Academic literature on the topic 'Gene co-expression pattern'
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Journal articles on the topic "Gene co-expression pattern"
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Roy, Swarup, Dhruba K. Bhattacharyya, and Jugal K. Kalita. "CoBi: Pattern Based Co-Regulated Biclustering of Gene Expression Data." Pattern Recognition Letters 34, no. 14 (October 2013): 1669–78. http://dx.doi.org/10.1016/j.patrec.2013.03.018.
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Muller, Heiko, and Francesco Acquati. "Topological Properties of Co-Occurrence Networks in Published Gene Expression Signatures." Bioinformatics and Biology Insights 2 (January 2008): BBI.S518. http://dx.doi.org/10.4137/bbi.s518.
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Meta-analysis of high-throughput gene expression data is often used for the interpretation of proprietary gene expression data sets. We have recently shown that co-occurrence patterns of gene expression in published cancer-related gene expression signatures are reminiscent of several cancer signaling pathways. Indeed, significant co-occurrence of up to ten genes in published gene expression signatures can be exploited to build a co-occurrence network from the sets of co-occurring genes (“co-occurrence modules”). Such co-occurrence network is represented by an undirected graph, where single genes are assigned to vertices and edges indicate that two genes are significantly co-occurring. Thus, graph-cut methods can be used to identify groups of highly interconnected vertices (“network communities”) that correspond to sets of genes that are significantly co-regulated in human cancer. Here, we investigate the topological properties of co-occurrence networks derived from published gene expression signatures and show that co-occurrence networks are characterized by scale-free topology and hierarchical modularity. Furthermore, we report that genes with a “promiscuous” or a “faithful” co-occurrence pattern can be distinguished. This behavior is reminiscent of date and party hubs that have been identified in protein-protein interaction networks.
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MA, PATRICK C. H., KEITH C. C. CHAN, and DAVID K. Y. CHIU. "CLUSTERING AND RE-CLUSTERING FOR PATTERN DISCOVERY IN GENE EXPRESSION DATA." Journal of Bioinformatics and Computational Biology 03, no. 02 (April 2005): 281–301. http://dx.doi.org/10.1142/s0219720005001053.
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The combined interpretation of gene expression data and gene sequences is important for the investigation of the intricate relationships of gene expression at the transcription level. The expression data produced by microarray hybridization experiments can lead to the identification of clusters of co-expressed genes that are likely co-regulated by the same regulatory mechanisms. By analyzing the promoter regions of co-expressed genes, the common regulatory patterns characterized by transcription factor binding sites can be revealed. Many clustering algorithms have been used to uncover inherent clusters in gene expression data. In this paper, based on experiments using simulated and real data, we show that the performance of these algorithms could be further improved. For the clustering of expression data typically characterized by a lot of noise, we propose to use a two-phase clustering algorithm consisting of an initial clustering phase and a second re-clustering phase. The proposed algorithm has several desirable features: (i) it utilizes both local and global information by computing both a "local" pairwise distance between two gene expression profiles in Phase 1 and a "global" probabilistic measure of interestingness of cluster patterns in Phase 2, (ii) it distinguishes between relevant and irrelevant expression values when performing re-clustering, and (iii) it makes explicit the patterns discovered in each cluster for possible interpretations. Experimental results show that the proposed algorithm can be an effective algorithm for discovering clusters in the presence of very noisy data. The patterns that are discovered in each cluster are found to be meaningful and statistically significant, and cannot otherwise be easily discovered. Based on these discovered patterns, genes co-expressed under the same experimental conditions and range of expression levels have been identified and evaluated. When identifying regulatory patterns at the promoter regions of the co-expressed genes, we also discovered well-known transcription factor binding sites in them. These binding sites can provide explanations for the co-expressed patterns.
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OLMAN, VICTOR, CHINDO HICKS, PENG WANG, and YING XU. "GENE EXPRESSION DATA ANALYSIS IN SUBTYPES OF OVARIAN CANCER USING COVARIANCE ANALYSIS." Journal of Bioinformatics and Computational Biology 04, no. 05 (October 2006): 999–1014. http://dx.doi.org/10.1142/s0219720006002296.
