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UnlabelledWe introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. The results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application.Availabilityhttp://www.genmapp.org/go_elite

Anaplastic lymphoma kinase (Alk) is a gene expressed in the nervous system that encodes a receptor tyrosine kinase commonly known for its oncogenic function in various human cancers. We have determined that Alk is associated with altered behavioral responses to ethanol in the fruit fly Drosophila melanogaster, in mice, and in humans. Mutant flies containing transposon insertions in dAlk demonstrate increased resistance to the sedating effect of ethanol. Database analyses revealed that Alk expression levels in the brains of recombinant inbred mice are negatively correlated with ethanol-induced ataxia and ethanol consumption. We therefore tested Alk gene knockout mice and found that they sedate longer in response to high doses of ethanol and consume more ethanol than wild-type mice. Finally, sequencing of human ALK led to the discovery of four polymorphisms associated with a low level of response to ethanol, an intermediate phenotype that is predictive of future alcohol use disorders (AUDs). These results suggest that Alk plays an evolutionary conserved role in ethanol-related behaviors. Moreover, ALK may be a novel candidate gene conferring risk for AUDs as well as a potential target for pharmacological intervention.

The role of alternative splicing in self-renewal, pluripotency and tissue lineage specification of human embryonic stem cells (hESCs) is largely unknown. To better define these regulatory cues, we modified the H9 hESC line to allow selection of pluripotent hESCs by neomycin resistance and cardiac progenitors by puromycin resistance. Exon-level microarray expression data from undifferentiated hESCs and cardiac and neural precursors were used to identify splice isoforms with cardiac-restricted or common cardiac/neural differentiation expression patterns. Splice events for these groups corresponded to the pathways of cytoskeletal remodeling, RNA splicing, muscle specification, and cell cycle checkpoint control as well as genes with serine/threonine kinase and helicase activity. Using a new program named AltAnalyze (http://www.AltAnalyze.org), we identified novel changes in protein domain and microRNA binding site architecture that were predicted to affect protein function and expression. These included an enrichment of splice isoforms that oppose cell-cycle arrest in hESCs and that promote calcium signaling and cardiac development in cardiac precursors. By combining genome-wide predictions of alternative splicing with new functional annotations, our data suggest potential mechanisms that may influence lineage commitment and hESC maintenance at the level of specific splice isoforms and microRNA regulation.

BackgroundMicroarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses.ResultsTo address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages.ConclusionGenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.

BackgroundThe ability of a neuron to regenerate functional connections after injury is influenced by both its intrinsic state and also by extrinsic cues in its surroundings. Investigations of the transcriptional changes undergone by neurons during in vivo models of injury and regeneration have revealed many transcripts associated with these processes. Because of the complex milieu of interactions in vivo, these results include not only expression changes directly related to regenerative outgrowth and but also unrelated responses to surrounding cells and signals. In vitro models of neurite outgrowth provide a means to study the intrinsic transcriptional patterns of neurite outgrowth in the absence of extensive extrinsic cues from nearby cells and tissues.ResultsWe have undertaken a genome-wide study of transcriptional activity in embryonic superior cervical ganglia (SCG) and dorsal root ganglia (DRG) during a time course of neurite outgrowth in vitro. Gene expression observed in these models likely includes both developmental gene expression patterns and regenerative responses to axotomy, which occurs as the result of tissue dissection. Comparison across both models revealed many genes with similar gene expression patterns during neurite outgrowth. These patterns were minimally affected by exposure to the potent inhibitory cue Semaphorin3A, indicating that this extrinsic cue does not exert major effects at the level of nuclear transcription. We also compared our data to several published studies of DRG and SCG gene expression in animal models of regeneration, and found the expression of a large number of genes in common between neurite outgrowth in vitro and regeneration in vivo.ConclusionMany gene expression changes undergone by SCG and DRG during in vitro outgrowth are shared between these two tissue types and in common with in vivo regeneration models. This suggests that the genes identified in this in vitro study may represent new candidates worthy of further study for potential roles in the therapeutic regrowth of neuronal connections.

