Relevant bibliographies by topics / Differential gene expression

Academic literature on the topic 'Differential gene expression'

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Published: 4 June 2021
Last updated: 20 February 2023

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Journal articles on the topic "Differential gene expression"

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Gammelgård, E., M. L. Mohan, R. A. Andersson, and J. P. T. Valkonen. "Host gene expression at an early stage of virus resistance induction." Plant Protection Science 38, SI 2 - 6th Conf EFPP 2002 (December 31, 2017): 502–3. http://dx.doi.org/10.17221/10535-pps.

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Suppression subtractive hybridization (SSH) was carried out to detect genes differentially expressed in plants expressing resistance to systemic infection with Potato virus A (PVA), genus Potyvirus. Differential screening has up to now revealed 19 putative differentially expressed genes. Nothern blot hybridization has confirmed the differential expression of seven genes. Three of them were only induced by the virus, but four genes were also wound-induced.
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Meade, Jonathan. "‘Differential Gene Expression 2002’." Pharmacogenomics 4, no. 2 (March 2003): 117–18. http://dx.doi.org/10.1517/phgs.4.2.117.22635.

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Chatterjee-Kishore, Moitreyee, and Maryann Z. Whitley. "From differential gene expression to differential gene function and back." Drug Discovery Today: Technologies 1, no. 2 (October 2004): 149–56. http://dx.doi.org/10.1016/j.ddtec.2004.09.005.

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Jakobs, T. C. "Differential Gene Expression in Glaucoma." Cold Spring Harbor Perspectives in Medicine 4, no. 7 (July 1, 2014): a020636. http://dx.doi.org/10.1101/cshperspect.a020636.

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Rihn, B. H., S. Mohr, S. A. McDowell, S. Binet, J. Loubinoux, F. Galateau, G. Keith, and G. D. Leikauf. "Differential gene expression in mesothelioma." FEBS Letters 480, no. 2-3 (August 30, 2000): 95–100. http://dx.doi.org/10.1016/s0014-5793(00)01913-x.

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Seroude, Laurent. "Differential Gene Expression and Aging." Scientific World JOURNAL 2 (2002): 618–31. http://dx.doi.org/10.1100/tsw.2002.135.

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It has been established that an intricate program of gene expression controls progression through the different stages in development. The equally complex biological phenomenon known as aging is genetically determined and environmentally modulated. This review focuses on the genetic component of aging, with a special emphasis on differential gene expression. At least two genetic pathways regulating organism longevity act by modifying gene expression. Many genes are also subjected to age-dependent transcriptional regulation. Some age-related gene expression changes are prevented by caloric restriction, the most robust intervention that slows down the aging process. Manipulating the expression of some age-regulated genes can extend an organism's life span. Remarkably, the activity of many transcription regulatory elements is linked to physiological age as opposed to chronological age, indicating that orderly and tightly controlled regulatory pathways are active during aging.
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Skubitz, Keith M., and Amy P. N. Skubitz. "Differential gene expression in leiomyosarcoma." Cancer 98, no. 5 (August 20, 2003): 1029–38. http://dx.doi.org/10.1002/cncr.11586.

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Campbell, W. G., S. E. Gordon, C. J. Carlson, J. S. Pattison, M. T. Hamilton, and F. W. Booth. "Differential global gene expression in red and white skeletal muscle." American Journal of Physiology-Cell Physiology 280, no. 4 (April 1, 2001): C763—C768. http://dx.doi.org/10.1152/ajpcell.2001.280.4.c763.

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The differences in gene expression among the fiber types of skeletal muscle have long fascinated scientists, but for the most part, previous experiments have only reported differences of one or two genes at a time. The evolving technology of global mRNA expression analysis was employed to determine the potential differential expression of ∼3,000 mRNAs between the white quad (white muscle) and the red soleus muscle (mixed red muscle) of female ICR mice (30–35 g). Microarray analysis identified 49 mRNA sequences that were differentially expressed between white and mixed red skeletal muscle, including newly identified differential expressions between muscle types. For example, the current findings increase the number of known, differentially expressed mRNAs for transcription factors/coregulators by nine and signaling proteins by three. The expanding knowledge of the diversity of mRNA expression between white and mixed red muscle suggests that there could be quite a complex regulation of phenotype between muscles of different fiber types.
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Lykhenko, O. "СONSECUTIVE INTEGRATION OF AVAILABLE MICROARRAY DATA FOR ANALYSIS OF DIFFERENTIAL GENE EXPRESSION IN HUMAN PLACENTA." Biotechnologia Acta 14, no. 1 (February 2021): 38–45. http://dx.doi.org/10.15407/biotech14.01.38.

