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1.
Hypertension ; 74(2): 375-383, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31230546

RESUMO

Hypertensive disorders of pregnancy (HDP) are associated with low birth weight, shorter gestational age, and increased risk of maternal and offspring cardiovascular diseases later in life. The mechanisms involved are poorly understood, but epigenetic regulation of gene expression may play a part. We performed meta-analyses in the Pregnancy and Childhood Epigenetics Consortium to test the association between either maternal HDP (10 cohorts; n=5242 [cases=476]) or preeclampsia (3 cohorts; n=2219 [cases=135]) and epigenome-wide DNA methylation in cord blood using the Illumina HumanMethylation450 BeadChip. In models adjusted for confounders, and with Bonferroni correction, HDP and preeclampsia were associated with DNA methylation at 43 and 26 CpG sites, respectively. HDP was associated with higher methylation at 27 (63%) of the 43 sites, and across all 43 sites, the mean absolute difference in methylation was between 0.6% and 2.6%. Epigenome-wide associations of HDP with offspring DNA methylation were modestly consistent with the equivalent epigenome-wide associations of preeclampsia with offspring DNA methylation (R2=0.26). In longitudinal analyses conducted in 1 study (n=108 HDP cases; 550 controls), there were similar changes in DNA methylation in offspring of those with and without HDP up to adolescence. Pathway analysis suggested that genes located at/near HDP-associated sites may be involved in developmental, embryogenesis, or neurological pathways. HDP is associated with offspring DNA methylation with potential relevance to development.

2.
PLoS One ; 12(10): e0185682, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29016655

RESUMO

Chronic obstructive pulmonary disease (COPD) occurs typically in current or former smokers, but only a minority of people with smoking history develops the disease. Besides environmental factors, genetics is an important risk factor for COPD. However, the relationship between genetics, environment and phenotypes is not well understood. Sample sizes for genome-wide expression studies based on lung tissue have been small due to the invasive nature of sample collection. Increasing evidence for the systemic nature of the disease makes blood a good alternative source to study the disease, but there have also been few large-scale blood genomic studies in COPD. Due to the complexity and heterogeneity of COPD, examining groups of interacting genes may have more relevance than identifying individual genes. Therefore, we used Weighted Gene Co-expression Network Analysis to find groups of genes (modules) that are highly connected. However, module definitions may vary between individual data sets. To alleviate this problem, we used a consensus module definition based on two cohorts, COPDGene and ECLIPSE. We studied the relationship between the consensus modules and COPD phenotypes airflow obstruction and emphysema. We also used these consensus module definitions on an independent cohort (TESRA) and performed a meta analysis involving all data sets. We found several modules that are associated with COPD phenotypes, are enriched in functional categories and are overrepresented for cell-type specific genes. Of the 14 consensus modules, three were strongly associated with airflow obstruction (meta p ≤ 0.0002), and two had some association with emphysema (meta p ≤ 0.06); some associations were stronger in the case-control cohorts, and others in the cases-only subcohorts. Gene Ontology terms that were overrepresented included "immune response" and "defense response." The cell types whose type-specific genes were overrepresented in modules (p < 0.05) included natural killer cells, dendritic cells, and neutrophils. Together, this is the largest investigation of gene blood expression in COPD with 469 cases in COPDGene, ECLIPSE and TESRA combined, with 6267 genes common to all data sets. Additional, we have 42 and 83 controls in COPDGene and ECLIPSE, respectively.