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Many studies have used microarray technology to identify the molecular signatures of human cancer, yet the critical features of these often unmanageably large set of signatures remain elusive. We have investigated co-expression pattern in four subtypes of ovarian cancer from 104 cancer patients using covariance analysis, treating each subtype of ovarian cancer as a distinct disease entity. We sought gene pairs that were transcriptionally co-expressed in one or multiple subtypes of ovarian cancer, establishing a high confidence network of 87 genes interconnected by significantly high co-expression links that were observed in at least two subtypes of ovarian cancer. We have shown that certain groups of co-expressed gene pairs are cancer subtype specific, through demonstrating significant differences in co-expression patterns of gene pairs between subtypes of ovarian cancer. In addition, we identified a set of 24 genes that classified patients into specific cancer subtypes with a misclassification error rate of less than 5%. Our findings illustrate how large public microarray gene expression datasets could be exploited for identification of cancer subtype specific molecular signatures, and how to classify cancer patients into specific subtypes of cancer using gene expression profiles.
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KUO, Ming-Wei, John POSTLETHWAIT, Wen-Chih LEE, Show-Wan LOU, Woon-Khiong CHAN, and Bon-chu CHUNG. "Gene duplication, gene loss and evolution of expression domains in the vertebrate nuclear receptor NR5A (Ftz-F1) family." Biochemical Journal 389, no. 1 (June 21, 2005): 19–26. http://dx.doi.org/10.1042/bj20050005.
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Fushi tarazu factor 1 (Ftz-F1, NR5A) is a zinc-finger transcription factor that belongs to the nuclear receptor superfamily and regulates genes that are involved in sterol and steroid metabolism in gonads, adrenals, liver and other tissues. To understand the evolutionary origins and developmental genetic relationships of the Ftz-F1 genes, we have cloned four homologous Ftz-f1 genes in zebrafish, called ff1a, ff1b, ff1c and ff1d. These four genes have different temporal and spatial expression patterns during development, indicating that they have distinct mechanisms of genetic regulation. Among them, the ff1a expression pattern is similar to mammalian Nr5a2, while the ff1b pattern is similar to that of mammalian Nr5a1. Genetic mapping experiments show that these four ff1 genes are located on chromosome segments conserved between the zebrafish and human genomes, indicating a common ancestral origin. Phylogenetic and conserved synteny analysis show that ff1a is the orthologue of NR5A2, and that ff1b and ff1d genes are co-orthologues of NR5A1 that arose by a gene-duplication event, probably a whole-genome duplication, in the ray-fin lineage, and each gene is located next to an NR6A1 co-orthologue as in humans, showing that the tandem duplication occurred before the divergence of human and zebrafish lineages. ff1c does not have a mammalian counterpart. Thus we have characterized the phylogenetic relationships, expression patterns and chromosomal locations of these Ftz-F1 genes, and have demonstrated their identities as NR5A genes in relation to the orthologous genes in other species.
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Raja, Komal K. B., Evan A. Bachman, Catrina E. Fernholz, David S. Trine, Rebecca E. Hobmeier, Nathaniel J. Maki, Timothy J. Massoglia, and Thomas Werner. "The Genetic Mechanisms Underlying the Concerted Expression of the yellow and tan Genes in Complex Patterns on the Abdomen and Wings of Drosophila guttifera." Genes 14, no. 2 (January 24, 2023): 304. http://dx.doi.org/10.3390/genes14020304.
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How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here, we sought to identify the genetic mechanisms that regulate the tan (t) gene in a multi-spotted pigmentation pattern on the abdomen and wings of Drosophila guttifera. Previously, we showed that yellow (y) gene expression completely prefigures the abdominal and wing pigment patterns of this species. In the current study, we demonstrate that the t gene is co-expressed with the y gene in nearly identical patterns, both transcripts foreshadowing the adult abdominal and wing melanin spot patterns. We identified cis-regulatory modules (CRMs) of t, one of which drives reporter expression in six longitudinal rows of spots on the developing pupal abdomen, while the second CRM activates the reporter gene in a spotted wing pattern. Comparing the abdominal spot CRMs of y and t, we found a similar composition of putative transcription factor binding sites that are thought to regulate the complex expression patterns of both terminal pigmentation genes y and t. In contrast, the y and t wing spots appear to be regulated by distinct upstream factors. Our results suggest that the D. guttifera abdominal and wing melanin spot patterns have been established through the co-regulation of y and t, shedding light on how complex morphological traits may be regulated through the parallel coordination of downstream target genes.
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Liu, Guo, Yaojian Xie, Xiuhua Shang, and Zhihua Wu. "Expression Patterns and Gene Analysis of the Cellulose Synthase Gene Superfamily in Eucalyptus grandis." Forests 12, no. 9 (September 15, 2021): 1254. http://dx.doi.org/10.3390/f12091254.