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The purpose of the study was to provide the pipeline for processing of publicly available unprocessed data on gene expression via integration and differential gene expression analysis. Data collection from open gene expression databases, normalization and integration into a single expression matrix in accordance with metadata and determination of differentially expressed genes were fulfilled. To demonstrate all stages of data processing and integrative analysis, there were used the data from gene expression in the human placenta from the first and second trimesters of normal pregnancy. The source code for the integrative analysis was written in the R programming language and publicly available as a repository on GitHub. Four clusters of functionally enriched differentially expressed genes were identified for the human placenta in the interval between the first and second trimester of pregnancy. Immune processes, developmental processes, vasculogenesis and angiogenesis, signaling and the processes associated with zinc ions varied in the considered interval between the first and second trimester of placental development. The proposed sequence of actions for integrative analysis could be applied to any data obtained by microarray technology.
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Jiang, Xue, Han Zhang, and Xiongwen Quan. "Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network." BioMed Research International 2016 (2016): 1–11. http://dx.doi.org/10.1155/2016/3962761.

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Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets.
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Dissertations / Theses on the topic "Differential gene expression"

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Al-Lawati, Sabah Ali Redha. "Differential gene expression in schizophrenia." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420028.

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Sweeney, Glen E. "Differential gene expression in Physarum." Thesis, University of Leicester, 1987. http://hdl.handle.net/2381/35166.

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Physarum polycephalum has a life-cycle that encompasses two very distinct vegetatively growing cell-types; uninucleate microscopic amoebae, and multinucleate macroscopic plasmodia. cDNA libraries have been prepared from both amoebae and plasmodia using the M13 vector mp8. Clones from the two libraries were screened using a differential hybridisation procedure that identifies clones derived from mRNAs much more abundant in one cell-type than in the other. For both the amoebal library and the plasmodial library it was found that about 5% of the clones represented genes preferentially expressed in the cell-type from which the library was prepared. Some of the cell-type-specific clones obtained were used to probe northern blots of amoebal and plasmodial RNA. Two of the plasmodial-specific clones were found to be derived from highly abundant mRNAs, constituting between 0.5% and 2% of total plasmodial mRNA. Selected clones were then used to look at changes in mRNA concentrations during development by probing northern blots of RNA from amoebae, plasmodia and intermediate cell-types. It was found that the plasmodial-specific mRNAs examined fell into two classes; those expressed early in development, and those expressed late in development. The amoebal-specific clones analysed constituted a single group, with each of the probes used detecting an mRNA whose concentration declined markedly in early development. Some of the changes in gene expression were examined more quantitatively by dot blotting. It was found that the difference in concentration of cell-type-specific mRNAs between amoebae and plasmodia varied from between 10 fold to greater than 100 fold. Analysis of the pattern of gene expression was begun in two mutant strains of Physarum which are unable to complete development. Results obtained from a strain which is arrested late in development (RA612) suggest that the developmentally arrested cells express the plasmodial-specific genes which are activated early in development, but not those that become active late in development. A few of the clones have been sequenced, but no homologies with genes sequenced in other systems were detected.
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Fung, Lai-fan. "Differential gene expression in nasopharyngeal carcinoma /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20604609.

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Liebermeister, Wolfram. "Analysis of optimal differential gene expression." Doctoral thesis, [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=97257347X.

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馮麗芬 and Lai-fan Fung. "Differential gene expression in nasopharyngeal carcinoma." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31220824.

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方佩儀 and Pui-yee Fong. "Differential gene expression in gestational trophoblastic disease." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B31224362.

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Hu, Yanmin. "Differential gene expression in dormant mycobacterium tuberculosis." Thesis, St George's, University of London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325140.

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Ghate, Aditée. "The opioid system and differential gene expression." Université Louis Pasteur (Strasbourg) (1971-2008), 2006. http://www.theses.fr/2006STR13019.

