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Journal articles on the topic 'Gens candidats'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Morin, Aurélie. "La participation politique au prisme de l’ethnicité : étude du discours des candidats issus de l’immigration maghrébine lors d’une échéance électorale en France." Notes de terrain 7, no. 1 (2007): 85–97. http://dx.doi.org/10.7202/016271ar.

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Résumé Lors des dernières élections françaises de 2004, la question de la place et du rôle des candidats d’origine maghrébine a été un enjeu controversé, relançant le débat sur le modèle universaliste français. Dans ce contexte, nous nous sommes interrogée sur l’importance accordée à l’ethnicité par les candidats d’origine maghrébine dans leur discours, à travers l’étude de leurs professions de foi et la réalisation d’entretiens. Trois types d’attitudes envers l’ethnicité ont ainsi été observés. Si la majorité des candidats ne mentionne aucun élément d’ordre ethnique, certains l’utilisent ponc

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Pelletier, Réjean. "Le personnel politique." Notes de recherche 25, no. 1 (2005): 83–102. http://dx.doi.org/10.7202/056072ar.

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Il est reconnu que, dans les grandes organisations à caractère bureaucratique, le pouvoir est détenu par une minorité. Il en est de même dans les régimes qui se définissent comme démocratiques où les représentants élus pour exercer le pouvoir politique ne constituent eux aussi qu'une minorité d'où est exclue d'une façon permanente la plus grande partie de la population. Bien plus, on a déjà montré qu'à chaque niveau politique — électeurs, adhérents, militants, cadres, députés, dirigeants nationaux — les caractéristiques sociales du groupe tendent à devenir moins « représentatives » de l'ensemb

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Zelenova, M. A., S. G. Vorsanova, and I. Y. Iourov. "Candidate processes for autism spectrum disorders revealed by copy number variation analysis." V.M. BEKHTEREV REVIEW OF PSYCHIATRY AND MEDICAL PSYCHOLOGY, no. 4-1 (December 9, 2019): 101–2. http://dx.doi.org/10.31363/2313-7053-2019-4-1-101-102.

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Despite the large number of candidate genes for mental disorders, molecular mechanisms of the majority remain unknown. To fill this gap, we have studied genomic networks-candidates (instead of genes) in a group of children with brain disorders. The identification of such processes seems to be more promising for developing therapeutic strategies in contrast to candidate gene identification.

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Chong, Veronica K., and John R. Stinchcombe. "Evaluating Population Genomic Candidate Genes Underlying Flowering Time in Arabidopsis thaliana Using T-DNA Insertion Lines." Journal of Heredity 110, no. 4 (2019): 445–54. http://dx.doi.org/10.1093/jhered/esz026.

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Abstract Population genomic scans have emerged as a powerful tool to detect regions of the genome that are potential targets of selection. Despite the success of genomic scans in identifying novel lists of loci potentially underlying adaptation, few studies proceed to validate the function of these candidate genes. In this study, we used transfer-DNA (T-DNA) insertion lines to evaluate the effects of 27 candidate genes on flowering time in North American accessions of Arabidopsis thaliana. We compared the flowering time of T-DNA insertion lines that knock out the function of a candidate gene o

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Thornblad, Tobias A., Kate S. Elliott, Jeremy Jowett, and Peter M. Visscher. "Prioritization of Positional Candidate Genes Using Multiple Web-Based Software Tools." Twin Research and Human Genetics 10, no. 6 (2007): 861–70. http://dx.doi.org/10.1375/twin.10.6.861.

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AbstractThe prioritization of genes within a candidate genomic region is an important step in the identification of causal gene variants affecting complex traits. Surprisingly, there have been very few reports of bioinformatics tools to perform such prioritization. The purpose of this article is to investigate the performance of 3 positional candidate gene software tools available, PosMed, GeneSniffer and SUSPECTS. The comparison was made for 40, 20 and 10 Mb regions in the human genome centred around known susceptibility genes for the common diseases breast cancer, Crohn's disease, age-relate

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Boultwood, Jacqueline, Carrie Fidler, Amanda J. Strickson, et al. "Narrowing and genomic annotation of the commonly deleted region of the 5q− syndrome." Blood 99, no. 12 (2002): 4638–41. http://dx.doi.org/10.1182/blood.v99.12.4638.

