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Academic literature on the topic 'EGene identification'
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Journal articles on the topic "EGene identification"
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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. Overall, 80 eGenes were identified to be associated with 20 HL GWAS signals. Enrichment analysis identified apoptosis, immune responses, and cytoskeletal processes as functions of these eGenes. The eGene of rs27524 encodes ERAP1 that can cleave peptides attached to human leukocyte antigen in immune responses; its minor allele may help Reed–Sternberg cells to escape the immune response. The eGene of rs7745098 encodes ALDH8A1 that can oxidize the precursor of acetyl-CoA for the production of ATP; its minor allele may increase oxidization activity to evade apoptosis of pre-apoptotic germinal center B cells. Thus, these minor alleles may be genetic risk factors for HL susceptibility. Experimental studies on genetic risk factors are needed to elucidate the underlying mechanisms of HL susceptibility and improve the accuracy of precision oncology.
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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 involved analyzing expression levels in relation to variant sites detected between populations from RNA-seq data. The second approach utilized kmers, which are sequences of length k derived from RNA-seq reads, to represent variant sites and associated these kmer genotypes with gene expression. We discovered 87 significant association signals involving eGene on the basis of the SNP-based eQTL analysis. These genes include DYNLT1, NMNAT1, and MRLC2, which are closely related to neurological functions such as motor coordination and homeostasis, play a role in cellular energy metabolism, and function in regulating calcium-dependent signaling in muscle contraction, respectively. This study compared the results obtained from eQTL mapping using RNA-seq identified SNPs and gene expression with those derived from kmers. We found that the vast majority (23/30) of the association signals overlapping the two methods could be verified by haplotype block analysis. This comparison elucidates the strengths and limitations of each method, providing insights into their relative efficacy for eQTL identification.
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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 regions in Russia (Western and Eastern Siberia) and Mongolia. This paper presents a concise diagnostic overview of the genus <em>Sphenoptera </em>Dejean, 1833, along with a brief description of the species. Using ArcGIS PRO 3.1.1, we created a distribution map and modeled the favorable habitat conditions for <em>Sphenoptera egena</em>. Additionally, we provide a description of the background vegetation in the species' collection site. Photographs of the jewel beetle were captured using a Canon Kiss X4 camera with a Canon 60 mm Macro USM lens, illustrating the collection site of <em>S. egena</em>. Furthermore, other species, such as <em>Agrilus sericans</em> Kiesenwetter, 1857, and <em>Meliboeus morawitzi</em> (Semenov, 1905), were concurrently identified in the fauna of these steppe slopes. The identification of <em>Sphenoptera egena</em> not only enriches the inventory of jewel beetles in Kazakhstan, which currently includes over 200 species and subspecies across five subfamilies, twelve tribes, and twenty-eight genera, but also extends the known distribution range of this species.
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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 PigGTEx database. Functional analyses revealed distinct genomic features: eQTLs were enriched near transcription start sites (TSSs) and associated with active TSS-proximal transcribed regions and enhancers, whereas sQTLs clustered at splice junctions, underscoring their distinct roles in gene expression and splicing regulation. Colocalization analysis of e/sQTLs with GWAS signals prioritized PHKG1 as a key candidate gene (PPH4 > 0.9) for glycogen metabolism. Notably, we confirmed that an sQTL-driven alternative splicing event in exon 10 of PHKG1 was significantly correlated with phenotypic variation (R = −0.39, p = 9.5 × 10−21). Collectively, this study provides novel insights into the genetic regulation of gene expression and alternative splicing in porcine muscle tissue, advancing our understanding of the molecular mechanisms underlying economically important meat quality traits.
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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 minimum length are of interest or short gaps are tolerable within spells. Many questions concerning spells are easy to answer given careful use of by: and appropriate sort order, selection of just 1 observation from each panel or spell, and appreciation of the many functions written for egen. Gaps before, between, and after spells can also be important, and I suggest a convention for handling them.