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Le système opioïde consiste en trois sous-types de récepteurs opioïdes (delta, mu et kappa) appartenant à la famille des récepteurs couplés aux protéines G, qui sont activés soit par une famille de peptides endogènes, soit par des ligands exogènes. Les récepteurs opioïdes médient les propriétés renforçantes de la morphine et de ses dérivés. L’administration répétée d’opiacés modifie le niveau de transcription de certains gènes dans certaines régions du cerveau de rongeurs, un effet qui serait une des bases moléculaires possibles de la plasticité neuronale associée au comportement addictif. La technologie des « microarrays » ou « puces » permet d’obtenir une image générale de l’expression de l’ensemble des transcrits dans une cellule. Nous avons observé que les souris déficientes en récepteurs mu ne répondent pas aux effets renforçants ou addictifs de la morphine. Des études ont montré que ces animaux mutantes ne montrent aucune préférence pour l’alcool, le THC et la nicotine. Notre hypothèse est que le récepteur mu serait un élément clé dans la mise en place du comportement addictif. Les souris déficientes en récepteur mu représentent un outil unique pour identifier des phénomènes adaptatifs communs à l’ensemble des drogues d’abus. Nous proposons d’utiliser cette lignée pour identifier une collection de gènes dépendants du système opioïde endogène, et dont l’expression est communément dérégulée par l’administration chronique de drogues par la technique des puces. Au cours de ma thèse, j’ai développé l’utilisation, des puces à ADNc et à oligonucléotides pour mes différents projets : l’analyse de la variation d'expression de gènes lors de l’activation de récepteurs opioïdes; l’identification de gènes dont l’expression est restreinte à une structure du cerveau impliquée dans l’addiction ; et l’étude du phénotype obèse de souris déficientes pour les trois récepteurs opioïdes
The opioid system consists of three G-protein coupled receptors, mu, delta, and kappa, which are stimulated by a family of endogenous opioid peptides like beta-endorphin and exogenous ligands such as morphine. It is believed that the repeated opiate administration alters gene expression in different brain regions of rodents, an effect which may contribute to plastic changes associated with addictive behaviour. Oligonucleotide and cDNA microarrays are the two most commonly used methods to profile the expression of thousands of genes in parallel. Gene expression studies performed by microarray analysis or by parallel measurements of the mRNA of multiple candidate genes have become a powerful tool to screen gene expression in the brain after application of drugs of abuse. Studies have shown that the reinforcing properties of morphine, alcohol, cannabinoids and nicotine are abolished or diminished in mice lacking the mu-opioid receptor. The genetic approach therefore highlights mu opioid receptors as convergent molecular switches which mediate reinforcement following direct (eg: morphine) or indirect activation (non-opioid drugs). Use of the mu-opioid receptor knockout mice would therefore help in identifying the genes, downstream of the mu-opioid receptor, that are commonly dysregulated following long term exposure to drugs of abuse. My thesis work involved establishment and use of cDNA and oligonucleotide microarrays screening tools in our laboratory to identify the transcriptional adaptations that occur on activation or in absence of the opioid receptors. I have also characterised obese phenotype observed in the triple opioid receptor knockout mice. Our laboratory is also interested in performing region-specific deletions of the opioid system and is therefore in the process of developing transgenic mice under region-specific promoters. A part of my thesis work also involved searching for region-specific markers for brain areas relevant in drug addiction
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Fong, Pui-yee. "Differential gene expression in gestational trophoblastic disease /." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk:8888/cgi-bin/hkuto%5Ftoc%5Fpdf?B23440132.

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Andersson, Tove. "Approaches to differential gene expression analysis in atherosclerosis." Doctoral thesis, KTH, Biotechnology, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3400.

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Today’s rapid development of powerful tools for geneexpression analysis provides unprecedented resources forelucidating complex molecular events.

The objective of this workhas been to apply, combine andevaluate tools for analysis of differential gene expressionusing atherosclerosis as a model system. First, an optimisedsolid-phase protocol for representational difference analysis(RDA) was applied to twoin vitromodel systems. Initially, The RDA enrichmentprocedure was investigated by shotgun cloning and sequencing ofsuccessive difference products. In the subsequent steps,combinations of RDA and microarray analysis were used tocombine the selectivity and sensitivity of RDA with thehigh-throughput nature of microarrays. This was achieved byimmobilization of RDA clones onto microarrays dedicated forgene expression analysis in atherosclerosis as well ashybridisation of labelled RDA products onto global microarrayscontaining more than 32,000 human clones. Finally, RDA wasapplied for the investigation of the focal localisation ofatherosclerotic plaques in mice usingin vivotissue samples as starting material.

A large number of differentially expressed clones wereisolated and confirmed by real time PCR. A very diverse rangeof gene fragments was identified in the RDA products especiallywhen they were screened with global microarrays. However, themicroarray data also seem to contain some noise which is ageneral problem using microarrays and should be compensated forby careful verification of the results.