BackgroundHigh-throughput mutagenesis of the mammalian genome is a powerful means to facilitate analysis of gene function. Gene trapping in embryonic stem cells (ESCs) is the most widely used form of insertional mutagenesis in mammals. However, the rules governing its efficiency are not fully understood, and the effects of vector design on the likelihood of gene-trapping events have not been tested on a genome-wide scale.Methodology/principal findingsIn this study, we used public gene-trap data to model gene-trap likelihood. Using the association of gene length and gene expression with gene-trap likelihood, we constructed spline-based regression models that characterize which genes are susceptible and which genes are resistant to gene-trapping techniques. We report results for three classes of gene-trap vectors, showing that both length and expression are significant determinants of trap likelihood for all vectors. Using our models, we also quantitatively identified hotspots of gene-trap activity, which represent loci where the high likelihood of vector insertion is controlled by factors other than length and expression. These formalized statistical models describe a high proportion of the variance in the likelihood of a gene being trapped by expression-dependent vectors and a lower, but still significant, proportion of the variance for vectors that are predicted to be independent of endogenous gene expression.Conclusions/significanceThe findings of significant expression and length effects reported here further the understanding of the determinants of vector insertion. Results from this analysis can be applied to help identify other important determinants of this important biological phenomenon and could assist planning of large-scale mutagenesis efforts.

BackgroundEarly transition to labor remains a major cause of infant mortality, yet the causes are largely unknown. Although several marker genes have been identified, little is known about the underlying global gene expression patterns and pathways that orchestrate these striking changes.ResultsWe performed a detailed time-course study of over 9,000 genes in mouse myometrium at defined physiological states: non-pregnant, mid-gestation, late gestation, and postpartum. This dataset allowed us to identify distinct patterns of gene expression that correspond to phases of myometrial 'quiescence', 'term activation', and 'postpartum involution'. Using recently developed functional mapping tools (HOPACH (hierarchical ordered partitioning and collapsing hybrid) and GenMAPP 2.0), we have identified new potential transcriptional regulatory gene networks mediating the transition from quiescence to term activation.ConclusionsThese results implicate the myometrium as an essential regulator of endocrine hormone (cortisol and progesterone synthesis) and signaling pathways (cyclic AMP and cyclic GMP stimulation) that direct quiescence via the transcriptional upregulation of both novel and previously associated regulators. With term activation, we observe the upregulation of cytoskeletal remodeling mediators (intermediate filaments), cell junctions, transcriptional regulators, and the coordinate downregulation of negative control checkpoints of smooth muscle contractile signaling. This analysis provides new evidence of multiple parallel mechanisms of uterine contractile regulation and presents new putative targets for regulating myometrial transformation and contraction.

MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP http://www.GenMAPP.org. The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged.

BackgroundSkeletal muscle remodeling is a critical component of an organism's response to environmental changes. Exercise causes structural changes in muscle and can induce phase shifts in circadian rhythms, fluctuations in physiology and behavior with a period of around 24 hours that are maintained by a core clock mechanism. Both exercise-induced remodeling and circadian rhythms rely on the transcriptional regulation of key genes.ResultsWe used DNA microarrays to determine the effects of resistance exercise (RE) on gene regulation in biopsy samples of human quadriceps muscle obtained 6 and 18 hours after an acute bout of isotonic exercise with one leg. We also profiled diurnal gene regulation at the same time points (2000 and 0800 hours) in the non-exercised leg. Comparison of our results with published circadian gene profiles in mice identified 44 putative genes that were regulated in a circadian fashion. We then used quantitative PCR to validate the circadian expression of selected gene orthologs in mouse skeletal muscle.ConclusionsThe coordinated regulation of the circadian clock genes Cry1, Per2, and Bmal1 6 hours after RE and diurnal genes 18 hours after RE in the exercised leg suggest that RE may directly modulate circadian rhythms in human skeletal muscle.

Many primary care physicians are not happy with some of the financial incentives they receive from their managed care organizations. A survey of 766 primary care physicians in California found that 38% received some type of bonus. Fifty-seven percent said they were being rewarded for limiting referrals and 17% of these physicians believed this compromised patient care. Three-quarters were pressured to see more patients and 24% of them believed this compromised patient care.