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The 5q− syndrome is the most distinct of the myelodysplastic syndromes, and the molecular basis for this disorder remains unknown. We describe the narrowing of the common deleted region (CDR) of the 5q− syndrome to the approximately 1.5-megabases interval at 5q32 flanked by D5S413 and theGLRA1 gene. The Ensembl gene prediction program has been used for the complete genomic annotation of the CDR. The CDR is gene rich and contains 24 known genes and 16 novel (predicted) genes. Of 40 genes in the CDR, 33 are expressed in CD34+ cells and, therefore, represent candidate genes since they are express

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Talwar, Puneet, Renu Gupta, Suman Kushwaha, et al. "Viral Induced Oxidative and Inflammatory Response in Alzheimer’s Disease Pathogenesis with Identification of Potential Drug Candidates: A Systematic Review using Systems Biology Approach." Current Neuropharmacology 17, no. 4 (2019): 352–65. http://dx.doi.org/10.2174/1570159x16666180419124508.

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Alzheimer’s disease (AD) is genetically complex with multifactorial etiology. Here, we aim to identify the potential viral pathogens leading to aberrant inflammatory and oxidative stress response in AD along with potential drug candidates using systems biology approach. We retrieved protein interactions of amyloid precursor protein (APP) and tau protein (MAPT) from NCBI and genes for oxidative stress from NetAge, for inflammation from NetAge and InnateDB databases. Genes implicated in aging were retrieved from GenAge database and two GEO expression datasets. These genes were individually used

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Díaz-Gay, Marcos, Sebastià Franch-Expósito, Coral Arnau-Collell, et al. "Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer." Cancers 11, no. 3 (2019): 362. http://dx.doi.org/10.3390/cancers11030362.

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Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial CRC. An integrated analysis of germline and tumor whole-exome sequencing data was performed in 18 unrelated CRC families. Deleterious single nucleotide variants (SNV), short insertions and deletions (indels), copy number variants (CNVs) and loss of heterozygosity (LOH) were assessed as candidates for first germline or second somatic hits. Candidate tumor suppressor genes we

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Blackwell, J. M., G. F. Black, C. S. Peacock, et al. "Immunogenetics of leishmanial and mycobacterial infections: the Belem Family Study." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 352, no. 1359 (1997): 1331–45. http://dx.doi.org/10.1098/rstb.1997.0118.

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In the 1970s and 1980s, analysis of recombinant inbred, congenic and recombinant haplotype mouse strains permitted us to effectively ‘scan’ the murine genome for genes controlling resistance and susceptibility to leishmanial infections. Five major regions of the genome were implicated in the control of infections caused by different Leishmania species which, because they show conserved synteny with regions of the human genome, immediately provides candidate gene regions for human disease susceptibility genes. A common intramacrophage niche for leishmanial and mycobacterial pathogens, and a sim

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10

Song, Long, Jing Qin Wu, Chong Mei Dong, and Robert F. Park. "Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina." Genes 11, no. 9 (2020): 1107. http://dx.doi.org/10.3390/genes11091107.

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The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and id

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Sykes, Jane E., Louise M. Ball, Nathan L. Bailiff, and Michael M. Fry. "‘Candidatus Mycoplasma haematoparvum’, a novel small haemotropic mycoplasma from a dog." International Journal of Systematic and Evolutionary Microbiology 55, no. 1 (2005): 27–30. http://dx.doi.org/10.1099/ijs.0.02989-0.

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A novel small haemoplasma was detected following cytological examination of blood smears from a splenectomized dog with haemic neoplasia. The 16S rRNA and rnpB genes of the organism were partially sequenced and a phylogenetic tree constructed. The organism was most closely related to the small feline haemoplasma, ‘Candidatus Mycoplasma haemominutum’ (94 % 16S rRNA gene nucleotide sequence identity; 75 % rnpB) and was only distantly related to Mycoplasma haemocanis (78 % 16S rRNA gene nucleotide sequence identity; 65 % rnpB). As this organism has not been cultured in vitro, the candidate specie

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Blackwell, J. M. "Genetic susceptibility to leishmanial infections: studies in mice and man." Parasitology 112, S1 (1996): S67—S74. http://dx.doi.org/10.1017/s0031182000076678.

