dna methylation genotype and gene expression

... both methylation and expression To better understand the role of genetic variation in controlling DNA methylation variation, and its resulting effects on gene expression variation, we studied DNA ... Second gene−expression quartile Third gene−expression quartile Highest gene−expression quartile (b) Methylation at the TSS Figure 2 DNA methylation is negatively correlated with gene expression ... [32] DNA methylation correlates with transcription and histone modifications Methylation has long been implicated in the regulation of gene expression To examine the role of methylation in gene expression...

Ngày tải lên: 09/08/2014, 22:23

... subnetwork- and gene-level overlap 73 4.3.2 Precision and recall 79 4.3.3 Comparing expression-difference, rank-difference t-test and Wilcoxon-like test 80 4.3.4 Comparing unweighted and weighted ... disease-related genes 2 1.1.2 A tool for clinical diagnosis 4 1.2 Research challenge and contributions 6 1.3 Thesis organization 7 2 Related Work and Definitions 9 2.1 Background on gene-expression ... differentially-expressed genes in BCR-ABL/E2A-PBX1 dataset 66 4.5 Consistency of subnetworks and their genes in DMD/NOR dataset 73 Trang 144.6 Consistency of subnetworks and their genes in ALL/AML...

Ngày tải lên: 09/09/2015, 10:15

... design and integration of DNA sequence databases, the alignment of protein and DNA sequences, the assembly of DNA fragments into genomic maps, and the prediction of the function of a gene based ... of gene expression or transcripts level is required for understanding gene regulatory networks High throughput analysis of differential gene expression is a powerful tool to identify new genes ... Expression profile of OsRIP genes upon ABA treatment and undervarious biotic and abiotic stresses 75 3.3 WRKY Gene Family of transcription factors 3.3.2 Genome wide identification of WRKY gene...

Ngày tải lên: 14/09/2015, 14:12

... understanding of thegenetic pathways that regulate pluripotency, self-renewal and differentiation Identifying “master regulators” and as yet undiscovered genes that control hESC self-renewal andimmortality ... organogenesis or somaticembryogenesis by tissue culture In somatic embryogenesis, regenerating tissuerecapitulates embryonic development while in organogenesis, organs form directlywithout embryogenesis ... with upregulated DNA repair, protein folding, ubiquitination, anddetoxifier systems, v) a remodeled chromatin, acted upon by DNA helicases, DNAmethylases, and histone deacetylases and vi) translation...

Ngày tải lên: 16/09/2015, 15:55

... % of RefSeq genes, with an average of 17 CpG sites per gene While the role of DNA methylation in promoter and CpG island is widely accepted, the importance of DNA methylation in gene body or ... correlates with gene expression, the role of DNA methylation in the gene body and intragenic regions is still under investigation Some recent papers report a direct correlation between DNA methylation ... DNA methylation in the gene body and associated gene expression [10–12].Accurate assessment of DNA methylation is critical for ing accurate data and for better understanding of disease, cellular...

Ngày tải lên: 14/05/2019, 14:35

... and de unigene library of fruit and seed of Davidia Moreover, we identified the differentially expressed genes (DEGs) between normal and abortive seeds Genes involved in cell proliferation, DNA ... seeds Among the DEGs, all genes encoding DNA polymerasealpha catalytic subunit, DNA replication licensing factor,ATP-dependent DNA helicase, DNA topoisomerase, Fig 5 Expression pattern of DEGs ... de-creased expression and two of them showed increasedexpression Seven genes encoding auxin response factorwere found; five of them were down-regulated and two syn-of them were up-regulated Three genes...

Ngày tải lên: 22/05/2020, 04:16

... that upon AtCHR23 over-expression also the variation of gene expression is increased in a subset of genes that associate with environmental stress The larger variation of gene expression is confirmed ... AtCHR23 over-expression is notably quantitative both in terms of growth phenotype as in terms of gene expression The over-expression of AtCHR23 increases the variability of growth and expression ... The larger expression differenceshown by the top 1% of the genes in wild-type (195 genes) was taken as cut-off for variability and used to se-lect the number (and identity) of the genes in all...