Quite a large number of candidate genes related to theatherosclerotic process were found by these studies. Inparticular several nuclear receptors with altered expression inresponse to oxidized LDL were identified and deserve furtherinvestigation. Extended functional annotation does not liewithin the scope of this thesis but raw data in the form ofnovel sequences and accession numbers of known sequences havebeen made publicly available in GenBank. Parts of the data arealso available for interactive exploration on-line through aninteractive software tool. The data generated thus constitute abase for new hypotheses to be tested in the field ofatherosclerosis.

Keywords:representational difference analysis, geneexpression profiling, microarray analysis, atherosclerosis,foam cell formation

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Books on the topic "Differential gene expression"

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Liauw, Jennifer Ann. Characterization of differential gene expression in presenilin 1-deficient mice. Ottawa: National Library of Canada, 2002.

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J, Leaver C., Boulter D, Flavell R. B, and Royal Society (Great Britain). Discussion Meeting, eds. Differential gene expression and plant development: Proceedings of a Royal Society discussion meeting held on 23 and 24 April 1986. London: The Society, 1986.

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Purzner, Andrew. Differential gene expression of LUCA-15 and other cancer related genes in primary breast tissue. Sudbury, Ont: Laurentian University, 2003.

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Colonna-Romano, Sergio. Differential-display reverse transcription-PCR (DDRT-PCR). Berlin: Springer-Verlag, 1998.

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Rintala, Nina. Differential gene expression in radiosensitive and radioresistant breast cancer cells using cDNA microarray analysis. Sudbury, Ont: Laurentian University, 2001.

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Brooks, P. R. Isozyme-specific polymerase chain reaction technology for theanalysis of differential ligninolytic gene expression inphanerochaete chrysosporium. Manchester: UMIST, 1994.

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Billia, Filio. Analysis of differential gene expression in a complex differentiating hierarchy by global amplification of cDNA from single hemopoietic precursors. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1997.

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Hampson, Lynne. Gene expression in haemopoiesis: Isolation and characterisation of differentially expressed sequences. Manchester: University of Manchester, 1996.

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Orsino, Angelina. Characterization and differential expression of connexin genes in the rodent uterus. Ottawa: National Library of Canada, 1995.

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E, Hansen, and Harper G, eds. Differentially expressed genes in plants: A bench manual. London: Taylor & Francis, 1997.

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Book chapters on the topic "Differential gene expression"

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Barah, Pankaj, Dhruba Kumar Bhattacharyya, and Jugal Kumar Kalita. "Differential Expression Analysis." In Gene Expression Data Analysis, 219–60. Boca Raton: Chapman and Hall/CRC, 2021. http://dx.doi.org/10.1201/9780429322655-6.

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Sanders Williams, R. "Differential Gene Expression in Muscle." In Contemporary Concepts in Cardiology, 315–31. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-5007-5_19.

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Gehrke, Lee. "Differential Translation of Eukaryotic Messenger RNAs." In Translational Regulation of Gene Expression, 367–78. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5365-2_16.

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Rickenberg, H. V., K. L. Schaller, and B. H. Leichtling. "Differential Cellular Distribution of Cyclic AMP-Dependent Protein Kinase During Development of Dictyostelium Discoideum." In Gene Manipulation and Expression, 289–304. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-011-6565-5_21.

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Arick, Mark, and Chuan-Yu Hsu. "Differential Gene Expression Analysis of Plants." In Methods in Molecular Biology, 279–98. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7834-2_14.

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Bennett, A., V. Gilman, N. Soch, D. Luo, and C. D. Eckhert. "Boron Stimulated Yeast Differential Gene Expression." In Trace Elements in Man and Animals 10, 1077. New York, NY: Springer US, 2002. http://dx.doi.org/10.1007/0-306-47466-2_328.

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Scholtens, D., and A. von Heydebreck. "Analysis of Differential Gene Expression Studies." In Bioinformatics and Computational Biology Solutions Using R and Bioconductor, 229–48. New York, NY: Springer New York, 2005. http://dx.doi.org/10.1007/0-387-29362-0_14.

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Schendel, D. J., M. Diedrichs, and J. P. Johnson. "Differential Expression of HLA-DR and DQ Molecules on Activated T Lymphocytes." In Regulation of Immune Gene Expression, 301–10. Totowa, NJ: Humana Press, 1986. http://dx.doi.org/10.1007/978-1-4612-5014-2_27.