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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. egena</i> (Weise, 1922), and <i>L.</i> <i>subcostata</i> (Pic, 1921a), <i>L.</i> <i>laticornis</i> (Gressit, 1942), <i>L.</i> <i>inflaticornis</i> Gressit and Kimoto, 1961, and <i>L.</i> <i>maai</i> Gressit and Kimoto, 1961 =<i> L. impressa </i>(Fabricius, 1787). Lectotypes of the following species are designated: <i>L.</i> <i>coomani </i>Pic, 1928; <i>L. impressa </i>(Fabricius, 1787); <i>L. laosensis</i> (Pic, 1916); <i>L. malabarica</i> (Jacoby, 1904); <i>L. ruficornis</i> (Pic, 1921b); <i>L. subcostata</i> (Pic, 1921a); <i>L. thibetana</i> (Pic, 1916); and <i>L. unicolor</i> (Hope, 1831).
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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 rakers on the first branchial arch; R. litteratus n. sp., from the upper rio Araguaia basin, is diagnosed by unique color patterns of flank in males and caudal fin in females; R. rutilicaudus n. sp., from the rio Verde drainage in Goiás, rio Paraná basin, is diagnosed by a unique color pattern of the caudal fin in females; R. scalaris n. sp., from the rio Sucuruí, rio Aporé, rio Correntes and rio Taquari drainages, rio Paraná basin, is diagnosed by a unique color pattern of the flank in males; and, R. egens n. sp., from the upper rio Verde drainage in Mato Grosso do Sul, rio Paraná basin, is distinguished by a combination of frontal E-scale pattern and the absence of red marks on the caudal fin in males. Combinations of other color patterns and morphological features, including number of scales of the longitudinal series, number of dorsal, anal, caudal and pectoral fin-rays, relative position of dorsal-fin origin and anal-fin rays, and number of vertebrae, are also useful in identification of the new species, but phylogenetic relationships among them are unknown at the present. A key to identification of species of Rivulus from the rio Paraná-Paraguay basin and adjacent headstreams is provided.
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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, isolate them and identify them based on morphology. Different species of insects; Carabid beetles - Stenolophus sp., Bembidion sp., Black ants - Camponotus sp., and Earwigs - Labidura riparia; were collected from different habitats of damp garden soil, river banks, light sources and entomological collection museum situated as different sites New Delhi. The insects were scrutinized for the presence of fungi through light and scanning electron microscopy. The morphological features of each fungus were recorded, and the species were characterized. The studies showed the presence of Laboulbenia anaplogenii and L. stenolophi on the legs of Stenolophus sp.; L. egens on Bembidion sp. legs; L. camponoti on the wings of black ants and Dimeromyces anisolabis on the legs of earwigs. The identification was made primarily based on the size, shape and structure of basal foot, receptacles, antheridia and foot of the thallus or it’s remnant scar found on the insect cuticle. This is the first Indian report of conducting scanning imaging of the Laboulbeniales fungi.
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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 available from auxiliary studies under the statistical framework of transfer learning. We apply TLegene to eGene identification in ten TCGA cancers which have an explicit relevant tissue in the GTEx project, and learn genetic effect of variant in TCGA from GTEx. We also adopt TLegene to the Geuvadis project to evaluate its usefulness in non-cancer studies. Results We observed substantial genetic effect correlation of cis-variants between TCGA and GTEx for a larger number of genes. Furthermore, consistent with the results of our simulations, we found that TLegene was more powerful than existing methods and thus identified 169 distinct candidate eGenes, which was much larger than the approach that did not consider knowledge transfer across target and auxiliary studies. Previous studies and functional enrichment analyses provided empirical evidence supporting the associations of discovered eGenes, and it also showed evidence of allelic heterogeneity of gene expression. Furthermore, TLegene identified more eGenes in Geuvadis and revealed that these eGenes were mainly enriched in cells EBV transformed lymphocytes tissue. Conclusion Overall, TLegene represents a flexible and powerful statistical method for eGene identification through transfer learning of genetic similarity shared across auxiliary and target studies.
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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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