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Cellulose is the world’s most abundant renewable energy resource, and a variety of cellulose synthase genes are involved in the biosynthesis of cellulose. In the process of cellulose synthesis, all cellulose synthases are interrelated and act synergistically. In this study, we analyzed the contents of cellulose, hemicellulose, and lignin in the different parts and tissues of E. grandis. The results showed that the cellulose content had greater differences among three different heights. On this basis, we carried out the transcriptome-wide profiling of gene expression patterns using RNA sequencing. A total of 2066 differentially expressed genes were identified for three pairwise comparisons between three different heights, most of which were related to the programmed photosynthetic membrane and photosystem. A total of 100 transcripts of CSs (58 CesA and 42 Csl) were obtained from transcriptome libraries. The expression pattern of these genes indicated that different CS genes had a wide range of expression profiles. A phylogenetic analysis of 135 reference CS genes showed that the CSs of E. grandis were clustered into six major groups (CesA1-9, CslA, CslB/H, CslD, CslE, and CslG). Based on the weighted gene co-expression network analysis, a dual-directional regulation mechanism between Csl and CesA proteins in the cellulose biosynthesis was identified. The gene expression profile analysis, using qRT-PCR in different tissues of E. grandis, demonstrated that the CSs were highly expressed in xylem, and CesAs had a higher relative expression than Csls. The analysis of sequence similarity combined with the expression pattern indicated that the CesA1, 3, and 6 transcripts were associated with the biosynthesis of the secondary cell wall, and CesA4, 5, and 7 transcripts were more likely to associate with the biosynthesis of the primary cell wall. Finally, the qRT-PCR analysis confirmed the expression of 11 selected CSs in three different parts of E. grandis.
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Donizetti, Aldo, Marcella Fiengo, Sergio Minucci, and Francesco Aniello. "Duplicated zebrafish relaxin-3 gene shows a different expression pattern from that of the co-orthologue gene." Development, Growth & Differentiation 51, no. 8 (September 23, 2009): 715–22. http://dx.doi.org/10.1111/j.1440-169x.2009.01131.x.
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Ma, Shisong, Smit Shah, Hans J. Bohnert, Michael Snyder, and Savithramma P. Dinesh-Kumar. "Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways." PLoS Genetics 9, no. 10 (October 3, 2013): e1003840. http://dx.doi.org/10.1371/journal.pgen.1003840.
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Rattay, Kristin, Hannah Verena Meyer, Philip Brennecke, Alejandro Reyes, Sheena Pinto, Benedikt Brors, Wolfgang Huber, Lars Steinmetz, and Bruno Kyewski. "Thymic expression of tissue-restricted self-antigens is a highly coordinated and evolutionary conserved process." Journal of Immunology 196, no. 1_Supplement (May 1, 2016): 186.15. http://dx.doi.org/10.4049/jimmunol.196.supp.186.15.
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Abstract Promiscuous gene expression (pGE) of tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs) is essential for tolerance imposition in the thymus. PGE is characterized on the one hand by inclusion of a broad range of TRAs and on the other hand by its mosaic patterns, whereby each antigen is only expressed in 1–3% of mTECs at a given point in time. Yet, this mosaic pattern at the single cell level faithfully adds up to the full repertoire of self-antigens at the population level. In order to analyze the regulatory mechanisms underlying this transcriptional heterogeneity among mTECs, we applied two complementing approaches, the isolation of minor mTEC subsets as defined by TRA-selected gene co-expression groups in conjunction with single cell mRNA sequencing. Different TRA-selected mTEC subfractions, each expressing distinct sets of genes in a mutually overlapping fashion, mapped to distinct stages of mTEC development. These co-expression patterns were evolutionary conserved between mouse and human (Rattay et al., J. Autoimmunity 2015). Applying an unbiased single cell mRNA sequencing approach, we extended these findings to the single cell level and showed that the mouse mTEC population essentially represents a composite of multiple co-expression groups (Brennecke et al., Nat. Immunology 2015). These co-expression groups may represent only snapshots of a continuum of changing co-expression groups along the lifetime of an individual mTEC, as captured in the model of “sliding co-expression groups” (Pinto et al., PNAS 2013). Continuous genome scanning would potentially enlarge the overall diversity of self-antigens displayed by a single mTEC.
Dissertations / Theses on the topic "Gene co-expression pattern"
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TRATTARO, SEBASTIANO. "BRAIN ORGANOID MODELLING OF HUMAN CORTICOGENESIS:THE PARADIGM OF WEAVER SYNDROME." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/875973.