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SUMMARYTwo important recent advances inLeishmaniaimmunology are: (i) the demonstration of a dramatic dichotomy in T helper 1 versus T helper 2 subset expansion leading to protection versus disease exacerbation; and (ii) analysis of the macrophage activation pathways leading to enhanced intracellular killing of parasites, in particular the tumour necrosis factor α (TNFα)-dependent sustained induction of the inducible nitric oxide synthase gene (Nos2) leading to the generation of large amounts of nitric oxide (NO). Given the broad spectrum of disease phenotypes in human leishmaniasis, one might

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Chen, Ren, Mayumi Gyokusen, Yoshihisa Nakazawa, and Koichiro Gyokusen. "Selection of Housekeeping Genes for Transgene Expression Analysis in Eucommia ulmoides Oliver Using Real-Time RT-PCR." Journal of Botany 2010 (March 17, 2010): 1–7. http://dx.doi.org/10.1155/2010/230961.

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In order to select appropriate housekeeping genes for accurate calibration of experimental variations in real-time (RT-) PCR results in transgene expression analysis, particularly with respect to the influence of transgene on stability of endogenous housekeeping gene expression in transgenic plants, we outline a reliable strategy to identify the optimal housekeeping genes from a set of candidates by combining statistical analyses of their (RT-) PCR amplification efficiency, gene expression stability, and transgene influences. We used the strategy to select two genes, ACTα and EF1α, from 10 can

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Li, M., X. Wu, X. Guo, et al. "Identification of optimal reference genes for examination of gene expression in different tissues of fetal yaks." Czech Journal of Animal Science 62, No. 10 (2017): 426–34. http://dx.doi.org/10.17221/75/2016-cjas.

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Reverse transcription quantitative real-time PCR (RT-qPCR) is widely used to study the relative abundance of mRNA transcripts because of its sensitivity and reliable quantification. However, the reliability of the interpretation of expression data is influenced by several complex factors, including RNA quality, transcription activity, and PCR efficiency, among others. To avoid experimental errors arising from potential variation, the selection of appropriate reference genes to normalize gene expression is essential. In this study, 10 commonly used reference genes – ACTB, B2M, HPRT1, GAPDH, 18S

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Treadwell, Julie A. "Integrative strategies to identify candidate genes in rodent models of human alcoholism." Genome 49, no. 1 (2006): 1–7. http://dx.doi.org/10.1139/g05-083.

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The search for genes underlying alcohol-related behaviours in rodent models of human alcoholism has been ongoing for many years with only limited success. Recently, new strategies that integrate several of the traditional approaches have provided new insights into the molecular mechanisms underlying ethanol's actions in the brain. We have used alcohol-preferring C57BL/6J (B6) and alcohol-avoiding DBA/2J (D2) genetic strains of mice in an integrative strategy combining high-throughput gene expression screening, genetic segregation analysis, and mapping to previously published quantitative trait

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Moseley, Robert C., Francis Motta, Gerald A. Tuskan, Steven B. Haase, and Xiaohan Yang. "Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi." Cells 10, no. 9 (2021): 2217. http://dx.doi.org/10.3390/cells10092217.

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The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we i

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Cooper, Bret, and Kimberly B. Campbell. "Protection Against Common Bean Rust Conferred by a Gene-Silencing Method." Phytopathology® 107, no. 8 (2017): 920–27. http://dx.doi.org/10.1094/phyto-03-17-0095-r.

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Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry. To assess their roles in pathogenicity, we have inserted small fragments of genes for five candidates into

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Zhang, Fan, Min Wu, Xue-Juan Li, Xiao-Li Li, Chee Keong Kwoh, and Jie Zheng. "Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates." Journal of Bioinformatics and Computational Biology 13, no. 03 (2015): 1541002. http://dx.doi.org/10.1142/s0219720015410024.

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A major goal of personalized anti-cancer therapy is to increase the drug effects while reducing the side effects as much as possible. A novel therapeutic strategy called synthetic lethality (SL) provides a great opportunity to achieve this goal. SL arises if mutations of both genes lead to cell death while mutation of either single gene does not. Hence, the SL partner of a gene mutated only in cancer cells could be a promising drug target, and the identification of SL pairs of genes is of great significance in pharmaceutical industry. In this paper, we propose a hybridized method to predict SL

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Bischof, Jocelyn M., and Rachel Wevrick. "Genome-wide analysis of gene transcription in the hypothalamus." Physiological Genomics 22, no. 2 (2005): 191–96. http://dx.doi.org/10.1152/physiolgenomics.00071.2005.