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Petersen, Robert B., and Susan Lindquist. "Differential mRNA Stability: A Regulatory Strategy for Hsp70 Synthesis." In Post-Transcriptional Control of Gene Expression, 83–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-75139-4_9.

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Gabashvili, Irene S., Richard J. Carter, Peter Markstein, and Anne B. S. Giersch. "Differential Gene Expression in the Auditory System." In Advances in Bioinformatics and Computational Biology, 1–8. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11532323_1.

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Conference papers on the topic "Differential gene expression"

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Odibat, Omar, Chandan K. Reddy, and Craig N. Giroux. "Differential biclustering for gene expression analysis." In the First ACM International Conference. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1854776.1854815.

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CHEN, TING, HONGYU L. HE, and GEORGE M. CHURCH. "MODELING GENE EXPRESSION WITH DIFFERENTIAL EQUATIONS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1998. http://dx.doi.org/10.1142/9789814447300_0004.

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"Differential gene expression analysis in barley Nud gene mutants." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-350.

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Karp, Richard M., Roland Stoughton, and Ka Yee Yeung. "Algorithms for choosing differential gene expression experiments." In the third annual international conference. New York, New York, USA: ACM Press, 1999. http://dx.doi.org/10.1145/299432.299485.

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Wibawa, N. A., Alhadi Bustamam, and Titin Siswantining. "Differential gene co-expression network using BicMix." In PROCEEDINGS OF THE SYMPOSIUM ON BIOMATHEMATICS (SYMOMATH) 2018. Author(s), 2019. http://dx.doi.org/10.1063/1.5094270.

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Liu, Xuejun, and Li Zhang. "An Improved Probabilistic Model for Finding Differential Gene Expression." In 2009 2nd International Conference on Biomedical Engineering and Informatics. IEEE, 2009. http://dx.doi.org/10.1109/bmei.2009.5302665.

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Isik, Riza, Isiksu Eksioglu, Bahattin Can Maral, Benan Bardak, and Mehmet Tan. "Chemical Induced Differential Gene Expression Prediction on LINCS Database." In 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2020. http://dx.doi.org/10.1109/bibe50027.2020.00026.

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Jiang, Dazhi, Zhijian Wu, and Lishan Kang. "Parameter Identifications In Differential Equations By Gene Expression Programming." In Third International Conference on Natural Computation (ICNC 2007) Vol V. IEEE, 2007. http://dx.doi.org/10.1109/icnc.2007.539.

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Zhang, Qiongyun, Chi Zhou, Weimin Xiao, and Peter C. Nelson. "Improving gene expression programming performance by using differential evolution." In Sixth International Conference on Machine Learning and Applications (ICMLA 2007). IEEE, 2007. http://dx.doi.org/10.1109/icmla.2007.62.

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Tedrow, J., K. Konishi, R. Landreneau, J. Luketich, N. Kaminski, and F. Sciurba. "Association of Radiographic COPD Phenotypes with Differential Gene Expression." In American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California. American Thoracic Society, 2009. http://dx.doi.org/10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a2996.

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Reports on the topic "Differential gene expression"

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Balfanz, Emma, Erin Sandford, Michael G. Kaiser, and Susan J. Lamont. Differential Immunological Gene Expression after Escherichia coli Infection in Chickens. Ames (Iowa): Iowa State University, January 2011. http://dx.doi.org/10.31274/ans_air-180814-668.

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Gottardo, Raphael, Adrian E. Raftery, Ka Y. Yeung, and Roger E. Bumgarner. Bayesian Robust Inference for Differential Gene Expression in cDNA Microarrays with Multiple Samples. Fort Belvoir, VA: Defense Technical Information Center, July 2004. http://dx.doi.org/10.21236/ada478418.

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Betzler, Christopher. Differential Gene Expression in Pancreatic Ductal Adenocarcinoma and Stromal Tissue: Prognostic and Therapeutic Implications. Science Repository, June 2019. http://dx.doi.org/10.31487/j.jso.2019.02.11.

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Vang, Lindsay K., P. Scott Pine, Sarah A. Munro, and Marc L. Salit. Preparation of a set of total RNA benchmarking samples for performance assessment of genome-scale differential gene expression. Gaithersburg, MD: National Institute of Standards and Technology, June 2017. http://dx.doi.org/10.6028/nist.sp.1200-23.

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Lers, Amnon, E. Lomaniec, S. Burd, A. Khalchitski, L. Canetti, and Pamela J. Green. Analysis of Senescence Inducible Ribonuclease in Tomato: Gene Regulation and Function. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7570563.bard.