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Multiple strategies of brain organoidogenesis have enabled the investigation of human cerebral corticogenesis in-vitro with increasing accuracy. However, little is yet known about how closely the gene co-expression patterns seen in brain organoids (BO) match those of fetal cortex. Here we benchmarked BO against fetal corticogenesis by integrating transcriptomes from in-house differentiated cortical BO (CBO), other BO systems, human fetal brain samples processed in-house, and pre-natal cortices from the BrainSpan Atlas. We identified and ranked co-expression patterns and hubs of corticogenesis and CBO differentiation, highlighting well-preserved and variable trends across BO protocols, and we found heterochronicity of differentiation across BO models compared to fetal cortex. Once performed this benchmarking, we used CBO for disease-modelling of Weaver syndrome (WS), a rare disease characterized by intellectual disability. WS is associated with mutations in Polycomb repressive complex 2, a repressor of gene expression through H3K27me3. We differentiated patient-derived CBO and profiled their transcriptome and epigenome at different time-points, revealing upregulation of genes involved in neuronal maturation and migration as well as alteration of glucose metabolism in WS. Intersection of differentially expressed genes between WS- and control-CBO across stages with H3K27me3 ChIP-seq peaks, DNA-methylation profiles and dysregulated genes in CBO from a CRISPR/Cas9-engineered EZH2 KO revealed a set of PRC2 targets possibly mediating the WS intellectual disability phenotype. Our approach identified commonalities and divergences between state-of-the-art BO systems, providing a resource to query when modelling human corticogenesis, and identified molecular phenotypes and targets relevant for WS, generating the framework for future potential therapeutic intervention.
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Thinesh, Peranantham. "Characterization of cell growth, substrate utilization, end-product synthesis and gene expression patterns in cellulose degrading co-cultures of Clostridium termitidis CT1112 and Clostridium intestinale URNW." 2015. http://hdl.handle.net/1993/30597.
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Co-cultures of selected fermentative bacteria have been shown to improve rates of substrate conversion and yields of some fermentation end-products. We have tested this hypothesis using a co-culture of the mesophilic, cellulolytic bacterium Clostridium termitidis CT1112 and the mesophilic, saccharophylic bacterium, Clostridium intestinale URNW. C. termitidis can utilize cellulose as a sole carbon source. It releases glycosyl hydrolases that hydrolyze cellulose, cellobiose and glucose. C. intestinale URNW, which was isolated as a contaminant from a cellobiose stock bottle of C. termitidis (Ramachandran et al., 2011), is not capable of hydrolyzing cellulose, but can utilize the cellobiose and glucose released by cellulose hydrolysis to grow in co-culture with C. termitidis. Based on the faster doubling-time of C. intestinale URNW on cellobiose, it was expected that the “soluble sugar free” environment will stimulate C. termitidis to hydrolyse cellulose at faster rate and which in-turn will result in increased substrate utilization and end-product synthesis compared to the monoculture of C. termitidis. The designed co-culture was characterized in depth with the use of microbial quantification studies (multiplex quantitative Real Time Polymerase Chain Reaction – qPCR) and ‘Omics techniques to understand the population dynamics and gene product expression in each species in the co-culture versus their respective monocultures at the molecular level. Inoculation of co-culture with diffferent initial ratios of the C. termitidis and C. intestinale resulted a fixed ratio of approximately 13:1 (C. termitidis : C. intestinale) at 168 hour post-inoculation (h pi). A statistical difference in substrate utilization and total cell mass production, but not end-product cocentrations, was observed at 168 h pi in cultures with an initial C. termitidis : C. intestinale ratio of 1:1 and 1:0.2). No statisical differences in substrate utilization, biomass accumulation, or end-product synthesis concentrations were observed for all other initial C. termitidis : C. intestinale ratios, or for co-cultures in where the C. termitidis : C. intestinale ratio was 1:25. Thus, the hypothesis that synergistic interactions between species in co-cultures can stimulate substrate consumption and end-product synthesis was supported under very limited conditions in this co-culutre system. Unlike other co-cultures reported in literature, the co-culture of C. termitidis and C. intestinale did not show large increases in substrate utilization or end-product concentrations synthesized when cultured on 2 g/L α-cellulose. This may be due to the slower cellulose degradation ability of C. termitidis in the co-culture, (compared to the cellulose degraders in other co-cultures such as C. thermocellum), which is the main contributor to the growth of C. intestinale in the co-culture and the competition for the same substrate (cellobiose) by both the species in the co-culture.October 2015
Book chapters on the topic "Gene co-expression pattern"
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Zhang, Shuzhong, Kun Wang, Bilian Chen, and Xiuzhen Huang. "A New Framework for Co-clustering of Gene Expression Data." In Pattern Recognition in Bioinformatics, 1–12. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-24855-9_1.