Assuntos
Interação Gene-Ambiente , Genômica , Doença Pulmonar Obstrutiva Crônica/sangue , Enfisema Pulmonar/sangue , Epistasia Genética , Expressão Gênica/genética , Ontologia Genética , Humanos , Monócitos/metabolismo , Monócitos/patologia , Neutrófilos/metabolismo , Neutrófilos/patologia , Doença Pulmonar Obstrutiva Crônica/genética , Doença Pulmonar Obstrutiva Crônica/fisiopatologia , Enfisema Pulmonar/genética , Fatores de Risco , Espirometria
3.
Sci Rep ; 7(1): 3633, 2017 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-28623356

RESUMO

Human papillomavirus (HPV) infection distinctly alters methylation patterns in HPV-associated cancer. We have recently reported that HPV E7-dependent promoter hypermethylation leads to downregulation of the chemokine CXCL14 and suppression of antitumor immune responses. To investigate the extent of gene expression dysregulated by HPV E7-induced DNA methylation, we analyzed parallel global gene expression and DNA methylation using normal immortalized keratinocyte lines, NIKS, NIKS-16, NIKS-18, and NIKS-16∆E7. We show that expression of the MHC class I genes is downregulated in HPV-positive keratinocytes in an E7-dependent manner. Methylome analysis revealed hypermethylation at a distal CpG island (CGI) near the HLA-E gene in NIKS-16 cells compared to either NIKS cells or NIKS-16∆E7 cells, which lack E7 expression. The HLA-E CGI functions as an active promoter element which is dramatically repressed by DNA methylation. HLA-E protein expression on cell surface is downregulated by high-risk HPV16 and HPV18 E7 expression, but not by low-risk HPV6 and HPV11 E7 expression. Conversely, demethylation at the HLA-E CGI restores HLA-E protein expression in HPV-positive keratinocytes. Because HLA-E plays an important role in antiviral immunity by regulating natural killer and CD8+ T cells, epigenetic downregulation of HLA-E by high-risk HPV E7 may contribute to virus-induced immune evasion during HPV persistence.

4.
Mamm Genome ; 27(9-10): 469-84, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27401171

RESUMO

Gene co-expression analysis has proven to be a powerful tool for ascertaining the organization of gene products into networks that are important for organ function. An organ, such as the liver, engages in a multitude of functions important for the survival of humans, rats, and other animals; these liver functions include energy metabolism, metabolism of xenobiotics, immune system function, and hormonal homeostasis. With the availability of organ-specific transcriptomes, we can now examine the role of RNA transcripts (both protein-coding and non-coding) in these functions. A systems genetic approach for identifying and characterizing liver gene networks within a recombinant inbred panel of rats was used to identify genetically regulated transcriptional networks (modules). For these modules, biological consensus was found between functional enrichment analysis and publicly available phenotypic quantitative trait loci (QTL). In particular, the biological function of two liver modules could be linked to immune response. The eigengene QTLs for these co-expression modules were located at genomic regions coincident with highly significant phenotypic QTLs; these phenotypes were related to rheumatoid arthritis, food preference, and basal corticosterone levels in rats. Our analysis illustrates that genetically and biologically driven RNA-based networks, such as the ones identified as part of this research, provide insight into the genetic influences on organ functions. These networks can pinpoint phenotypes that manifest through the interaction of many organs/tissues and can identify unannotated or under-annotated RNA transcripts that play a role in these phenotypes.


Assuntos
Fígado/metabolismo , RNA/metabolismo , Animais , Feminino , Ontologia Genética , Sistema Imunitário/metabolismo , Desequilíbrio de Ligação , Fígado/imunologia , Escore Lod , Masculino , Locos de Características Quantitativas , RNA/genética , Ratos Endogâmicos SHR , Análise de Sequência de RNA , Transcriptoma
5.
J Invest Dermatol ; 135(8): 2068-2076, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25822579