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Natural leaf senescence has a negative influence on yield. Postharvest induced senescence contributes to the losses of quality in flowers, foliage, and vegetables. Strategies designed to control the senescence process in crop plants could therefore have great applied significance. Senescence is regulated by differential gene expression yet, functional characterization of the genes specifically induced and study of their expression control, is still in its infancy. Study of senescence-specific genes is required to allow identification of regulatory elements participating in senescence-induced expression and thus provide insights into the genetic regulation of senescence. A main feature of senescence is the hydrolysis of macromolecules by hydrolases of various types such as RNases and proteases. This study was aimed a analysis of senescence-inducible RNases in tomato with the following objectives: Isolation of senescence-inducible RNase cDNA clones; Expression analyses of RNase genes during senescence; Identification of sequences required for senescence-induced gene expression; Functional analyses of senescence-inducible RNases. We narrowed our aims somewhat to focus on the first three objectives because the budget we were awarded was reduced from that requested. We have expanded our research for identification senescence-related RNase/nuclease activities as we thought it will direct us to new RNase/nuclease genes. We have also carried out research in Arabidopsis and parsley, which enabled us to draw mire general conclusions. We completed the first and second objectives and have made considerable progress on the remaining two. We have defined growth conditions suitable for this research and defined the physiological and biochemical parameters characteristic to the advance of leaf senescence. In tomato and arabidopsis we have focused on natural leaf senescence. Parsley was used mainly for study of postharvest senescence in detached leaves. We have identified a 41-kD a tomato nuclease, LeNUCI, specifically induced during senescence which can degrade both RNA and DNA. This activity could be induced by ethylene in young leaves and was subjected to detailed analysis, which enabled its classification as Nuclease I enzyme. LeNUCI may be involved in nucleic acid metabolism during tomato leaf senescence. In parsley senescing leaves we identified 2 main senescence-related nuclease activities of 41 and 39-kDa. These activities were induced in both naturally or artificially senescing leaves, could degrade both DNA and RNA and were very similar in their characteristics to the LeNUCI. Two senescence-induced RNase cDNAs were cloned from tomato. One RNase cDNA was identical to the tomato LX RNase while the second corresponded to the LE RNase. Both were demonstrated before to be induced following phosphate starvation of tomato cell culture but nothing was known about their expression or function in plants. LX gene expression was much more senescence specific and ethylene could activate it in detached young leaves. LE gene expression, which could be transiently induced by wounding, appeared to be activated by abscisic acid. We suggest that the LX RNase has a role in RNA catabolism in the final stage of senescence, and LE may be a defense-related protein. Transgenic plants were generated for altering LX gene expression. No major visible alterations in the phenotype were observed so far. Detailed analysis of senescence in these plants is performed currently. The LX promoter was cloned and its analysis is performed currently for identification of senescence-specific regulatory elements. In Arabidopsis we have identified and characterized a senescence-associated nuclease 1 gene, BFN1, which is highly expressed during leaf and stem senescence. BFN1, is the first example of a senescence- associated gene encoding a nuclease I enzyme as well as the first nuclease I cloned and characterized from Arabidopsis. Our progress should provide excellent tools for the continued analysis of regulation and function of senescence-inducible ribonucleases and nucleases in plants. The cloned genes can be used in reverse genetic approaches, already initiated, which can yield a more direct evidence for the function of these enzymes. Another contribution of this research will be in respect to the molecular mechanism, which controls senescence. We had already initiated in this project and will continue to identify and characterize regulatory elements involved in senescence-specific expression of the genes isolated in this work.
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6

Raghothama, Kashchandra G., Avner Silber, and Avraham Levy. Biotechnology approaches to enhance phosphorus acquisition of tomato plants. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7586546.bard.