Physicians who serve large numbers of uninsured patients may be denied participation in a managed care organization. Researchers surveyed 947 primary care physicians to see how many had been excluded from participation in managed care. Twenty-two percent had been denied a contract or terminated from one with a managed care organization. Those in solo practice were most likely to denied a contract and were those who served many uninsured patients and non-white patients., Context.--Little is known about the problems physicians may be encountering in gaining access to managed care networks and whether the process used by managed care plans to select physicians is discriminatory. Objective.--To investigate the incidence and predictors of denials or terminations of physicians' managed care contracts and the impact these denials and terminations had on primary care physicians' involvement with managed care. Design.--Cross-sectional mail survey of a probability sample of primary care physicians. Setting.--A total of 13 large urban counties in California. Participants.--Primary care physicians (family practice, internal medicine, obstetrics and gynecology, or pediatrics) who work in off ice-based practice. Main Outcome Measures.--Denial or termination from a contract with an independent practice association (IPA) or health maintenance organization (HMO) and managed care contracts. Results.--Of the 947 respondents (response rate, 71%), 520 were involved in office-based primary care. After adjusting for sampling and response rate, 22% of primary care physicians had been denied or terminated from a contract with an IPA or HMO, but 87% of office-based primary care physicians had at least 1 IPA or direct HMO contract. Solo practice was the strongest predictor of having experience a denial or termination and of having neither an IPA nor a direct HMO contract. Physician age, sex, and race did not predict the level of involvement with managed care. However, physicians' patient demographics were associated with managed care participation; physicians in managed care had significantly lower percentages of uninsured and nonwhite patients in their practices. Physicians experiencing a denial or termination had fewer capitated patients in their practice. Conclusions.--Denials and terminations, although relatively common, do not preclude most primary care physicians from participating in managed care. Managed care selective contracting does not appear to be systematically discriminatory based on physician characteristics, but it may be biased against physicians who provide greater amounts of care to the underserved. JAMA. 1998;279:675-679

The dismantling of affirmative action programs may reduce access to health care for the poor and minorities. Researchers used Census data to analyze the racial distribution of 394 California communities and data from the American Medical Association to determine the number of physicians practicing in those areas. The lowest number of physicians per 100,000 people occurred in areas with large numbers of black and Hispanic residents. This was true in urban and rural areas. A survey of 718 primary care physicians in 51 California communities found that black physicians practiced in areas with a high percentage of Blacks and cared for almost six times as many Blacks as other physicians. They also cared for more Medicaid patients than other physicians. Hispanic physicians practiced in areas with a high percentage of Hispanics and cared for almost three times as many Hispanics as other physicians. They also cared for more uninsured patients. Black and Hispanic physicians may be filling an important role in underserved areas.

About half of the physicians nationwide appear to remain in the state where they received their graduate medical education. Researchers drew data from two national physician databases, and analyzed a sample of 97,947 physicians. Between 1980 and 1992, 51% percent of physicians practiced in the state where they received their graduate education, although the rates ranged from 71% in California to 6% in Nevada. The states which trained the largest number of physicians, New York and Massachusetts, had average retention rates. California and Texas, which train far fewer physicians, had high retention rates. General practice physicians were more likely than specialists to stay in the state where they received their graduate medical education. National policies should be formulated to distribute physicians more evenly between states., Objective.--To determine the relationship between graduate medical education and physician practice location. Design.--Cross-sectional analysis of physicians in active practice in 1993, classified by state of graduate medical education and stratified by specialty and professional activity. Logistic regression analysis was used to examine predictors of physicians remaining to practice in the same state in which they trained. Setting.--There were 82871 allopathic physicians (national random sample) and 15076 osteopathic physicians (universe) who completed graduate medical education between 1980 and 1992. Main Outcome Measure.--Practice location in the same state as graduate medical education. Results.--Overall, 51% of physicians are practicing in the state in which they obtained their graduate medical education (range among states, 6% to 71%). Generalist physicians are more likely than specialists to remain in their state of graduate medical education (odds ratio [OR], 1.36; 95% confidence interval [CI], 1.33 to 1.40) There is a weak negative association between the number of physicians in training per capita in a state and the likelihood of a physician remaining in the state to practice (OR, 0.90; 95% CI, 0.90 to 0.91, for an increment in resident supply of 10 per 100 000 population). New York and Massachusetts, the states with the highest numbers of residents per capita, retained 51% and 49%, respectively, of their graduates, placing them near the median among states. Conclusions.--Most physician training and practice locations function as a national market, with physicians dispersing relatively widely after completing graduate medical education. States that produce high numbers of physicians per capita do not appear to play a unique role in training physicians to serve a national market. These findings pose challenges for states attempting to modify their physician supply and specialty mix. (JAMA. 1995;274:685-691)