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Low, Felicia M., Peter D. Gluckman, and Mark A. Hanson. "A life course approach to public health: why early life matters." In Oxford Textbook of Nature and Public Health, edited by Matilda van den Bosch and William Bird, 11–25. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198725916.003.0031.
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This chapter describes the theoretical and mechanistic basis, and public health implications, of the Developmental Origins of Health and Disease (DOHaD) paradigm, which has emerged from overwhelming epidemiological, clinical, and experimental evidence demonstrating the importance of early life development in influencing an individual’s susceptibility to later life disease risk. DOHaD is underpinned by the evolutionarily conserved processes of developmental plasticity. These enable phenotypic adjustment to match the environment and are effected, in part, by epigenetic mechanisms that modulate patterns of gene expression. This chapter uses obesity and its co-morbidities to illustrate how a life course approach can provide an effective strategy for reducing disease risk and have major policy implications. It focuses on early life as a critical intervention point, and recognizes the importance of taking into consideration the full range of influencial biological, behavioural, and contextual factors that operate across the life course.
Conference papers on the topic "Gene co-expression pattern"
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Bhattacharyya, Malay, and Sanghamitra Bandyopadhyay. "Integration of Co-expression Networks for Gene Clustering." In 2009 Seventh International Conference on Advances in Pattern Recognition (ICAPR). IEEE, 2009. http://dx.doi.org/10.1109/icapr.2009.55.
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Becker, Nicole Bernd, Allan Marinho Alcará, Isadora Ghilardi, Vitoria Pimentel, Giulia Pinzetta, Laura Provenz, Gabriel Leal, et al. "Mesenchymal stem cells modulate the gene expression of cationchloride co-transporter KCC2 in epileptogenesis." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.693.
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Background: Temporal Lobe Epilepsy (TLE), by firing of neuronal populations, leads to spontaneous and recurrent seizures1 . As 30% of TLE patients do not respond to pharmacotherapy2,3, it is necessary to search for alternatives. Mesenchymal stem cells (MSCs) are an attractive approach in this context, due to their less invasive character and its ability to modulate diseased niches. Objective: Analyze the gene expression related to the cation-chloride cotransporter KCC2 in TLE induced by pilocarpine model in rats. Design and Setting: Experimental study, Brain Institute of Rio Grande do Sul. Methods: MSCs were extracted from the bone marrow of Wistar rats, cultured and transplanted intravenously and intranasally into healthy and epileptic Wistar rats. Results: It was observed a decrease in the expression of KCC2 in the brain of the animals at 1-day post-transplant, which refers to a down-regulation, and an increase at 7 days post-transplant, representing an up-regulation. The loss of function of KCC2 decreases the release of chloride with difficulty in inhibiting GABAergic inhibition, resulting in hyperexcitability of neuronal circuits. In this case, MSCs can promote rearrangement in gamma-aminobutyric acid-mediated inhibition, reducing hyperexcitability and hypersynchronicity. Hence, KCC2 down-regulation is associated with epileptiform activity, while up-regulation can be related to the MSCs effects. Also, KCC2 expression showed a kind of pattern at 1-day post- transplant in both routes of administration, providing the possibility that KCC2 can be explored as a biomarker for epilepsy. Conclusion: KCC2 is an important target for epilepsy, as well MSCs have a modulatory function on the levels of the expression of this gene in animals induced to status epilepticus by pilocarpine.
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Lai, Yinglei. "The analysis of ordered changes of gene expression and gene-gene co-expression patterns." In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2011. http://dx.doi.org/10.1109/iccabs.2011.5729863.
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Xin Xu, Ying Lu, A. K. H. Tung, and Wei Wang. "Mining Shifting-and-Scaling Co-Regulation Patterns on Gene Expression Profiles." In 22nd International Conference on Data Engineering (ICDE'06). IEEE, 2006. http://dx.doi.org/10.1109/icde.2006.98.