RESUMO

In vitiligo, the autoimmune destruction of epidermal melanocytes produces white spots that can be repigmented by melanocyte precursors from the hair follicles, following stimulation with UV light. We examined by immunofluorescence the distribution of melanocyte markers (C-KIT, DCT, PAX3, and TYR) coupled with markers of proliferation (KI-67) and migration (MCAM) in precursors and mature melanocytes from the hair follicle and the epidermis of untreated and narrow band UVB (NBUVB)-treated human vitiligo skin. NBUVB was associated with a significant increase in the number of melanocytes in the infundibulum and with restoration of the normal melanocyte population in the epidermis, which was lacking in the untreated vitiligo. We identified several precursor populations (melanocyte stem cells, melanoblasts, and other immature phenotypes), and progressively differentiating melanocytes, some with putative migratory and/or proliferative abilities. The primary melanocyte germ was present in the untreated and treated hair follicle bulge, whereas a possible secondary melanocyte germ composed of C-KIT+ melanocytes was found in the infundibulum and interfollicular epidermis of UV-treated vitiligo. This is an exceptional model for studying the mobilization of melanocyte stem cells in human skin. Improved understanding of this process is essential for designing better treatments for vitiligo, ultimately based on melanocyte stem cell activation and mobilization.


Assuntos
Melanócitos/patologia , Células-Tronco/patologia , Raios Ultravioleta , Terapia Ultravioleta , Vitiligo/patologia , Vitiligo/radioterapia , Diferenciação Celular/efeitos da radiação , Movimento Celular/efeitos da radiação , Proliferação de Células/efeitos da radiação , Epiderme/metabolismo , Epiderme/patologia , Epiderme/efeitos da radiação , Folículo Piloso/metabolismo , Folículo Piloso/patologia , Folículo Piloso/efeitos da radiação , Humanos , Oxirredutases Intramoleculares/metabolismo , Melanócitos/metabolismo , Melanócitos/efeitos da radiação , Fator de Transcrição PAX3 , Fatores de Transcrição Box Pareados/metabolismo , Fenótipo , Proteínas Proto-Oncogênicas c-kit/metabolismo , Células-Tronco/metabolismo , Células-Tronco/efeitos da radiação , Vitiligo/metabolismo
6.
Nucleic Acids Res ; 42(17): e133, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25063298

RESUMO

microRNAs (miRNAs) regulate expression by promoting degradation or repressing translation of target transcripts. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using various algorithms. Several online resources provide collections of multiple databases but need to be imported into other software, such as R, for processing, tabulation, graphing and computation. Currently available miRNA target site packages in R are limited in the number of databases, types of databases and flexibility. We present multiMiR, a new miRNA-target interaction R package and database, which includes several novel features not available in existing R packages: (i) compilation of nearly 50 million records in human and mouse from 14 different databases, more than any other collection; (ii) expansion of databases to those based on disease annotation and drug microRNAresponse, in addition to many experimental and computational databases; and (iii) user-defined cutoffs for predicted binding strength to provide the most confident selection. Case studies are reported on various biomedical applications including mouse models of alcohol consumption, studies of chronic obstructive pulmonary disease in human subjects, and human cell line models of bladder cancer metastasis. We also demonstrate how multiMiR was used to generate testable hypotheses that were pursued experimentally.


Assuntos
Regiões 3' não Traduzidas , Bases de Dados de Ácidos Nucleicos , MicroRNAs/metabolismo , Software , Consumo de Bebidas Alcoólicas/genética , Animais , Antineoplásicos/farmacologia , Linhagem Celular Tumoral , Humanos , Camundongos , Metástase Neoplásica , Doença Pulmonar Obstrutiva Crônica/genética , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/patologia
7.
OMICS ; 17(12): 619-26, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24138069

RESUMO

Interleukin-16 (IL-16) is a multifunctional cytokine that has been associated with autoimmune and allergic diseases. To investigate comprehensively whether IL-16 is also associated with chronic obstructive pulmonary disease (COPD) and emphysema, we performed an integrated analysis of multiple "omics" data. Over 500 subjects participating in the COPDGene® study donated blood and were clinically characterized and genetically profiled. IL-16 mRNA levels were measured in peripheral blood mononuclear cells (PBMC), and protein levels were measured in fresh frozen plasma. A multivariate analysis found plasma IL-16 positively associated with age and body mass index, and negatively associated with current smoking and emphysema in the upper lobes. PBMC IL-16 expression was positively associated with gender and a composite score for airflow obstruction, emphysema, and gas trapping. Whole-genome expression quantitative trait locus (eQTL) analysis identified a novel IL-16 missense SNP (rs11556218) associated with lower IL-16 in plasma. In summary, an integrated "omics" analysis in a very large cohort identified an association between decreased IL-16 and emphysema and discovered a novel IL-16 cis-eQTL. Thus IL-16 plasma levels and IL-16 genotyping may be useful in a personalized medicine approach for lung disease.


