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Journal articles on the topic 'Functionnal genes'

Author: Grafiati

Published: 11 January 2025

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1

Sitnicka, Dorota, Katarzyna Figurska, and Slawomir Orzechowski. "Functional Analysis of Genes." Advances in Cell Biology 2, no. 1 (January 1, 2010): 1–16. http://dx.doi.org/10.2478/v10052-010-0001-y.

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SummaryThe aim of this article is to present the current literature concerning the expression analysis and methods of functional characteristics of genes. The progress in the analysis of gene expression within cells or whole tissues is undisputed and leads to a constant improvement of our understanding of the function of particular gene. The traditional methods of the functional characteristics of genes such as homology, inactivation and overexpression are more frequently being replaced by microarray and DNA chip analysis, which are extensively supported by bioinformatics tools. Knowledge of the functions and changes in gene expression has applications in medical diagnostics, the pharmaceutical industry and in plant and animal biotechnology.

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2

Jeong, Soon-Seog, and Ridong Chen. "Functional misassignment of genes." Nature Biotechnology 19, no. 2 (February 2001): 95. http://dx.doi.org/10.1038/84480.

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3

Scott, Rodney J. "Cancer genes: Functional aspects." European Journal of Cancer 33, no. 10 (September 1997): 1706–7. http://dx.doi.org/10.1016/s0959-8049(97)00259-1.

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4

Carpenter, D., R. S. McIntosh, R. J. Pleass, and J. A. L. Armour. "Functional effects of CCL3L1 copy number." Genes & Immunity 13, no. 5 (April 5, 2012): 374–79. http://dx.doi.org/10.1038/gene.2012.5.

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5

Klee, Eric W., Stephen C. Ekker, and Lynda B. M. Ellis. "Target selection forDanio rerio functional genomics." genesis 30, no. 3 (2001): 123–25. http://dx.doi.org/10.1002/gene.1045.

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6

Montgomery, Nathan D. "Functional genomics: A rose by another name." genesis 33, no. 3 (July 2002): 140. http://dx.doi.org/10.1002/gene.10101.

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7

Purnell, Beverly A. "Functional screen for microcephaly genes." Science 370, no. 6519 (November 19, 2020): 926.3–926. http://dx.doi.org/10.1126/science.370.6519.926-c.

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8

Camilleri, M., and A. R. Zinsmeister. "Candidate genes and functional dyspepsia." Neurogastroenterology & Motility 21, no. 1 (January 2009): 94. http://dx.doi.org/10.1111/j.1365-2982.2008.01205.x.

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9

Oliveira, Daniela M., and Margaret A. Goodell. "Transient RNA interference in hematopoietic progenitors with functional consequences." genesis 36, no. 4 (August 2003): 203–8. http://dx.doi.org/10.1002/gene.10212.

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10

Vudattu, N. K., I. Magalhaes, H. Hoehn, D. Pan, and M. J. Maeurer. "Expression analysis and functional activity of interleukin-7 splice variants." Genes & Immunity 10, no. 2 (December 18, 2008): 132–40. http://dx.doi.org/10.1038/gene.2008.90.

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11

Troshchynsky, A., I. Dzneladze, L. Chen, Y. Sheng, V. Saridakis, and G. E. Wu. "Functional analyses of polymorphic variants of human terminal deoxynucleotidyl transferase." Genes & Immunity 16, no. 6 (September 2015): 388–98. http://dx.doi.org/10.1038/gene.2015.19.

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12

Gujarati, Nehaben A., Alexandra R. Leonardo, Jessica M. Vasquez, Yiqing Guo, Bismark O. Frimpong, Elbek Fozilov, Monica P. Revelo, et al. "Loss of Functional SCO2 Attenuates Oxidative Stress in Diabetic Kidney Disease." Diabetes 71, no. 1 (October 26, 2021): 142–56. http://dx.doi.org/10.2337/db21-0316.