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Salazar Moscoso, Marcela, Silvia Joly Ruiz Castellanos, Guillem Anglada Escudé, and Laia Ribas Cabezas. "Hypergravity induces changes in physiology, gene expression and epigenetics in zebrafish." In Symposium on Space Educational Activities (SSAE). Universitat Politècnica de Catalunya, 2022. http://dx.doi.org/10.5821/conference-9788419184405.044.
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All living organisms that inhabit Earth have evolved under a common value of gravity, which amounts to an acceleration of 9.81 m/s2 at mean sea level. Changes on it could cause important alterations that affect vital biological functions. The crescent interest in spatial exploration has opened the question of how exactly these changes in gravity would affect Earth life forms on space environments. This work is the result of a collaborative co-supervision of a master thesis between experts in the area of space sciences and biology, and it can serve as a case study for training experts in such interdisciplinary environments. In particular, we focus on the effect of gravity as a pressure factor in the development of zebrafish (Danio rerio) in the larval stage as a model organism using up-to-date (genomic and epigenetic) techniques. Given the high cost of any experiment in true low gravity (which would require a space launch), we performed an initial experiment in hypergravity to develop the methodologies and identify good (epi)genetic markers of the effect of gravity in our model organism. Previous studies in zebrafish have shown how alteration in gravity effects the development and the gene expression of important regulatory genes. For this study, we firstly customized a small laboratory scale centrifuge to study changes in fish physiology together with changes at molecular levels. We exposed zebrafish larvae from 0 to 6 days post fertilization to the simulated hypergravity (SHG) (100 rpm 3g). After 6 days of hypergravity exposition the larvae showed changes in their swimming and flotation patterns, and presented corporal alterations. Then, we assessed gene expression of genes implicated in important biological processes, (e.g., epigenetics), and an upregulation were observed when compared to the control. Taken together, these preliminary findings show how gravity alterations could affect some basic biological responses, and illustrate the potential of developing new science cases to be developed by students at postgraduate level (MSc and beyond) in a multidisciplinary environment
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Banerjee, P., B. Premanand, S. A. Wicher, R. D. Britt, C. M. Pabelick, Y. S. Prakash, and V. Sathish. "Identifying Asthma Genetic Signature Patterns by Mining Gene Co-Expression in Airway Smooth Muscle Cells." In American Thoracic Society 2021 International Conference, May 14-19, 2021 - San Diego, CA. American Thoracic Society, 2021. http://dx.doi.org/10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4496.
Full textReports on the topic "Gene co-expression pattern"
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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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Sessa, Guido, and Gregory Martin. role of FLS3 and BSK830 in pattern-triggered immunity in tomato. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604270.bard.
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Pattern-recognition receptors (PRRs) located on the plant cell surface initiate immune responses by perceiving conserved pathogen molecules known as pathogen-associated molecular patterns (PAMPs). PRRs typically function in multiprotein complexes that include transmembrane and cytoplasmickinases and contribute to the initiation and signaling of pattern-triggered immunity (PTI). An important challenge is to identify molecular components of PRR complexes and downstream signaling pathways, and to understand the molecular mechanisms that mediate their function. In research activities supported by BARD-4931, we studied the role of the FLAGELLIN SENSING 3 (FLS3) PRR in the response of tomato leaves to flagellin-derivedPAMPs and PTI. In addition, we investigated molecular properties of the tomato brassinosteroid signaling kinase 830 (BSK830) that physically interacts with FLS3 and is a candidate for acting in the FLS3 signaling pathway. Our investigation refers to the proposal original objectives that were to: 1) Investigate the role of FLS3 and its interacting proteins in PTI; 2) Investigate the role of BSK830 in PTI; 3) Examine molecular and phosphorylation dynamics of the FLS3-BSK830 interaction; 4) Examine the possible interaction of FLS3 and BSK830 with Pstand Xcveffectors. We used CRISPR/Cas9 techniques to develop plants carrying single or combined mutations in the FLS3 gene and in the paralogsFLS2.1 and FLS2.2 genes, which encode the receptor FLAGELLIN SENSING2 (FLS2), and analyzed their function in PTI. Domain swapping analysis of the FLS2 and FLS3 receptors revealed domains of the proteins responsible for PAMP detection and for the different ROS response initiated by flgII-28/FLS3 as compared to flg22/FLS2. In addition, in vitro kinase assays and point mutations analysis identified FLS2 and FLS3 domains required for kinase activity and ATP binding. In research activities on tomato BSK830, we found that it interacts with PRRs and with the co-receptor SERK3A and PAMP treatment affects part of these interactions. CRISPR/Cas9 bsk830 mutant plants displayed enhanced pathogen susceptibility and reduced ROS production upon PAMP treatment. In addition, BSK830 interacted with 8 Xanthomonastype III secreted effectors. Follow up analysis revealed that among these effectors XopAE is part of an operon, is translocated into plant cells, and displays E3 ubiquitinligase activity. Our investigation was also extended to other Arabidopsis and tomato BSK family