Ngày tải lên: 27/05/2020, 01:33

... transcript abundance in the CJ06 and TN1 plants Upon WBPH infestation, 432 genes in CJ06 and 257 genes in TN1 were significantly up-regulated, while 802 genes in CJ06 and 398 genes in TN1 were significantly ... levels of expression in TN1 Some of the differentially expressed genes in CJ06 and TN1 are listed in Table 3 Genes related to defense, second-ary metabolism, transcription, and cell and hormone ... important role in WBPH resistance Expression patterns of the candidate genes in the 122-kb region Special attention was paid to the expression patterns of the candidate genes in the 122-kb region The...

Ngày tải lên: 27/05/2020, 02:02

... ER, PR and Ki67 and mRNA gene expression. Methods Immunohistochemistry comparison between core biopsy and resection specimens To re-evaluate the consistency of staining between core biopsy and breast ... 2987 gene sets collectively representing most known biological and metabolic pathways in Gene Ontology (GO, http:// www.geneontology.org) To be included, a GO gene set required a minimum of 10 and ... Scotland Authors’ contributions SH, PGR, SMT and AMT conceived and designed the studies; LBJ and CP provided expert pathology for the IHC; TI and LP provided microarray analytical support; SH and...

Ngày tải lên: 20/09/2020, 18:06

... of DNA methylation and aCGH experiments, performed the experiments, DNA methylation and aCGH data analysis and interpretation, drafted and revised the manuscript TM participated in analyzing and ... gen-omic DNA of samples and female reference DNA (a normal control DNA) (Promega, Madison, WI) were first fragmented for 30 s at 95 °C and 30 min at 95 °C re-spectively, and then the reference and ... have closely related DNA methylation patterns and profiles In this study, we set out to compare DNA methylation profiling and aCGH as tools to distinguish between de novo and recurrent tumours...

Ngày tải lên: 28/09/2020, 09:25

... both proliferation-related gene expression and associated intrinsic subtypes (Basal-like and Luminal B), was negatively associated with estrogen-related gene expression and associated intrinsic ... underweight and tumor gene expression is largely unknown Strengths of this study include being the first to examine the relationship between obesity around breast cancer diagnosis and tumor gene expression, ... have breast tumors with greater expression of proliferation genes and lesser expression ofESR1, and pos-sible increased odds of being diagnosed with Basal-like and Luminal B tumor subtypes These...

Ngày tải lên: 30/09/2020, 12:46

... R T I C L E Open AccessYanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis Mohamed K Gunady1,2, Stephen M Mount3and Héctor Corrada Bravo1,2* Abstract ... two specific expression analyses – alternative splicing and gene differential expression – without the need of a transcript quantification step Our experiments based on simulated and experimental ... effect of genetic or environmental changes on gene expression Transcript-level analysis and abundance estimation can play a central role in both fine-grained analysis of local splicing events and global...

Ngày tải lên: 25/11/2020, 12:41

... metadata information on the genes and metabolites 2) Filter data: gene expression and metabolomics data are optionally filtered by gene and metabolite abundances and missing values 3) Run IntLIM: ... unique genes and 155 gene-metabolites of which 35 are unidentified) with relatively high correlations in tumor samples and mostly negative correlations in gene-metabolite pairs (479 unique genes and ... probes mapped to a single gene This re-sulted in 20,254 genes measured in tumor and non-tumor tissue After removing the 10% lowest expression genes, we analyzed 18,228 genes With this breast cancer...

Ngày tải lên: 25/11/2020, 15:16

... studied and syntenic blocks constructed Homologs that are candidates for being PM susceptibility genes were inferred by phylogenetic relationships with functionally characterized MLO genes and, ... apple [8], and P leucotricha strains able to breakdown Pl-1 and Pl-2, two major PM R-genes of apple [9] An alternative to the use of R-genes is based on plant susceptibility genes (S-genes), defined ... VII and VIII (not shown) Four apple MLO homologs (MdMLO5, MdMLO7, MdMLO11 and MdMLO19) and three MLO homologs from peach (PpMLO1, PpMLO3 and PpMLO4), apricot (PaMLO1, PaMLO3 and PaMLO4) and woodland...