People who live in areas where they have poor access to health care may have high rates of avoidable hospitalizations for chronic disorders. Researchers analyzed census and hospital discharge data, and conducted surveys of physicians and community residents in 41 ZIP code areas. They identified five chronic disorders for which hospitalization is preventable: asthma, chronic obstructive pulmonary disease, congestive heart failure, diabetes mellitus, and hypertension. The median rate of preventable hospitalization for chronic disorders ranged from 13 per 10,000 to 59 per 10,000. According to the resident survey, the average community access to health care ranged from 3.7 to 4.3 on a scale of zero to five. The areas with the highest rates of preventable hospitalization tended to have the lowest rates of health care accessibility. This inverse relationship was maintained even when statistics were adjusted to account for differences in income, demographics, the tendency to seek care, and the tendency of physicians to refer patients to hospitals.

An association has been observed between dietary fat and increased risk for coronary heart disease. In addition to recommendations for reducing fat in the diet, the National Cholesterol Education Program's Adult Treatment Guidelines maintain that consumption of monounsaturated and polyunsaturated fats should be carefully controlled. To assess the influence of the type of fat consumed, 19 men and 20 women were evaluated. None of the subjects had cardiovascular abnormalities or high blood pressure, and the total blood cholesterol levels of the groups were comparable. The subjects were put on a polyunsaturated fat-enriched diet for 12 weeks, followed by a 12-week diet rich in monounsaturated fat; the cholesterol and saturated fat contents in both diets remained the same. Measurements of blood lipid (fat) components were taken before and after each of the diets. After the diet of polyunsaturated fat and monounsaturated fat, no significant differences were found in concentrations of (the more harmful) low-density lipoprotein (LDL) cholesterol or mass, or in (the more beneficial) high-density lipoprotein (HDL) cholesterol or mass. An increase of 50 percent of HDL-2 concentration was associated with the polyunsaturated fat diet; decreases in HDL-3 concentration also accompanied this diet. The results of this study offer no support for the benefits of a predominantly monounsaturated fat diet, rather than a predominantly polyunsaturated fat diet. No benefits of the monounsaturated fat diet were noted with regard to HDL blood concentration levels, compared with the polyunsaturated fat diet. (Consumer Summary produced by Reliance Medical Information, Inc.)

Abstract Background The ability of a neuron to regenerate functional connections after injury is influenced by both its intrinsic state and also by extrinsic cues in its surroundings. Investigations of the transcriptional changes undergone by neurons during in vivo models of injury and regeneration have revealed many transcripts associated with these processes. Because of the complex milieu of interactions in vivo, these results include not only expression changes directly related to regenerative outgrowth and but also unrelated responses to surrounding cells and signals. In vitro models of neurite outgrowth provide a means to study the intrinsic transcriptional patterns of neurite outgrowth in the absence of extensive extrinsic cues from nearby cells and tissues. Results We have undertaken a genome-wide study of transcriptional activity in embryonic superior cervical ganglia (SCG) and dorsal root ganglia (DRG) during a time course of neurite outgrowth in vitro. Gene expression observed in these models likely includes both developmental gene expression patterns and regenerative responses to axotomy, which occurs as the result of tissue dissection. Comparison across both models revealed many genes with similar gene expression patterns during neurite outgrowth. These patterns were minimally affected by exposure to the potent inhibitory cue Semaphorin3A, indicating that this extrinsic cue does not exert major effects at the level of nuclear transcription. We also compared our data to several published studies of DRG and SCG gene expression in animal models of regeneration, and found the expression of a large number of genes in common between neurite outgrowth in vitro and regeneration in vivo. Conclusion Many gene expression changes undergone by SCG and DRG during in vitro outgrowth are shared between these two tissue types and in common with in vivo regeneration models. This suggests that the genes identified in this in vitro study may represent new candidates worthy of further study for potential roles in the therapeutic regrowth of neuronal connections.

Abstract Background Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses. Results To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. Conclusion GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.