The BLUEPRINT Data Analysis Portal.

The impact of large and complex epigenomic datasets on biological insights or clinical applications is limited by the lack of accessibility by easy, intuitive, and fast tools. Here, we describe an epigenomics comparative cyber-infrastructure (EPICO), an open-access reference set of libraries to develop comparative epigenomic data portals. Using EPICO, large epigenome projects can make available their rich datasets to the community without requiring specific technical skills. As a first instance of EPICO, we implemented the BLUEPRINT Data Analysis Portal (BDAP). BDAP provides a desktop for the comparative analysis of epigenomes of hematopoietic cell types based on results, such as the position of epigenetic features, from basic analysis pipelines. The BDAP interface facilitates interactive exploration of genomic regions, genes, and pathways in the context of differentiation of hematopoietic lineages. This work represents initial steps toward broadly accessible integrative analysis of epigenomic data across international consortia. EPICO can be accessed at https://github.com/inab, and BDAP can be accessed at http://blueprint-data.bsc.es.

Scientific competency questions as the basis for semantically enriched open pharmacological space development.

Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of an open pharmacological space (OPS) information system. The focus of this work is the integration of compound-target-pathway-disease/phenotype data for public and industrial drug discovery research. Typical scientific competency questions provided by the consortium members will be analyzed based on the underlying data concepts and associations needed to answer the questions. Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented.

Chapter 14: Cancer genome analysis.

Although there is great promise in the benefits to be obtained by analyzing cancer genomes, numerous challenges hinder different stages of the process, from the problem of sample preparation and the validation of the experimental techniques, to the interpretation of the results. This chapter specifically focuses on the technical issues associated with the bioinformatics analysis of cancer genome data. The main issues addressed are the use of database and software resources, the use of analysis workflows and the presentation of clinically relevant action items. We attempt to aid new developers in the field by describing the different stages of analysis and discussing current approaches, as well as by providing practical advice on how to access and use resources, and how to implement recommendations. Real cases from cancer genome projects are used as examples.

Mutated genes, pathways and processes in tumours.

Integration of the many available sources of cancer gene information--such as large-scale tumour-resequencing studies--identifies the 'usual suspect' genes, mutated in many tumour types, as well as different sets of mutated genes according to the specific tumour type. Scaling-up the analysis reveals that this large collection of mutated genes cluster into a smaller number of signalling pathways and processes. From this, we draw a map of the altered processes, and their combinations, in more than 10 tumours types. Literature searches identify pathways and processes that are covered sparsely in the literature, and invite the proposal of new hypotheses to investigate cancer initiation and progression.

FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

BACKGROUND: FragKB (Fragment Knowledgebase) is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

Hamartoma mesenquimal rabdomiomatoso / Rhabdomyomatous mesenchymal hamartoma

El Hamartoma Mesenquimal Rabdomiomatoso, representa un raro tipo de hamartoma consistenteen la presencia de fibras musculares estriadas dispuestas al azar en la dermis y tejidosubcutáneo, asociadas con elementos mesenquimales de apariencia normal. Se han descrito 24casos en la literatura. La mayoría en el recién nacido, a veces asociados con otras anomalíascongénitas y sólo tres en el adulto. Presentamos un nuevo caso en un neonato sin evidencia deotras lesiones

Rhabdomyomatous mesenchymal hamartoma is a rare type of hamartoma consisting of striatedmuscle fibers arranged randomly within the dermis and subcutaneous tissue, associated withnormal-appearing mesenchymal elements. Only 24 cases are described in the literature, most ofthem in newborn, sometimes associated with other congenital abnormalities and only three inadults. We report a new case in a newborn without evidence of other lesions

Hamartoma mesenquimal rabdomiomatoso / Rhabdomyomatous mesenchymal hamartoma

El Hamartoma Mesenquimal Rabdomiomatoso, representa un raro tipo de hamartoma consistente en la presencia de fibras musculares estriadas dispuestas al azar en la dermis y tejido subcutáneo, asociadas con elementos mesenquimales de apariencia normal. Se han descrito 24 casos en la literatura. La mayoría en el recién nacido, a veces asociados con otras anomalías congénitas y sólo tres en el adulto. Presentamos un nuevo caso en un neonato sin evidencia de otras lesiones

Rhabdomyomatous mesenchymal hamartoma is a rare type of hamartoma consisting of striated muscle fibers arranged randomly within the dermis and subcutaneous tissue, associated with normal-appearing mesenchymal elements. Only 24 cases are described in the literature, most of them in newborn, sometimes associated with other congenital abnormalities and only three in adults. We report a new case in a newborn without evidence of other lesions