members. Arabidopsis BSK5 localized to the plant cell periphery, interacted with receptor-like kinases, and it was phosphorylatedin vitro by the PEPR1 and EFRPRRs. bsk5 mutant plants displayed enhanced susceptibility to pathogens and were impaired in several, but not all, PAMP-induced responses. Conversely, BSK5 overexpression conferred enhanced disease resistance and caused stronger PTI responses. Genetic complementation suggested that proper localization, kinase activity, and phosphorylation by PRRs are critical for BSK5 function. BSK7 and BSK8 specifically interacted with the FLS2 PRR, their respective mutant plants were more susceptible to B. cinereaand displayed reduced flg22-induced responses. The tomato BSK Mai1 was found to interact with the M3KMAPKKK, which is involved in activation of cell death associated with effector-triggered immunity. Silencing of Mai1 in N. benthamianaplants compromised cell death induced by a specific class of immune receptors. In addition, co-expression of Mai1 and M3Kin leaves enhanced MAPKphosphorylation and cell death, suggesting that Mai1 acts as a molecular link between pathogen recognition and MAPK signaling. Finally, We identified the PP2C phosphatase Pic1 that acts as a negative regulator of PTI by interacting with and dephosphorylating the receptor-like cytoplasmickinase Pti1, which is a positive regulator of plant immunity. The results of this investigation shed new light on the molecular characteristics and interactions of components of the immune system of crop plants providing new knowledge and tools for development of novel strategies for disease control.
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Lichter, Amnon, Gopi K. Podila, and Maria R. Davis. Identification of Genetic Determinants that Facilitate Development of B. cinerea at Low Temperature and its Postharvest Pathogenicity. United States Department of Agriculture, March 2011. http://dx.doi.org/10.32747/2011.7592641.bard.
Full textAbstract:
Botrytis cinerea is the postharvest pathogen of many agricultural produce with table grapes, strawberries and tomatoes as major targets. The high efficiency with which B. cinerea causes disease on these produce during storage is attributed in part due to its exceptional ability to develop at very low temperature. Our major goal was to understand the genetic determinants which enable it to develop at low temperature. The specific research objectives were: 1. Identify expression pattern of genes in a coldenriched cDNA library. 2. Identify B. cinerea orthologs of cold-induced genes 3. Profile protein expression and secretion at low temperature on strawberry and grape supplemented media. 4. Test novel methods for the functional analysis of coldresponsive genes. Objective 1 was modified during the research because a microarray platform became available and it allowed us to probe the whole set of candidate genes according to the sequence of 2 strains of the fungus, BO5.10 and T4. The results of this experiment allowed us to validate some of our earlier observations which referred to genes which were the product of a SSH suppression-subtraction library. Before the microarray became available during 2008 we also analyzed the expression of 15 orthologs of cold-induced genes and some of these results were also validated by the microarray experiment. One of our goals was also to perform functional analysis of cold-induced genes. This goal was hampered for 3 years because current methodology for transformation with ‘protoplasts’ failed to deliver knockouts of bacteriordopsin-like (bR) gene which was our primary target for functional analysis. Consequently, we developed 2 alternative transformation platforms, one which involves an air-gun based technique and another which involves DNA injection into sclerotia. Both techniques show great promise and have been validated using different constructs. This contribution is likely to serve the scientific community in the near future. Using these technologies we generated gene knockout constructs of 2 genes and have tested there effect on survival of the fungus at low temperature. With reference to the bR genes our results show that it has a significant effect on mycelial growth of the B. cinerea and the mutants have retarded development at extreme conditions of ionic stress, osmotic stress and low temperature. Another gene of unknown function, HP1 is still under analysis. An ortholog of the yeast cold-induced gene, CCH1 which encodes a calcium tunnel and was shown to be cold-induced in B. cinerea was recently cloned and used to complement yeast mutants and rescue them from cold-sensitivity. One of the significant findings of the microarray study involves a T2 ribonuclease which was validated to be cold-induced by qPCR analysis. This and other genes will serve for future studies. In the frame of the study we also screened a population of 631 natural B. cinerea isolates for development at low temperature and have identified several strains with much higher and lower capacity to develop at low temperature. These strains are likely to be used in the future as candidates for further functional analysis. The major conclusions from the above research point to specific targets of cold-induced genes which are likely to play a role in cold tolerance. One of the most significant observations from the microarray study is that low temperature does not induce ‘general stress response in B. cinerea, which is in agreement to its exceptional capacity to develop at low temperature. Due to the tragic murder of the Co-PI Maria R. Davis and GopiPodila on Feb. 2010 it is impossible to deliver their contribution to the research. The information of the PI is that they failed to deliver objective 4 and none of the information which relates to objective 3 has been delivered to the PI before the murder or in a visit to U. Alabama during June, 2010. Therefore, this report is based solely on the IS data.