Assuntos
Enfisema/sangue , Interleucina-16/sangue , Doença Pulmonar Obstrutiva Crônica/sangue , Corticosteroides/farmacologia , Corticosteroides/uso terapêutico , Idoso , Biomarcadores/sangue , Enfisema/tratamento farmacológico , Enfisema/genética , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Humanos , Leucócitos Mononucleares/metabolismo , Masculino , Pessoa de Meia-Idade , Fenótipo , Polimorfismo de Nucleotídeo Único , Proteômica , Doença Pulmonar Obstrutiva Crônica/tratamento farmacológico , Doença Pulmonar Obstrutiva Crônica/genética , Locos de Características Quantitativas , Fumar/efeitos adversos , Fumar/sangue
8.
PLoS One ; 8(9): e72751, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24019874

RESUMO

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and ß-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies.


Assuntos
Nitrogenase/química , Alinhamento de Sequência , Sequência de Aminoácidos , Modelos Moleculares , Nitrogenase/classificação , Homologia de Sequência de Aminoácidos , Relação Estrutura-Atividade
9.
Stat Med ; 32(23): 4057-70, 2013 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-23703923

RESUMO

Although genome-wide expression data sets from multiple species are now more commonly generated, there have been few studies on how to best integrate this type of correlated data into models. Starting with a single-species, linear regression model that predicts transcription factor binding sites as a case study, we investigated how best to take into account the correlated expression data when extending this model to multiple species. Using a multivariate regression model, we accounted for the phylogenetic relationships among the species in two ways: (i) a repeated-measures model, where the error term is constrained; and (ii) a Bayesian hierarchical model, where the prior distributions of the regression coefficients are constrained. We show that both multiple-species models improve predictive performance over the single-species model. When compared with each other, the repeated-measures model outperformed the Bayesian model. We suggest a possible explanation for the better performance of the model with the constrained error term.


Assuntos
Teorema de Bayes , Interpretação Estatística de Dados , Perfilação da Expressão Gênica/métodos , Modelos Lineares , Análise Multivariada , Filogenia , Animais , Proteínas de Choque Térmico/genética , Humanos , Saccharomyces/genética
10.
Am J Respir Cell Mol Biol ; 49(2): 316-23, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23590301

RESUMO

Although most cases of chronic obstructive pulmonary disease (COPD) occur in smokers, only a fraction of smokers develop the disease. We hypothesized distinct molecular signatures for COPD and emphysema in the peripheral blood mononuclear cells (PBMCs) of current and former smokers. To test this hypothesis, we identified and validated PBMC gene expression profiles in smokers with and without COPD. We generated expression data on 136 subjects from the COPDGene study, using Affymetrix U133 2.0 microarrays (Affymetrix, Santa Clara, CA). Multiple linear regression with adjustment for covariates (gender, age, body mass index, family history, smoking status, and pack-years) was used to identify candidate genes, and ingenuity pathway analysis was used to identify candidate pathways. Candidate genes were validated in 149 subjects according to multiplex quantitative real-time polymerase chain reaction, which included 75 subjects not previously profiled. Pathways that were differentially expressed in subjects with COPD and emphysema included those that play a role in the immune system, inflammatory responses, and sphingolipid (ceramide) metabolism. Twenty-six of the 46 candidate genes (e.g., FOXP1, TCF7, and ASAH1) were validated in the independent cohort. Plasma metabolomics was used to identify a novel glycoceramide (galabiosylceramide) as a biomarker of emphysema, supporting the genomic association between acid ceramidase (ASAH1) and emphysema. COPD is a systemic disease whose gene expression signatures in PBMCs could serve as novel diagnostic or therapeutic targets.