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As the genomic regions containing loci predisposing to obesity-related traits are mapped in human population screens and mouse genetic studies, identification of susceptibility genes will increasingly be facilitated by bioinformatic methods. We hypothesized that candidate genes can be prioritized by their expression levels in tissues of central importance in obesity. Our objective was to develop a combined bioinformatics and molecular paradigm to identify novel genes as candidates for murine or human obesity genetic modifiers based on their differential expression patterns in the hypothalamus

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Xie, Hao, Bo Li, Yu Chang, et al. "Selection and Validation of Reference Genes for RT-qPCR Analysis in Spinacia oleracea under Abiotic Stress." BioMed Research International 2021 (February 3, 2021): 1–12. http://dx.doi.org/10.1155/2021/4853632.

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Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and convenient method for mRNA quantification. Selection of optimal reference gene(s) is an important step in RT-qPCR experiments. However, the stability of housekeeping genes in spinach (Spinacia oleracea) under various abiotic stresses is unclear. Evaluating the stability of candidate genes and determining the optimal gene(s) for normalization of gene expression in spinach are necessary to investigate the gene expression patterns during development and stress response. In this study, ten housekeep

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Nageswara-Rao, Madhugiri, Mike Irey, Stephen M. Garnsey, and Siddarame Gowda. "Candidate gene makers for Candidatus Liberibacter asiaticus for detecting citrus greening disease." Journal of Biosciences 38, no. 2 (2013): 229–37. http://dx.doi.org/10.1007/s12038-013-9315-x.

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Khan, Sawar, Ayesha Nisar, Jianqi Yuan, et al. "A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus." Genes 11, no. 4 (2020): 367. http://dx.doi.org/10.3390/genes11040367.

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The most important and broad-spectrum drug used to control the parasitic worms to date is ivermectin (IVM). Resistance against IVM has emerged in parasites, and preserving its efficacy is now becoming a serious issue. The parasitic nematode Haemonchus contortus (Rudolphi, 1803) is economically an important parasite of small ruminants across the globe, which has a successful track record in IVM resistance. There are growing evidences regarding the multigenic nature of IVM resistance, and although some genes have been proposed as candidates of IVM resistance using lower magnification of genome,

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Žlůvová, J. "Heterologous approach in the search for (candidate) genes." Plant, Soil and Environment 53, No. 8 (2008): 361–64. http://dx.doi.org/10.17221/2216-pse.

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To answer many questions of evolutionary developmental biology, it is necessary to identify genes which could be responsible for the studied traits. In this review, I have summarised the methods that are currently used to identify these genes. Mainly the PCR-based methods of gene cloning are discussed here, with the special attention given to the comparison of primer design strategies and PCR amplification strategies. In addition to the review of methods used by other authors, an overview of our experience with PCR-based gene cloning in dioecious model plant species <i>Silene latifolia&l

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Huang, Zhenyu, Fei Shen, Yuling Chen, Ke Cao, and Lirong Wang. "Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study." Plants 10, no. 2 (2021): 242. http://dx.doi.org/10.3390/plants10020242.

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Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key genes related to peach pollen fertility trait. The significant association peak was detected at Chr.06: 2,116,368 bp, which was in accordance with the previous genetic mapping results, but displayed largely improved precision, allowing for the identification of n

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Liu, Junjie, Peng Li, Liuyang Lu, Lanfen Xie, Xiling Chen, and Baizhong Zhang. "Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua Linn." Plant Protection Science 55, No. 1 (2018): 61–71. http://dx.doi.org/10.17221/20/2018-pps.

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Eight commonly used candidate reference genes, 18S ribosomal RNA (rRNA) (18S), 28S rRNA (28S), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1α), ribosomal protein L7 (RPL7), Alpha-tubulin (α-TUB), and TATA box binding protein-associated factor (TBP), were evaluated under various experimental conditions to assess their suitability in different developmental stages, tissues and herbicide treatments in Avena fatua. The results indicated the most suitable reference genes for the different experimental conditions. For developmental stages, 28S and EF1α

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Bubenikova, Jana, Jana Vrabelova, Karla Stejskalova, et al. "Candidate Gene Markers Associated with Fecal Shedding of the Feline Enteric Coronavirus (FECV)." Pathogens 9, no. 11 (2020): 958. http://dx.doi.org/10.3390/pathogens9110958.

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The Feline coronavirus (FCoV) can cause a fatal disease, the Feline Infectious Peritonitis. Persistent shedders represent the most important source of infection. The role of the host in FCoV fecal shedding is unknown. The objective of this study was to develop gene markers and to test their associations with FCoV shedding patterns. Fecal samples were taken from 57 cats of 12 breeds on the day 0 and after 2, 4 and 12 months. Variation from persistent and/or high-intensity shedding to no shedding was observed. Thirteen immunity-related genes were selected as functional and positional/functional

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Kirschbaum-Slager, Natanja, Raphael Bessa Parmigiani, Anamaria Aranha Camargo, and Sandro José de Souza. "Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data." Physiological Genomics 21, no. 3 (2005): 423–32. http://dx.doi.org/10.1152/physiolgenomics.00237.2004.