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Increased oxidative stress in glomerular endothelial cells (GEnCs) contributes to early diabetic kidney disease (DKD). While mitochondrial respiratory complex IV activity is reduced in DKD, it remains unclear whether it is a driver or a consequence of oxidative stress in GEnCs. Synthesis of cytochrome C oxidase 2 (SCO2), a key metallochaperone in the electron transport chain, is critical to the biogenesis and assembly of subunits required for functional respiratory complex IV activity. Here, we investigated the effects of Sco2 hypomorphs (Sco2KO/KI, Sco2KI/KI), with a functional loss of SCO2, in the progression of DKD by using a model of type 2 diabetes, db/db mice. Diabetic Sco2KO/KI and Sco2KI/KI hypomorphs exhibited a reduction in complex IV activity but an improvement in albuminuria, serum creatinine, and histomorphometric evidence of early DKD compared with db/db mice. Single-nucleus RNA sequencing using gene set enrichment analysis of differentially expressed genes in the endothelial cluster of Sco2KO/KI;db/db mice demonstrated an increase in genes involved in VEGF-VEGFR2 signaling and reduced oxidative stress compared with db/db mice. These data suggest that reduced complex IV activity as a result of a loss of functional SCO2 might be protective in GEnCs in early DKD.

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13

Wang, S., I. Adrianto, G. B. Wiley, C. J. Lessard, J. A. Kelly, A. J. Adler, S. B. Glenn, et al. "A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus." Genes & Immunity 13, no. 5 (April 5, 2012): 380–87. http://dx.doi.org/10.1038/gene.2012.6.

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14

Agrawal, N., and M. A. Brown. "Genetic associations and functional characterization of M1 aminopeptidases and immune-mediated diseases." Genes & Immunity 15, no. 8 (August 21, 2014): 521–27. http://dx.doi.org/10.1038/gene.2014.46.

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15

Jones, Julie R., Kathy D. Shelton, Youfei Guan, Matthew D. Breyer, and Mark A. Magnuson. "Generation and functional confirmation of a conditional null PPAR? allele in mice." genesis 32, no. 2 (February 2002): 134–37. http://dx.doi.org/10.1002/gene.10042.

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16

Sokolowski, Marla B. "Functional testing of ASD-associated genes." Proceedings of the National Academy of Sciences 117, no. 1 (December 10, 2019): 26–28. http://dx.doi.org/10.1073/pnas.1919695117.

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17

Cole, Shannon H., Ginger E. Carney, Colleen A. McClung, Stacey S. Willard, Barbara J. Taylor, and Jay Hirsh. "Two Functional but NoncomplementingDrosophilaTyrosine Decarboxylase Genes." Journal of Biological Chemistry 280, no. 15 (February 3, 2005): 14948–55. http://dx.doi.org/10.1074/jbc.m414197200.

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18

Liebregts, T., B. Adam, and G. Holtmann. "Susceptibility genes and functional gastrointestinal disorders." Journal of Gastroenterology and Hepatology 20, no. 11 (November 2005): 1792–93. http://dx.doi.org/10.1111/j.1440-1746.2005.04163.x.

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19

Jeon, Hyejin, Younghoon Go, Minchul Seo, Won-Ha Lee, and Kyoungho Suk. "Functional Selection of Phagocytosis-Promoting Genes." Journal of Biomolecular Screening 15, no. 8 (July 26, 2010): 949–55. http://dx.doi.org/10.1177/1087057110376090.

