Data integration

Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions

M. Jargosch, Kröger, S., Gralinska, E., Klotz, U., Fang, Z., Chen, W., Leser, U., Selbig, J., Groth, D., Baumgrass, R., Jargosch, M., Kröger, S., Gralinska, E., Klotz, U., Fang, Z., Chen, W., Leser, U., Selbig, J., Groth, D., and Baumgrass, R., “Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions”, vol. 15, p. -, 2016.

Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of Stat6-knockout mouse studies together with STAT6 ChIP-seq data and our own gene expression time series data during Th2 cell differentiation.

An integrated model for cellular analysis

E. Battistella, de Souza, J. G. C., Barcellos, C. K., Lemke, N., and Mombach, J. C. M., “An integrated model for cellular analysis”, vol. 4, pp. 506-513, 2005.

We present the MOlecular NETwork (MONET) ontology as a model to integrate data from different networks that govern cell function. To achieve this, different existing ontologies were analyzed and an integrated ontology was built in a way to make it possible to share and reuse knowledge, support interoperability between systems, and also allow the formulation of hypotheses through inferences.

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases

A. Barbosa-Silva, Pafilis, E., Ortega, J. M., and Schneider, R., “Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases”, vol. 6, pp. 1142-1150, 2007.

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS).

BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database

A. C. Faria-Campos, Gomes, R. R., Moratelli, F. S., Rausch-Fernandes, H., Franco, G. R., and Campos, S. V. A., “BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database”, vol. 6. pp. 937-945, 2007.

Proteomics correspond to the identification and quantitative analysis of proteins expressed in different conditions or life stages of a cell or organism. Methods used in proteomics analysis include mainly chromatography, two-dimensional electrophoresis and mass spectrometry. Data generated in proteomics analysis vary significantly, and to identify a protein it is often necessary to perform a series of experiments, comparing its results to those found in proteomics databases.

Data integration