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Alternative splicing is one of the major sources of the large transcriptional diversity found in human cells. Splicing variants have been shown to be associated with features like spreading and progression in several human tumors. Therefore, such variants may be of great importance as both diagnostic and therapeutic tools. Here, by using a set of criteria regarding the expression pattern of splicing variants and statistical analyses, we were able to screen the genome for exons overexpressed in tumors of specific tissues. However, as in other analyses attempting to identify tumor-associated var

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Gibson, Kate F., Anita Dos Santos, Nunu Lund, Rigmor Jensen, and Ioannis M. Stylianou. "Genetics of cluster headache." Cephalalgia 39, no. 10 (2019): 1298–312. http://dx.doi.org/10.1177/0333102418815503.

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Background Cluster headache is the most severe primary headache disorder. A genetic basis has long been suggested by family and twin studies; however, little is understood about the genetic variants that contribute to cluster headache susceptibility. Methods We conducted a literature search of the MEDLINE database using the PubMed search engine to identify all human genetic studies for cluster headache. In this article we provide a review of those genetic studies, along with an overview of the pathophysiology of cluster headache and a brief review of migraine genetics, which have both been sig

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Sim, Cheolho, David S. Kang, Sungshil Kim, Xiaodong Bai, and David L. Denlinger. "Identification of FOXO targets that generate diverse features of the diapause phenotype in the mosquito Culex pipiens." Proceedings of the National Academy of Sciences 112, no. 12 (2015): 3811–16. http://dx.doi.org/10.1073/pnas.1502751112.

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Insulin and juvenile hormone signaling direct entry of the mosquito Culex pipiens into its overwintering adult diapause, and these two critical signaling pathways appear to do so by converging on the regulation of forkhead transcription factor (FOXO). Diapause is a complex phenotype, and FOXO emerges as a prime candidate for activating many of the diverse physiological pathways that generate the diapause phenotype. Here, we used ChIP sequencing to identify direct targets of FOXO. The nearest gene in a 10-kb region surrounding a predicted binding site was extracted for each binding site, result

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Dang, Hong, Deepika Polineni, Rhonda G. Pace, et al. "Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation." PLOS ONE 15, no. 11 (2020): e0239189. http://dx.doi.org/10.1371/journal.pone.0239189.

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Genome wide association studies (GWAS) have identified several genomic loci with candidate modifiers of cystic fibrosis (CF) lung disease, but only a small proportion of the expected genetic contribution is accounted for at these loci. We leveraged expression data from CF cohorts, and Genotype-Tissue Expression (GTEx) reference data sets from multiple human tissues to generate predictive models, which were used to impute transcriptional regulation from genetic variance in our GWAS population. The imputed gene expression was tested for association with CF lung disease severity. By comparing and

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Tan, Kuibi, Jing Chen, Wuxian Li, et al. "Genome-wide analysis of microRNAs expression profiling in patients with primary IgA nephropathy." Genome 56, no. 3 (2013): 161–69. http://dx.doi.org/10.1139/gen-2012-0159.

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The aim of this study was to investigate the differential expression characteristics and the roles of the genome-wide microRNAs (miRNAs) in immunoglobulin A nephropathy (IgAN) kidney tissues. We used Illumina high-throughput sequencing technology to evaluate the miRNAs expression of six biopsy tissues from IgAN and six normal renal cortex specimens from patients with renal cell carcinoma. We observed a total of 85 miRNAs that were differentially expressed in the six IgAN patients, of which 11 miRNAs were up-regulated and 74 miRNAs were down-regulated in patients' tissues compared with control

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González-Giraldo, Yeimy, Andrés Camargo, Sandra López-León, and Diego A. Forero. "No Association ofBDNF,COMT,MAOA,SLC6A3, andSLC6A4Genes and Depressive Symptoms in a Sample of Healthy Colombian Subjects." Depression Research and Treatment 2015 (2015): 1–5. http://dx.doi.org/10.1155/2015/145483.