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Phagocytosis is a critical host defense mechanism that clears invading pathogens, apoptotic cells, and cell debris; it is an essential process for normal development, tissue remodeling, immune response, and inflammation. Here, a functional selection strategy was used to isolate novel phagocytosis-promoting genes. After the retroviral transfer of mouse brain cDNA library into NIH3T3 mouse fibroblast cells, cell sorting was used to select the cells that phagocytosed fluorescent zymosan particles. The cDNAs were retrieved from the selected cells and identified by DNA sequencing as eIF5A, Meg3, Tubb5, Sparcl-1, Uchl-1, Bsg (CD147), Ube2v1, and Pamr1. The phagocytosis-promoting activity for some of these cDNAs was confirmed by transient transfection in the independent phagocytosis assays. Thus, the unbiased selection procedure successfully identified multiple phagocytosis-promoting genes. The selection method can be applied to other cell-based assays where cells with a desired phenotype can be physically separated. Moreover, the new gene targets uncovered in this study could be relevant to biomolecule screening in search of phagocytosis-regulating agents. In a small-scale screen, a series of imidazopyridine compounds was tested to identify the small molecules that modulate eIF5A-mediated phagocytic activity. Several compounds that influenced the phagocytic activity can be further used as chemical-genetic tools to delineate the mechanisms of eIF5A action and be potential drug candidates that are capable of therapeutically modulating phagocytic activity.

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20

Ichikawa, Naoya, and Tatsuhiko Kadowaki. "Functional analysis of mouse Mahya genes." Neuroscience Research 58 (January 2007): S51. http://dx.doi.org/10.1016/j.neures.2007.06.299.

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21

Burgess, Darren J. "Leveraging functional data for driver genes." Nature Reviews Genetics 16, no. 1 (December 9, 2014): 5. http://dx.doi.org/10.1038/nrg3875.

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22

Weiner, David M., Matilda W. Goodman, Tonya M. Colpitts, Michelle A. Feddock, Kate L. Duggento, Norman R. Nash, Allan I. Levey, and Mark R. Brann. "Functional Screening of Drug Target Genes." American Journal of PharmacoGenomics 4, no. 2 (2004): 119–28. http://dx.doi.org/10.2165/00129785-200404020-00006.

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23

Stepanenko, A. A., Y. S. Vassetzky, and V. M. Kavsan. "Antagonistic functional duality of cancer genes." Gene 529, no. 2 (October 2013): 199–207. http://dx.doi.org/10.1016/j.gene.2013.07.047.

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24

Kiss-Toth, Endre, Eva E. Qwarnstrom, and Steven K. Dower. "Hunting for genes by functional screens." Cytokine & Growth Factor Reviews 15, no. 2-3 (April 2004): 97–102. http://dx.doi.org/10.1016/j.cytogfr.2004.02.002.

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25

Gao, Y., F. Lin, J. Su, Z. Gao, Y. Li, J. Yang, Z. Deng, B. Liu, A. Tsun, and B. Li. "Molecular mechanisms underlying the regulation and functional plasticity of FOXP3+ regulatory T cells." Genes & Immunity 13, no. 1 (November 3, 2011): 1–13. http://dx.doi.org/10.1038/gene.2011.77.

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26

Briggs, F. B. S., L. J. Leung, and L. F. Barcellos. "Annotation of functional variation within non-MHC MS susceptibility loci through bioinformatics analysis." Genes & Immunity 15, no. 7 (July 17, 2014): 466–76. http://dx.doi.org/10.1038/gene.2014.37.

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27

Zhao, Ming, Cynthia R. Shirley, Shotaro Hayashi, Ludovic Marcon, Bhagyalaxmi Mohapatra, Ryota Suganuma, Richard R. Behringer, Guylain Boissonneault, Ryuzo Yanagimachi, and Marvin L. Meistrich. "Transition nuclear proteins are required for normal chromatin condensation and functional sperm development." genesis 38, no. 4 (2004): 200–213. http://dx.doi.org/10.1002/gene.20019.

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28

M. Zimmerman, Sarah, Roberta Besio, Melissa E. Heard-Lipsmeyer, Milena Dimori, Patrizio Castagnola, Frances L. Swain, Dana Gaddy, Alan B. Diekman, and Roy Morello. "Expression characterization and functional implication of the collagen-modifying Leprecan proteins in mouse gonadal tissue and mature sperm." AIMS Genetics 5, no. 1 (2018): 24–40. http://dx.doi.org/10.3934/genet.2018.1.24.