Assuntos
Gangliosídeos/sangue , Regulação da Expressão Gênica , Leucócitos Mononucleares/metabolismo , Doença Pulmonar Obstrutiva Crônica/sangue , Idoso , Idoso de 80 Anos ou mais , Biomarcadores/sangue , Feminino , Humanos , Masculino , Metabolômica/métodos , Pessoa de Meia-Idade , Doença Pulmonar Obstrutiva Crônica/diagnóstico , Enfisema Pulmonar/sangue , Enfisema Pulmonar/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real
11.
Bioinformatics ; 28(22): 2986-8, 2012 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-22954632

RESUMO

SUMMARY: comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher's exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications. AVAILABILITY: comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues. CONTACT: bpederse@gmail.com


Assuntos
Genômica/métodos , Software , Sondas de DNA/análise , Sondas de DNA/genética , Estudo de Associação Genômica Ampla , Humanos , Linguagens de Programação , Análise de Sequência de DNA
12.
Alcohol Clin Exp Res ; 36(9): 1519-29, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22530671

RESUMO

BACKGROUND: Prenatal alcohol exposure can result in fetal alcohol spectrum disorders (FASD). Not all women who consume alcohol during pregnancy have children with FASD and studies have shown that genetic factors can play a role in ethanol teratogenesis. We examined gene expression in embryos and placentae from C57BL/6J (B6) and DBA/2J (D2) mice following prenatal alcohol exposure. B6 fetuses are susceptible to morphological malformations following prenatal alcohol exposure while D2 are relatively resistant. METHODS: Male and female B6 and D2 mice were mated for 2 hours in the morning, producing 4 embryonic genotypes: true-bred B6B6 and D2D2, and reciprocal B6D2 and D2B6. On gestational day 9, dams were intubated with 5.8 g/kg ethanol, an isocaloric amount of maltose dextrin, or nothing. Four hours later, dams were sacrificed and embryos and placentae were harvested. RNA was extracted, labeled and hybridized to Affymetrix Mouse Genome 430 v2 microarray chips. Data were normalized, subjected to analysis of variance and tested for enrichment of gene ontology molecular function and biological process using the Database for Annotation, Visualization and Integrated Discovery (DAVID). RESULTS: Several gene classes were differentially expressed in B6 and D2 regardless of treatment, including genes involved in polysaccharide binding and mitosis. Prenatal alcohol exposure altered expression of a subset of genes, including genes involved in methylation, chromatin remodeling, protein synthesis, and mRNA splicing. Very few genes were differentially expressed between maltose-exposed tissues and tissues that received nothing, so we combined these groups for comparisons with ethanol. While we observed many expression changes specific to B6 following prenatal alcohol exposure, none were specific for D2. Gene classes up- or down-regulated in B6 following prenatal alcohol exposure included genes involved in mRNA splicing, transcription, and translation. CONCLUSIONS: Our study identified several classes of genes with altered expression following prenatal alcohol exposure, including many specific for B6, a strain susceptible to ethanol teratogenesis. Lack of strain specific effects in D2 suggests there are few gene expression changes that confer resistance. Future studies will begin to analyze functional significance of the expression changes.


Assuntos
Expressão Gênica/efeitos dos fármacos , Efeitos Tardios da Exposição Pré-Natal/genética , Análise de Variância , Animais , Depressores do Sistema Nervoso Central/toxicidade , Etanol/toxicidade , Feminino , Transtornos do Espectro Alcoólico Fetal/genética , Regulação da Expressão Gênica no Desenvolvimento/efeitos dos fármacos , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos DBA , Análise em Microsséries , Placenta/metabolismo , Reação em Cadeia da Polimerase , Gravidez , RNA/biossíntese , RNA/genética , Especificidade da Espécie , Teratogênios/toxicidade
13.
PLoS One ; 6(11): e26105, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-22069446