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Abstract: Phosphorus is one of the least available macronutrient in the soil. The high affinity phosphate transporters are known to be associated with phosphate acquisition under natural conditions. Due to unique interactions of phosphate with soil particles, up to 80% of the applied phosphates may be fixed forcing the farmers to apply 4 to 5 times the fertilizers necessary for crop production. Efficient uptake and utilization of this essential nutrient is essential for sustainability and profitability of agriculture. Many predictions point to utilization/exhaustion of high quality phosphate rocks within this century. This calls for efforts to improve the ability of plants to acquire and utilize limiting sources of phosphate in the rhizosphere. Two important molecular and biochemical components associated with phosphate efficiency are phosphate transporters and phosphatases. This research project is aimed at defining molecular determinants of phosphate acquisition and utilization in addition to generating phosphate uptake efficient plants. The main objectives of the project were; Creation and analysis of transgenic tomato plants over-expressing phosphatases and transporters Characterization of the recently identified members (LePT3 and LePT4) of the Pi transporter family Generate molecular tools to study genetic responses of plants to Pi deficiency During the project period we have successfully identified and characterized a novel phosphate transporter associated with mycorrhizal symbiosis. The expression of this transporter increases with mycorrhizal symbiosis. A thorough characterization of mutant tomato lacking the expression of this gene revealed the biological significance of LePT3 and another novel gene LePT4. In addition we have isolated and characterized several phosphate starvation induced genes from tomato using a combination of differential and subtractive mRNA hybridization techniques. One of the genes, LePS2 belongs to the family of phospho-protein phosphatase. The functionality of the recombinant protein was determined using synthetic phosphor-peptides. Over expression of this gene in tomato resulted in significant changes in growth, delay in flowering and senescence. It is anticipated that phospho-protein phosphatase may have regulatory role in phosphate deficiency responses of plants. In addition a novel phosphate starvation induced glycerol 3-phosphate permease gene family was also characterized. Two doctoral research students are continuing the characterization and functional analysis of these genes. Over expression of high affinity phosphate transporters in tobacco showed increased phosphate content under hydroponic conditions. There is growing evidence suggesting that high affinity phosphate transporters are crucial for phosphate acquisition even under phosphate sufficiency conditions. This project has helped train several postdoctoral fellows and graduate students. Further analysis of transgenic plants expressing phosphatases and transporters will not only reveal the biological function of the targeted genes but also result in phosphate uptake and utilization efficient plants.
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Sadka, Avi, Mikeal L. Roose, and Yair Erner. Molecular Genetic Analysis of Citric Acid Accumulation in Citrus Fruit. United States Department of Agriculture, March 2001. http://dx.doi.org/10.32747/2001.7573071.bard.

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The acid content of the juice sac cells is a major determinant of maturity and fruit quality in citrus. Many citrus varieties accumulate acid in concentrations that exceed market desires, reducing grower income and consumer satisfaction. Pulp acidity is thought to be dependent on two mechanisms: the accumulation of citric acid in the vacuoles of the juice sac cells, and acidification of the vacuole. The major aim of the project was to direct effort toward understanding the mechanism of citric acid accumulation in the fruit. The following objectives were suggested: Measure the activity of enzymes likely to be involved in acid accumulation and follow their pattern of expression in developing fruit (Sadka, Erner). Identify and clone genes which are associated with high and low acid phenotypes and with elevated acid level (Roose, Sadka, Erner). Convert RAPD markers that map near a gene that causes low acid phenotype to specific co dominant markers (Roose). Use genetic co segregation to test whether specific gene products are responsible for low acid phenotype (Roose and Sadka). Objective 1 was fully achieved. Most of the enzymes of organic acid metabolism were cloned from lemon pulp. Their expression was studied during fruit development in low and high acid varieties. The activity and expression of citrate synthase, aconitase and NADP-isocitrate dehydrogenase (IDH) were studied in detail. The role that each enzyme plays in acid accumulation and decline was evaluated. As a result, a better understanding of the metabolic changes that contribute to acid accumulation was achieved. It was found that the activity of the mitochondrial aconitase is greatly reduced early in high-acid fruits, but not in acidless ones, suggesting that this enzyme plays an important role in acid accumulation. In addition, it was demonstrated that increases in the cytosolic forms of aconitase and NADP-IDH towards fruit maturation play probably a major role in acid decline. Our studies also demonstrated that the two mechanisms that contribute to fruit acidity, vacuolar acidification and citric acid accumulation, are independent, although they are tightly co-regulated. Additional, we demonstrated that sodium arsenite, which reduce fruit acidity, causes a transient inhibition in the activity of citrate synthase, but an induction in the gene expression. This part of the work has resulted in 4 papers. Objective 3 was also fully achieved. Using bulked segregant analysis, three random amplified polymorphic DNA (RAPD) markers were identified as linked to acitric, a gene controlling the acidless phenotype of pummelo 2240. One of them, which mapped 1.2 cM from acitric was converted into sequence characterized amplified region (SCAR marker, and into co dominant restriction length polymorphism (RFLP) marker. These markers were highly polymorphic among 59 citrus accessions, and therefore, they should be useful for selecting seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 and other citrus genotypes. This part of the project resulted in one paper. Objective 4 was also fully achieved. Clones isolated by the Israeli group were sent to the American laboratory for co segregation analysis. However, none of them seemed to co segregate with the low acid phenotype. Both laboratories invested much effort in achieving the goals of Objective 2, namely the isolation of genes that are elevated in expression in low and high acid phenotypes, and in tissue cultures treated with arsenite (a treatment which reduces fruit acidity). However, conventional differential display and restriction fragment differential display analyses could not identify any differentially expressed genes. The isolation of such genes was the major aim of a continuation project, which was recently submitted.
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8