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Background. Major depressive disorder (MDD) is the second cause of years lived with disability around the world. A large number of studies have been carried out to identify genetic risk factors for MDD and related endophenotypes, mainly in populations of European and Asian descent, with conflicting results. The main aim of the current study was to analyze the possible association of five candidate genes and depressive symptoms in a Colombian sample of healthy subjects.Methods and Materials. The Spanish adaptation of the Hospital Anxiety and Depression Scale (HADS) was applied to one hundred ei

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Amuzu, Setor, Euridice Carmona, Anne-Marie Mes-Masson, Celia M. T. Greenwood, Patricia N. Tonin, and Jiannis Ragoussis. "Candidate Markers of Olaparib Response from Genomic Data Analyses of Human Cancer Cell Lines." Cancers 13, no. 6 (2021): 1296. http://dx.doi.org/10.3390/cancers13061296.

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The benefit of PARP inhibitor olaparib in relapsed and advanced high-grade serous ovarian carcinoma (HGSOC) is well established especially in BRCA1/2 mutation carriers. Identification of additional biomarkers can help expand the population of patients most likely to benefit from olaparib treatment. To identify candidate markers of olaparib response we analyzed genomic and in vitro olaparib response data from two independent groups of cancer cell lines. Using pan-cancer cell lines (n = 896) from the Genomics of Drug Sensitivity in Cancer database, we applied linear regression methods to identif

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Terenina, Elena, Stephane Fabre, Agnès Bonnet, et al. "Differentially expressed genes and gene networks involved in pig ovarian follicular atresia." Physiological Genomics 49, no. 2 (2017): 67–80. http://dx.doi.org/10.1152/physiolgenomics.00069.2016.

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Ovarian folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration, this latter process being called atresia. Even if atresia involves apoptosis, its mechanism is not well understood. The objective of this study was to analyze global gene expression in pig granulosa cells of ovarian follicles during atresia. The transcriptome analysis was performed on a 9,216 cDNA microarray to identify gene networks and candidate genes involved in pig ovarian follicular atresia. We found 1,684 significantly regulated genes to be differentially regulated between sm

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Florez, Liz M., Reiny W. A. Scheper, Brent M. Fisher, Paul W. Sutherland, Matthew D. Templeton, and Joanna K. Bowen. "Reference genes for gene expression analysis in the fungal pathogen Neonectria ditissima and their use demonstrating expression up-regulation of candidate virulence genes." PLOS ONE 15, no. 11 (2020): e0238157. http://dx.doi.org/10.1371/journal.pone.0238157.

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European canker, caused by the necrotrophic fungal phytopathogen Neonectria ditissima, is one of the most damaging apple diseases worldwide. An understanding of the molecular basis of N. ditissima virulence is currently lacking. Identification of genes with an up-regulation of expression during infection, which are therefore probably involved in virulence, is a first step towards this understanding. Reverse transcription quantitative real-time PCR (RT-qPCR) can be used to identify these candidate virulence genes, but relies on the use of reference genes for relative gene expression data normal

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Zhang, Hongjia, Mar Lar San, Seong-Gyu Jang, et al. "Genome-Wide Association Study of Root System Development at Seedling Stage in Rice." Genes 11, no. 12 (2020): 1395. http://dx.doi.org/10.3390/genes11121395.

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Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million h

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Eckert, Elias Simon Peter, Peer Wünsche, Manfred Schmidt, Claudia Ball, Friederike Herbst, and Hanno Glimm. "Identification and Validation of Novel Hematopoietic Stem Cell Regulatory microRNAs." Blood 128, no. 22 (2016): 3872. http://dx.doi.org/10.1182/blood.v128.22.3872.3872.

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Abstract Within this study we have developed a novel approach to identify hematopoietic regulatory genes by re-analyzing genome-wide viral integration site (IS) data from a clinical gene therapy trial of 10 Wiskott-Aldrich syndrome patients. We observed a statistically enriched contribution of individual cell clones marked by IS to benign human long-term hematopoiesis within a dataset comprising 130,699 unique IS in the proximity of 12,437 genes. Furthermore, when we assessed the genomic distribution of the IS, we found that clusters of IS (CIS) are significantly over-represented at certain co

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Farber, James E., and Robert P. Lane. "Bioinformatics Discovery of Putative Enhancers within Mouse Odorant Receptor Gene Clusters." Chemical Senses 44, no. 9 (2019): 705–20. http://dx.doi.org/10.1093/chemse/bjz043.