RESUMO

Transcriptional regulation depends upon the binding of transcription factor (TF) proteins to DNA in a sequence-dependent manner. Although many experimental methods address the interaction between DNA and proteins, they generally do not comprehensively and accurately assess the full binding repertoire (the complete set of sequences that might be bound with at least moderate strength). Here, we develop and evaluate through simulation an experimental approach that allows simultaneous high-throughput quantitative analysis of TF binding affinity to thousands of potential DNA ligands. Tens of thousands of putative binding targets can be mixed with a TF, and both the pre-bound and bound target pools sequenced. A hierarchical Bayesian Markov chain Monte Carlo approach determines posterior estimates for the dissociation constants, sequence-specific binding energies, and free TF concentrations. A unique feature of our approach is that dissociation constants are jointly estimated from their inferred degree of binding and from a model of binding energetics, depending on how many sequence reads are available and the explanatory power of the energy model. Careful experimental design is necessary to obtain accurate results over a wide range of dissociation constants. This approach, which we call Simultaneous Ultra high-throughput Ligand Dissociation EXperiment (SULDEX), is theoretically capable of rapid and accurate elucidation of an entire TF-binding repertoire.


Assuntos
Teorema de Bayes , DNA/metabolismo , Regulação da Expressão Gênica , Cadeias de Markov , Fatores de Transcrição/metabolismo , Sítios de Ligação , DNA/genética , Humanos , Ligação Proteica , Fatores de Transcrição/genética
14.
Addict Biol ; 16(3): 393-404, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21054686

RESUMO

The identification of genes that contribute to polygenic (complex) behavioral phenotypes is a key goal of current genetic research. One approach to this goal is to combine gene expression information with genetic information, i.e. to map chromosomal regions that regulate gene expression levels. This approach has been termed 'genetical genomics', and, when used in conjunction with the identification of genomic regions (QTLs) that regulate the complex physiological trait under investigation, provides a strong basis for candidate gene discovery. In this paper, we describe the implementation of the genetical genomic/phenotypic approach to identify candidate genes for sensitivity to the analgesic effect of morphine in BXD recombinant inbred mice. Our analysis was performed 'in silico', using an online interactive resource called PhenoGen (http://phenogen.ucdenver.edu). We describe in detail the use of this resource, which identified a set of candidate genes, some of whose products regulate the cellular localization and activity of the mu opiate receptor. The results demonstrate how PhenoGen can be used to identify a novel set of genes that can be further investigated for their potential role in pain, morphine analgesia and/or morphine tolerance.


Assuntos
Analgésicos Opioides/farmacologia , Bases de Dados Genéticas , Perfilação da Expressão Gênica/métodos , Estudos de Associação Genética/métodos , Genoma , Internet , Morfina/farmacologia , Limiar da Dor/efeitos dos fármacos , Animais , Encéfalo/metabolismo , Mapeamento Encefálico , Expressão Gênica/genética , Camundongos , Camundongos Endogâmicos , Análise de Sequência com Séries de Oligonucleotídeos , Fenótipo , Locos de Características Quantitativas/genética , Desenho de Programas de Computador , Sensação Térmica/efeitos dos fármacos , Sensação Térmica/genética
15.
Behav Genet ; 41(4): 625-8, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21184165

RESUMO

Our laboratory has developed an online interactive resource called PhenoGen ( http://phenogen.ucdenver.edu ) which provides an archive of brain and other organ gene expression data from a panel of 20 common inbred mouse strains, and three recombinant inbred (RI) panels (two mouse and one rat). DNA microarray data can also be uploaded to the site where numerous analytical tools can be implemented. An important advantage to the archived data is that each array represents data from a single animal and each strain was sampled 4-7 times, providing an estimate of genetic variance (heritability) of individual transcript levels. These panels also allow genetic mapping of expression QTLs. Overlap of eQTLs with phenotypic QTLs provides a powerful approach to candidate gene identification. These methods are briefly described here and we encourage the use of our site for both scientific discovery and as a teaching tool in quantitative genetics.