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29

Mrazek, F., A. Stahelova, E. Kriegova, R. Fillerova, M. Zurkova, V. Kolek, and M. Petrek. "Functional variant ANXA11 R230C: true marker of protection and candidate disease modifier in sarcoidosis." Genes & Immunity 12, no. 6 (May 12, 2011): 490–94. http://dx.doi.org/10.1038/gene.2011.27.

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30

Kłossowicz, M., K. Marek-Bukowiec, M. M. Arbulo-Echevarria, B. Ścirka, M. Majkowski, A. F. Sikorski, E. Aguado, and A. Miazek. "Identification of functional, short-lived isoform of linker for activation of T cells (LAT)." Genes & Immunity 15, no. 7 (July 10, 2014): 449–56. http://dx.doi.org/10.1038/gene.2014.35.

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31

Nguyen, T. N., S. Baaklini, F. Koukouikila-Koussounda, M. Ndounga, M. Torres, L. Pradel, F. Ntoumi, and P. Rihet. "Association of a functional TNF variant with Plasmodium falciparum parasitaemia in a congolese population." Genes & Immunity 18, no. 3 (July 13, 2017): 152–57. http://dx.doi.org/10.1038/gene.2017.13.

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32

Gul, Zareen, Muhammad Younas Khan Barozai, and Muhammad Din. "In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)." AIMS Genetics 4, no. 2 (2017): 138–65. http://dx.doi.org/10.3934/genet.2017.2.138.

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33

De Santi, Chiara, Sucharitha Gadi, Agnieszka Swiatecka-Urban, and Catherine M. Greene. "Identification of a novel functional miR-143-5p recognition element in the Cystic Fibrosis Transmembrane Conductance Regulator 3’UTR." AIMS Genetics 5, no. 1 (2018): 53–62. http://dx.doi.org/10.3934/genet.2018.1.53.

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34

Conde, Susana, Shahin Tavakoli, and Daphne Ezer. "Functional regression clustering with multiple functional gene expressions." PLOS ONE 19, no. 11 (November 25, 2024): e0310991. http://dx.doi.org/10.1371/journal.pone.0310991.

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Gene expression data is often collected in time series experiments, under different experimental conditions. There may be genes that have very different gene expression profiles over time, but that adjust their gene expression patterns in the same way under experimental conditions. Our aim is to develop a method that finds clusters of genes in which the relationship between these temporal gene expression profiles are similar to one another, even if the individual temporal gene expression profiles differ. We propose a K-means-type algorithm in which each cluster is defined by a function-on-function regression model, which, inter alia, allows for multiple functional explanatory variables. We validate this novel approach through extensive simulations and then apply it to identify groups of genes whose diurnal expression pattern is perturbed by the season in a similar way. Our clusters are enriched for genes with similar biological functions, including one cluster enriched in both photosynthesis-related functions and polysomal ribosomes, which shows that our method provides useful and novel biological insights.

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35

Early, S. B., P. Huyett, K. Brown-Steinke, L. Borish, and J. W. Steinke. "Functional analysis of −351 interleukin-9 promoter polymorphism reveals an activator controlled by NF-κB." Genes & Immunity 10, no. 4 (April 23, 2009): 341–49. http://dx.doi.org/10.1038/gene.2009.28.

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36

Eerligh, P., M. van Lummel, A. Zaldumbide, A. K. Moustakas, G. Duinkerken, G. Bondinas, B. P. C. Koeleman, G. K. Papadopoulos, and B. O. Roep. "Functional consequences of HLA-DQ8 homozygosity versus heterozygosity for islet autoimmunity in type 1 diabetes." Genes & Immunity 12, no. 6 (May 12, 2011): 415–27. http://dx.doi.org/10.1038/gene.2011.24.

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37

Nishijima, Ichiko, Alea Mills, Yi Qi, Michael Mills, and Allan Bradley. "Two new balancer chromosomes on mouse chromosome 4 to facilitate functional annotation of human chromosome1p." genesis 36, no. 3 (July 2003): 142–48. http://dx.doi.org/10.1002/gene.10207.