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Abstract Olfactory neuronal function depends on the expression and proper regulation of odorant receptor (OR) genes. Previous studies have identified 54 putative intergenic enhancers within or flanking 40 mouse OR clusters. At least 2 of these putative enhancers have been shown to regulate the expression of a small subset of proximal OR genes. In recognition of the large size of the mouse OR gene family (~1400 OR genes distributed across multiple chromosomal loci), it is likely that there remain many additional not-as-yet discovered OR enhancers. We utilized 23 of the previously identified enh

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Yuan, Fang, Mingliang Li, and Jing Li. "Identifying Disease Genes Based on Functional Annotation and Text Mining." International Journal of Advanced Pervasive and Ubiquitous Computing 3, no. 1 (2011): 45–54. http://dx.doi.org/10.4018/japuc.2011010106.

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The identification of disease genes from candidated regions is one of the most important tasks in bioinformatics research. Most approaches based on function annotations cannot be used to identify genes for diseases without any known pathogenic genes or related function annotations. The authors have built a new web tool, DGHunter, to predict genes associated with these diseases which lack detailed function annotations. Its performance was tested with a set of 1506 genes involved in 1147 disease phenotypes derived from the morbid map table in the OMIM database. The results show that, on average,

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OCHAGAVÍA, MARÍA ELENA, JAMILET MIRANDA, MARCELO NAZÁBAL, et al. "A METHODOLOGY BASED ON MOLECULAR INTERACTIONS AND PATHWAYS TO FIND CANDIDATE GENES ASSOCIATED TO DISEASES: ITS APPLICATION TO SCHIZOPHRENIA AND ALZHEIMER'S DISEASE." Journal of Bioinformatics and Computational Biology 09, no. 04 (2011): 541–57. http://dx.doi.org/10.1142/s0219720011005392.

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Experimental techniques for the identification of genes associated with diseases are expensive and have certain limitations. In this scenario, computational methods are useful tools to identify lists of promising genes for further experimental verification. This paper describes a flexible methodology for the in silico prediction of genes associated with diseases combining the use of available tools for gene enrichment analysis, gene network generation and gene prioritization. A set of reference genes, with a known association to a disease, is used as bait to extract candidate genes from molecu

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Lawniczak, Mara KN, and David J. Begun. "A genome-wide analysis of courting and mating responses in Drosophila melanogaster females." Genome 47, no. 5 (2004): 900–910. http://dx.doi.org/10.1139/g04-050.

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In Drosophila melanogaster, seminal fluid proteins influence several components of female physiology and behavior, including re-mating rates, ovulation and oviposition, and sperm use. It is well-known that female flies are not simply passive vessels and that female-mediated interactions with male products are important to female (and thus male) reproductive success. While the population genetics, molecular evolution and physiological effects of seminal fluid proteins have been examined, the genetics and evolution of the female side of these post-mating interactions is unexplored in spite of wo

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Jensen, Lea Møller, Barbara Ann Halkier, and Meike Burow. "How to discover a metabolic pathway? An update on gene identification in aliphatic glucosinolate biosynthesis, regulation and transport." Biological Chemistry 395, no. 5 (2014): 529–43. http://dx.doi.org/10.1515/hsz-2013-0286.

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Abstract Identification of enzymes, regulators and transporters involved in different metabolic processes is the foundation to understand how organisms function. There are, however, many difficulties in identifying candidate genes as well as in proving their in vivo roles. In this review, we describe different approaches utilized in Arabidopsis thaliana to identify gene candidates and experiments required to prove the function of a given candidate. For example, we use the production of methionine-derived aliphatic glucosinolates that represent major defence compounds in A. thaliana. Nearly all

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Wang, Yan, Li, et al. "GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies." Genes 10, no. 10 (2019): 803. http://dx.doi.org/10.3390/genes10100803.

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Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyp

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Jiang, Huanhuan, Xiaoyun Jin, Xiaofeng Shi, et al. "Transcriptomic Analysis Reveals Candidate Genes Responsive to Sclerotinia scleroterum and Cloning of the Ss-Inducible Chitinase Genes in Morus laevigata." International Journal of Molecular Sciences 21, no. 21 (2020): 8358. http://dx.doi.org/10.3390/ijms21218358.