Assuntos
Genoma , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Animais , Mapeamento Cromossômico , Cruzamentos Genéticos , Perfilação da Expressão Gênica , Genética Comportamental , Internet , Camundongos , Modelos Genéticos , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , RNA Mensageiro/metabolismo , Software
16.
Stat Appl Genet Mol Biol ; 9: Article29, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20812907

RESUMO

High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.


Assuntos
Drosophila/genética , Perfilação da Expressão Gênica/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Animais , Sítios de Ligação , Interpretação Estatística de Dados , Fatores de Transcrição/genética
17.
Stat Appl Genet Mol Biol ; 8: Article 36, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-19799555

RESUMO

De novo identification of transcription factor binding sites (TFBS) is a challenging computational problem because TFBSs are relatively short sequences buried in long genomic regions. Earlier methods incorporated genome-wide expression data and promoter sequences into a linear-model framework, regressing expression on counts of putative TFBSs in promoters for a single species. More recently, it has been shown that examining sequence data across multiple species improves the prediction of TFBSs. In this work, we describe an extension of the single-species, linear-model framework for the analysis of paired cross-species sequence and expression data. A repeated measures model for gene-expression measurements across species is used, accounting for phylogenetic relationships among species through the error covariance structure. This multiple-species algorithm is applied to a data set of four yeast species grown under heat-shock conditions and comparisons are made to the single species algorithm. Using evaluations based on transcription factor binding strength and an independent source of expression data, we find the multiple species results show an improvement in the prediction of TFBS.


Assuntos
Expressão Gênica , Saccharomyces/genética , Fatores de Transcrição/genética , Algoritmos , Sítios de Ligação , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Modelos Lineares , Estresse Oxidativo , Filogenia , Saccharomyces/química , Análise de Sequência de DNA , Fatores de Transcrição/química
18.
PLoS One ; 4(7): e6136, 2009 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-19578539

RESUMO

BACKGROUND: This study examines the structural features and phylogeny of the alpha subunits of 69 full-length NifD (MoFe subunit), VnfD (VFe subunit), and AnfD (FeFe subunit) sequences. METHODOLOGY/PRINCIPAL FINDINGS: The analyses of this set of sequences included BLAST scores, multiple sequence alignment, examination of patterns of covariant residues, phylogenetic analysis and comparison of the sequences flanking the conserved Cys and His residues that attach the FeMo cofactor to NifD and that are also conserved in the alternative nitrogenases. The results show that NifD nitrogenases fall into two distinct groups. Group I includes NifD sequences from many genera within Bacteria, including all nitrogen-fixing aerobes examined, as well as strict anaerobes and some facultative anaerobes, but no archaeal sequences. In contrast, Group II NifD sequences were limited to a small number of archaeal and bacterial sequences from strict anaerobes. The VnfD and AnfD sequences fall into two separate groups, more closely related to Group II NifD than to Group I NifD. The pattern of perfectly conserved residues, distributed along the full length of the Group I and II NifD, VnfD, and AnfD, confirms unambiguously that these polypeptides are derived from a common ancestral sequence. CONCLUSIONS/SIGNIFICANCE: There is no indication of a relationship between the patterns of covariant residues specific to each of the four groups discussed above that would give indications of an evolutionary pathway leading from one type of nitrogenase to another. Rather the totality of the data, along with the phylogenetic analysis, is consistent with a radiation of Group I and II NifDs, VnfD and AnfD from a common ancestral sequence. All the data presented here strongly support the suggestion made by some earlier investigators that the nitrogenase family had already evolved in the last common ancestor of the Archaea and Bacteria.


Assuntos
Sequência Conservada , Molibdoferredoxina/química , Nitrogenase/química , Oxirredutases/química , Sequência de Aminoácidos , Dados de Sequência Molecular , Filogenia
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