Ngày tải lên: 01/11/2022, 09:02

... Ufret-Vincenty1* Abstract goal was to study the spatial and temporal distribution, the phenotype, and gene expression of subretinal MG/MΦ in mice with normal retinas and compare them to mice with known retinal ... mutation in the Crb1 gene (which, in the presence of yet unidentified permissive/modifying genes, leads to a retinal degeneration), and documented their fundus appearance and the change with aging ... distribution, and pheno-type/morphology of subretinal MG/MΦ in C57BL/6N versus C57BL/6J mice We also analyzed the expression of complement activation and inflammation-related genes in the retina and in...

Ngày tải lên: 01/11/2022, 09:49

... localizes in the nucleus and binds to and regulates basal expression via HSEs of target genes [26] Deletion of the HSF gene is lethal to cells, even at physiological temperatures The genes targeted by ... levels of gene expression and probably in distinguishing target genes by mammalian HSFs In response to stress, yeast HSF bound to an HSE recruits the general transcription factors and Pol II ... of the chicken HSF3 gene; however, the human HSF3 gene is a pseudogene [41] Mouse HSF3 translocates into the nucleus upon heat shock and may activate nonclassical heat shock genes, but does not...

Ngày tải lên: 18/02/2014, 04:20

... of gene expression of a certain gene (X) normalized to the mean of the control gene PDI1 and the steady-state sample of the chemostat culture (Eqns and 7) We have normalized to steady state and ... versus gene expression before examining specific metabolites Earlier regulation analysis studies of nitrogen starvation in yeast revealed mixed and diverse regulation [9] Both gene expression and ... subtle and cannot be attributed to a single process in the gene expression cascade Discussion Time-dependent regulation analysis quantifies the relative importance of metabolism and gene expression...

Ngày tải lên: 18/02/2014, 06:20

... oxidative stress and alterations of mitochondria and gene expression in brown and white adipose tissues Particle and Fibre Toxicology 2011 8:20 Submit your next manuscript to BioMed Central and take ... family of genes, and it is recognized as WAT-specific marker in primary adipocyte cultures [29] DPT serves as a good gene marker for white adipogenesis and can be seen as a reference gene for ... differences in the gene expressions of Hoxc9 or Igfbp3 in the WAT, neither was the gene expression of Dpt in BAT or WAT Xu et al Particle and Fibre Toxicology 2011, 8:20 http://www.particleandfibretoxicology.com/content/8/1/20...

Ngày tải lên: 06/03/2014, 19:20

... and hnRNP U Moreover, it has been shown that actin, hnRNP U and PCAF associate with the Ser2 ⁄ 5and Ser2-phosphorylated Pol II C-terminal domain hnRNP U and PCAF are present at the promoter and ... activation and actin polymerization [55] Recently, MRTF-A and -B were shown to serve as a link between STARS and SRF In NIH 3T3 cells cotransfected with expression plasmids encoding MRTFs and STARS, ... includes lung and liver [58] Both ABLIM-2 and -3 strongly bind F-actin and colocalize with actin stress fibers The interaction of STARS with ABLIM-2 and -3 was confirmed by coimmunoprecipitation and further...

Ngày tải lên: 07/03/2014, 01:20

... NODAL, and ACVR2B [32-35] The node containing genes upregulated in EB (node C) included the genes HAND1, HOXA1, HOXB2, MSX1, MSX2, MEIS1, FGF9 and FREM1 which are involved in morphogenesis and development ... miR-130a and miR-190, the difference in their expression between EB and hES cells and between EB and adult cells were significant (P < 0.05) The difference in expression of miR-17-5p between EB and ... differences in expression of these miRNA expression between adult cells and hES cells and between adult cells and EB were significant (P < 0.05) Of note, the expression levels of let-7b and let-7i...

Ngày tải lên: 18/06/2014, 15:20