. 2 (2021). http://dx.doi.org/10.1161/circgen.120.003196.

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Background: Randomized clinical trials indicate that the immune response plays a significant role in coronary artery disease (CAD), a disorder impacting the lifespan potential. However, the identification of targets critical to the immune response in atheroma is still hampered by a lack of solid inference. Methods: Herein, we implemented a system genetics approach to identify causally associated immune targets implicated in atheroma. We leveraged genome-wide association studies to perform mapping and Mendelian randomization to assess causal associations between gene expression in blood cells w

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16

BABB, JEFF, CHRISTOPHER MEIKLEJOHN, HANS CHRISTIAN PETERSEN, and MAUREEN BABB. "Strøby Egede, Vedbæk-Bøgebakken and Relationships among Scandinavian Mesolithic Skeletal Material." Proceedings of the Prehistoric Society, December 6, 2024, 1–19. https://doi.org/10.1017/ppr.2024.12.

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This paper derives from new work on Mesolithic human skeletal material from Strøby Egede, a near coastal site in eastern Sjælland, with two foci. The first confirms sex identifications from original work carried out in 1986. The second, and central focus, re-examines comments by one of us (CM) based on work in 1992, and a new statistical analysis including data from the two Strøby Egede adults. In 1998 it was suggested that the Strøby Egede sample more closely resembled Skateholm, on the coast of Skåne in southern Sweden, than Vedbæk-Bøgebakken on Sjælland, fitting lithic patterns noted earlie

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17

EGEDE, LEONARD E., and REBEKAH J. WALKER. "595-P: Creation of a Food Insecurity Risk Score for Adults with Diabetes." Diabetes 71, Supplement_1 (2022). http://dx.doi.org/10.2337/db22-595-p.

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Current measurement of food insecurity in the US has largely focused the USDA scales. However, these scales do not capture multidimensional risk associated with food insecurity, account for stigma associated with being considered food insecure, or adequately capture the idea of nutrition security which is particularly important for individuals with diabetes. We aimed to create a more comprehensive set of questions allowing identification of an individual as being food insecure without reliance on questions only focused on food quantity and cost. We used data collected from 614 adults with type

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18

Karl, Julie A., Trent M. Prall, Hailey E. Bussan, et al. "Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype." Genome Research, February 28, 2023, gr.277429.122. http://dx.doi.org/10.1101/gr.277429.122.

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Macaques provide the most widely used nonhuman primate models for studying immunology and pathogenesis of human diseases. While the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004, the structural diversity of MHC genomic organization in macaques remains poorly understood due to a lack of adequate genomic reference sequences. We used ultra-long Oxford Nanopore and high-accuracy Pac

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19

WILLIAMS, JONI S., REBEKAH J. WALKER, and LEONARD E. EGEDE. "190-OR: Development and Validation of a Social Risk Screening Tool for Adults with Type 2 Diabetes." Diabetes 73, Supplement_1 (2024). http://dx.doi.org/10.2337/db24-190-or.

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Introduction & Objective: Social risk factors are the adverse social conditions associated with poor health including poor diabetes outcomes. Despite being important for assessing social needs and integrating social care into medical care, most measures that assess social determinants of health and social risk factors are lengthy and difficult to administer in clinical settings. Therefore, the objective of this study was to develop and validate a screening tool useful for identifying social risk factors and social needs among adults with type 2 diabetes. Methods: Cross-sectional data from

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20

Liu, Dengying, Zhenliang Chen, Wei Zhao, et al. "Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-08042-x.

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Abstract Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures

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