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Sclerotinia sclerotiorum (Ss) is a devastating fungal pathogen that causes Sclerotinia stem rot in rapeseed (Brassica napus), and is also detrimental to mulberry and many other crops. A wild mulberry germplasm, Morus laevigata, showed high resistance to Ss, but the molecular basis for the resistance is largely unknown. Here, the transcriptome response characteristics of M. laevigata to Ss infection were revealed by RNA-seq. A total of 833 differentially expressed genes (DEGs) were detected after the Ss inoculation in the leaf of M. laevigata. After the GO terms and KEGG pathways enrichment ana

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Dorsman, Josephine C., Marieke Levitus, Davy Rockx, et al. "Identification of the Fanconi Anemia Complementation Group I Gene, FANCI." Analytical Cellular Pathology 29, no. 3 (2007): 211–18. http://dx.doi.org/10.1155/2007/151968.

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To identify the gene underlying Fanconi anemia (FA) complementation group I we studied informative FA-I families by a genome-wide linkage analysis, which resulted in 4 candidate regions together encompassing 351 genes. Candidates were selected via bioinformatics and data mining on the basis of their resemblance to other FA genes/proteins acting in the FA pathway, such as: degree of evolutionary conservation, presence of nuclear localization signals and pattern of tissue-dependent expression. We found a candidate, KIAA1794 on chromosome 15q25-26, to be mutated in 8 affected individuals previous

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Carlevaro-Fita, Joana, Leibo Liu, Yuan Zhou, et al. "LnCompare: gene set feature analysis for human long non-coding RNAs." Nucleic Acids Research 47, W1 (2019): W523—W529. http://dx.doi.org/10.1093/nar/gkz410.

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Abstract Interest in the biological roles of long noncoding RNAs (lncRNAs) has resulted in growing numbers of studies that produce large sets of candidate genes, for example, differentially expressed between two conditions. For sets of protein-coding genes, ontology and pathway analyses are powerful tools for generating new insights from statistical enrichment of gene features. Here we present the LnCompare web server, an equivalent resource for studying the properties of lncRNA gene sets. The Gene Set Feature Comparison mode tests for enrichment amongst a panel of quantitative and categorical

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Yoshioka, Hiroki, Yin-Ying Wang, Akiko Suzuki, et al. "Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta." International Journal of Molecular Sciences 22, no. 4 (2021): 2202. http://dx.doi.org/10.3390/ijms22042202.

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Amelogenesis imperfecta is a congenital form of enamel hypoplasia. Although a number of genetic mutations have been reported in humans, the regulatory network of these genes remains mostly unclear. To identify signatures of biological pathways in amelogenesis imperfecta, we conducted bioinformatic analyses on genes associated with the condition in humans. Through an extensive search of the main biomedical databases, we found 56 genes in which mutations and/or association/linkage were reported in individuals with amelogenesis imperfecta. These candidate genes were further grouped by function, p

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Steensel, Maurice AM van, J. Celli, JH van Bokhoven, and HG Brunner. "Probing the Gene eXpression Database for candidate genes." European Journal of Human Genetics 7, no. 8 (1999): 910–19. http://dx.doi.org/10.1038/sj.ejhg.5200405.

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Fung, Jenny N., Yadav Sapkota, Dale R. Nyholt, and Grant W. Montgomery. "Genetic Risk Factors for Endometriosis." Journal of Endometriosis and Pelvic Pain Disorders 9, no. 2 (2017): 69–76. http://dx.doi.org/10.5301/je.5000273.

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Advances in genetics and genomics are driving progress in understanding genetic risk factors for endometriosis. Genome-wide association scans (GWAS) in endometriosis have identified 11 genomic regions associated with increased risk of disease. Many of the regions contain interesting candidate genes, but the risk alleles may not always act through the obvious candidates. Functional evidence to identify the causal gene(s) will require multiple steps including better mapping precision, genetic studies on gene expression and epigenetic marks, chromatin looping and functional studies. Evidence from

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MATSUNAGA, TSUTOMU, SHUHEI KUWATA, and MASAAKI MURAMATSU. "COMPUTATIONAL GENE KNOCKOUT REVEALS TRANSDISEASE–TRANSGENE ASSOCIATION STRUCTURE." Journal of Bioinformatics and Computational Biology 08, no. 05 (2010): 843–66. http://dx.doi.org/10.1142/s0219720010004975.

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Genome-wide association studies for a variety of diseases are identifying increasing numbers of candidate genes. Now we are confronted with the fact that some genes are common candidates across diseases. Thus there is a strong need to develop a hypothesis formulation methodology to comprehend multifaceted associations between genes and diseases. We have developed a computational method for building transdisease–transgene association structure. By introducing the basic rationale underlying the gene knockout approach as an information processing procedure to a network constructed on the basis of

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