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38

KOWALEWSKA-ŁUCZAK, Inga, and Ewa Czerniawska-Piątkowska. "THE POLYMORPHISM C9681T IN THE PROLACTIN RECEPTOR GENE AND FUNCTIONAL TRAITS OF DAIRY CATTLE." Folia Pomeranae Universitatis Technologiae Stetinensis Agricultura, Alimentaria, Piscaria et Zootechnica 334, no. 42 (June 30, 2017): 73–78. http://dx.doi.org/10.21005/aapz2017.42.2.08.

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39

Brand, Cara L., and Mia T. Levine. "Functional Diversification of Chromatin on Rapid Evolutionary Timescales." Annual Review of Genetics 55, no. 1 (November 23, 2021): 401–25. http://dx.doi.org/10.1146/annurev-genet-071719-020301.

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Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat–packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.

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40

Zendo, Takeshi, Shun Iwatani, and Kenji Sonomoto. "Functional analysis of biosynthetic genes for bacteriocins." Japanese Journal of Lactic Acid Bacteria 30, no. 1 (March 14, 2019): 18–26. http://dx.doi.org/10.4109/jslab.30.18.

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41

Kim, Tae Im, Byoung-Kuk Na, and Sung-Jong Hong. "Functional Genes and Proteins of Clonorchis sinensis." Korean Journal of Parasitology 47, Suppl (2009): S59. http://dx.doi.org/10.3347/kjp.2009.47.s.s59.

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42

Capellini, Alexandra, Matthew Williams, Kenan Onel, and Kuan-Lin Huang. "The Functional Hallmarks of Cancer Predisposition Genes." Cancer Management and Research Volume 13 (June 2021): 4351–57. http://dx.doi.org/10.2147/cmar.s311548.

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43

Rud, Daniel, Paul Marjoram, Kimberly Siegmund, and Darryl Shibata. "Functional human genes typically exhibit epigenetic conservation." PLOS ONE 16, no. 9 (September 14, 2021): e0253250. http://dx.doi.org/10.1371/journal.pone.0253250.

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Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.

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44

Crooijmans, R. P. M. A., J. J. Poel, and M. A. M. Groenen. "Functional genes mapped on the chicken genome." Animal Genetics 26, no. 2 (April 24, 2009): 73–78. http://dx.doi.org/10.1111/j.1365-2052.1995.tb02636.x.

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45

SMITH, EUGENE J., HANS H. CHENG, and ROGER L. VALLEJO. "Mapping Functional Chicken Genes: An Alternative Approach." Poultry Science 75, no. 5 (May 1996): 642–47. http://dx.doi.org/10.3382/ps.0750642.

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46

Zhang, H., J. M. Maniar, and A. Z. Fire. "'Inc-miRs': functional intron-interrupted miRNA genes." Genes & Development 25, no. 15 (August 1, 2011): 1589–94. http://dx.doi.org/10.1101/gad.2058711.

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47

Dannenfelser, Ruth, Neil R. Clark, and Avi Ma'ayan. "Genes2FANs: connecting genes through functional association networks." BMC Bioinformatics 13, no. 1 (2012): 156. http://dx.doi.org/10.1186/1471-2105-13-156.

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48

Lee, I. "A Probabilistic Functional Network of Yeast Genes." Science 306, no. 5701 (November 26, 2004): 1555–58. http://dx.doi.org/10.1126/science.1099511.

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49

Cuperus, Josh T., Noah Fahlgren, and James C. Carrington. "Evolution and Functional Diversification of MIRNA Genes." Plant Cell 23, no. 2 (February 2011): 431–42. http://dx.doi.org/10.1105/tpc.110.082784.

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50

Terrazas, Sari, and Saumya Ramanathan. "Functional Characterization of X Antigen Genes (XAGEs)." FASEB Journal 34, S1 (April 2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.05192.

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