Whitham, Steven A., Amit Gal-On, and Victor Gaba. Post-transcriptional Regulation of Host Genes Involved with Symptom Expression in Potyviral Infections. United States Department of Agriculture, June 2012. http://dx.doi.org/10.32747/2012.7593391.bard.

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Understanding how RNA viruses cause disease symptoms in their hosts is expected to provide information that can be exploited to enhance modern agriculture. The helper component-proteinase (HC-Pro) protein of potyviruses has been implicated in symptom development. Previously, we demonstrated that symptom expression is associated with binding of duplex small-interfering-RNA (duplex-siRNA) to a highly conserved FRNK amino acid motif in the HC-Pro of Zucchini yellow mosaic virus (ZYMV). This binding activity also alters host microRNA (miRNA) profiles. In Turnip mosaic virus (TuMV), which infects the model plant Arabidopsis, mutation of the FRNK motif to FINK was lethal providing further indication of the importance of this motif to HC-Pro function. In this continuation project, our goal was to further investigate how ZYMV and TuMV cause the mis-expression of genes in cucurbits and Arabidopsis, respectively, and to correlate altered gene expression with disease symptoms. Objective 1 was to examine the roles of aromatic and positively charged residues F164RNH and K215RLF adjacent to FR180NK in small RNA binding. Objective 2 was to determine the target genes of the miRNAs which change during HC-Pro expression in infected tissues and transgenic cucumber. Objective 3 was to characterize RNA silencing mechanisms underlying differential expression of host genes. Objective 4 was to analyze the function of miRNA target genes and differentially expressed genes in potyvirus-infected tissues. We found that the charged K/R amino acid residues in the FKNH and KRLF motifs are essential for virus viability. Replacement of K to I in FKNH disrupted duplex-siRNA binding and virus infectivity, while in KRLF mutants duplex-siRNA binding was maintained and virus infectivity was limited: symptomless following a recovery phenomenon. These findings expanded the duplex-siRNA binding activity of HC-Pro to include the adjacent FRNK and FRNH sites. ZYMV causes many squash miRNAs to hyper-accumulate such as miR166, miR390, mir168, and many others. Screening of mir target genes showed that only INCURVATA-4 and PHAVOLUTA were significantly upregulated following ZYMVFRNK infection. Supporting this finding, we found similar developmental symptoms in transgenic Arabidopsis overexpressing P1-HC-Pro of a range of potyviruses to those observed in miR166 mutants. We characterized increased transcription of AGO1 in response to infection with both ZYMV strains. Differences in viral siRNA profiles and accumulation between mild and severe virus infections were characterized by Illumina sequencing, probably due to the differences in HC-Pro binding activity. We determined that the TuMV FINK mutant could accumulate and cause symptoms in dcl2 dcl4 or dcl2 dcl3 dcl4 mutants similar to TuMV FRNK in wild type Arabidopsis plants. These dcl mutant plants are defective in antiviral defenses, and the results show that factors other than HC-ProFRNK motif can induce symptoms in virus-infected plants. As a result of this work, we have a better understanding of the FRNK and FKNH amino acid motifs of HC-Pro and their contributions to the duplex-siRNA binding functions. We have identified plant genes that potentially contribute to infectivity and symptoms of virus infected plants when they are mis-expressed during potyviral infections. The results establish that there are multiple underlying molecular mechanisms that lead viral pathogenicity, some dependent on HC-Pro. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.
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9

Lee, Yong J., S. S. Galoforo, and C. M. Berns. Differential effect of 1{alpha},25-dihydroxyvitamin D{sub 3} on Hsp28 and PKC{beta} gene expression in the phorbol ester-resistant human myeloid HL-525 leukemic cells. Office of Scientific and Technical Information (OSTI), August 1997. http://dx.doi.org/10.2172/522765.

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10

Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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