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Reisch, Bruce, Avichai Perl, Julie Kikkert, Ruth Ben-Arie, and Rachel Gollop. Use of Anti-Fungal Gene Synergisms for Improved Foliar and Fruit Disease Tolerance in Transgenic Grapes. United States Department of Agriculture, August 2002. http://dx.doi.org/10.32747/2002.7575292.bard.
Full textAbstract:
Original objectives . 1. Test anti-fungal gene products for activity against Uncinula necator, Aspergillus niger, Rhizopus stolonifer and Botrytis cinerea. 2. For Agrobacterium transformation, design appropriate vectors with gene combinations. 3. Use biolistic bombardment and Agrobacterium for transformation of important cultivars. 4. Characterize gene expression in transformants, as well as level of powdery mildew and Botrytis resistance in foliage of transformed plants. Background The production of new grape cultivars by conventional breeding is a complex and time-consuming process. Transferring individual traits via single genes into elite cultivars was proposed as a viable strategy, especially for vegetatively propagated crops such as grapevines. The availability of effective genetic transformation procedures, the existence of genes able to reduce pathogen stress, and improved in vitro culture methods for grapes, were combined to serve the objective of this proposal. Effective deployment of resistance genes would reduce production costs and increase crop quality, and several such genes and combinations were used in this project. Progress The efficacy of two-way combinations of Trichoderma endochitinase (CHIT42), synthetic peptide ESF12 and resveratrol upon the control of growth of Botrytis cinerea and Penicillium digitatum were evaluated in vitro. All pairwise interactions were additive but not synergistic. Per objective 2, suitable vectors with important gene combinations for Agrobacterium transformation were designed. In addition, multiple gene co-transformation by particle bombardment was also tested successfully. In New York, transformation work focused on cultivars Chardonnay and Merlot, while the technology in Israel was extended to 41B, R. 110, Prime, Italia, Gamay, Chardonnay and Velika. Transgenic plant production is summarized in the appendix. Among plants developed in Israel, endochitinase expression was assayed via the MuchT assay using material just 1-5 days after co-cultivation. Plants of cv. Sugraone carrying the gene coding for ESF12, a short anti-fungal lytic peptide under the control of the double 358 promoter, were produced. Leaf extracts of two plants showed inhibition zones that developed within 48 h indicating the inhibitory effect of the leaf extracts on the six species of bacteria. X fastidiosa, the causal organism of Pierce's disease, was very sensitive to leaf extracts from ESF12 transformed plants. Further work is needed to verify the agricultural utility of ESF12 transformants. In New York, some transformants were resistant to powdery mildew and Botrytis fruit rot. Major conclusions, solutions, achievements and implications The following scientific achievements resulted from this cooperative BARD project: 1. Development and improvement of embryogenesis and tissue culture manipulation in grape, while extending these procedures to several agriculturally important cultivars both in Israel and USA. 2. Development and improvement of novel transformation procedures while developing transformation techniques for grape and other recalcitrant species. 3. Production of transgenic grapevines, characterization of transformed vines while studying the expression patterns of a marker gene under the control of different promoter as the 35S CaMV in different part of the plants including flowers and fruits. 4. Expression of anti-fungal genes in grape: establishment of transgenic plants and evaluation of gene expression. Development of techniques to insert multiple genes. 5. Isolation of novel grape specific promoter to control the expression of future antimicrobial genes. It is of great importance to report that significant progress was made in not only the development of transgenic grapevines, but also in the evaluation of their potential for increased resistance to disease as compared with the non engineered cultivar. In several cases, increased disease resistance was observed. More research and development is still needed before a product can be commercialized, yet our project lays a framework for further investigations.
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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.
Full textAbstract:
To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.