BISC: Binary SubComplexes in proteins database

Binary subcomplexes in proteins database (BISC) is a new protein–protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces. Among other uses we envision that this resource can help identify possible false positive PPI in current database records. BISC is freely available at http://bisc.cse.ucsc.edu

Ensembl 2014

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

A doutrina intelectualista de Descartes consiste, em parte, na crença de que para que as pessoas executem adequadamente uma tarefa, elas devem antes refletir sobre as regras de bom desempenho que se aplicam à tarefa. Neste sentido, um bom desempenho em qualquer tarefa dependeria sempre da consciência, por parte do indivíduo, das prescrições para a ação, sendo consciência entendida como um processo interno, isento de erros quanto à sua capacidade de perceber o fluxo da vida mental, de admitir para si mesmo certas prescrições acerca do que vai ser feito. De acordo com essa interpretação da doutrina, os episódios da vida imaterial, como pensar e julgar, seriam responsáveis pelas ações, os episódios da vida material. Um dos problemas relacionados com esta doutrina intelectualista, de acordo com Ryle, é que muitas ações ditas inteligentes não são precedidas por quaisquer conhecimentos anteriores dos princípios que se lhes aplicam. Outro problema mais relevante se refere ao fato de tal doutrina gerar uma regressão teórica infinita, isto é, se ações inteligentes são necessariamente precedidas por considerações teóricas inteligentes, estas, para serem inteligentes, teriam que ser também precedidas por outras considerações teóricas inteligentes. Visto que a psicologia cognitiva, representada por exemplo por teorias de processamento de informação, sofreu influência da doutrina intelectualista, as críticas mencionadas podem ser também aplicadas a ela. Sugere-se que uma análise dos usos dos conceitos psicológicos na linguagem cotidiana pode ser útil para a solução de algumas dessas dificuldades conceituais.Descartes´ intellectualistic doctrine consists in part in the belief that in order for people to adequately execute a task, they first have to reflect on the rules of good performance that apply to that task. Therefore, good performance on any task would always depend on the individual's consciousness of the prescriptions for the actions, consciousness being understood as an internal process, free from mistakes concerning its ability to perceive the flow of mental life, of admitting for oneself certain prescriptions about what will be done. According to this doctrine's interpretation, immaterial life episodes, such as thinking and judging, would be responsible for actions, material life episodes. One of the problems related to this intellectualistic doctrine, according to Ryle, is that many of the so-called intelligent actions are not preceded by any previous knowledge of the applicable principles. Another more relevant problem refers to the fact that such doctrine may generate an infinite theoretical regression, that is, if intelligent actions are necessarily preceded by intelligent theoretical considerations, the latter, in order to be considered intelligent, would also have to be preceded by other intelligent theoretical considerations. Since Cognitive Psychology, represented for example by information processing theories, was influenced by the intellectualistic doctrine, the criticism mentioned previously can also be applied to it. It is suggested that an analysis of the uses of psychological concepts in ordinary language may be useful in solving some of these conceptual difficulties

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the version 8 data, examining 15,201 RNA-sequencing samples from 49 tissues of 838 postmortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue specificity of genetic effects and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues