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We propose potential directions for statistical data integration. doi: 10.1186/gm413 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Sikora-Wohlfeld, W., Ackermann, M., Christodoulou, E. We discuss the importance of incorporating underestimated aspects (such as alternative splicing and long-range chromatin interactions). The majority of the identified loci are heat-inducibly bound by yeast HSF, and the target genes encode proteins that have a broad range of biological functions including protein folding and degradation, energy generation, protein trafficking, maintenance of cell integrity, small molecule transport, cell signaling, and transcription.This genome-wide identification of HSF target genes provides novel insights into the role of HSF in growth, development, disease, and aging and in the complex metabolic reprogramming that occurs in all cells in response to stress.
The visualization of several tracks allows qualitatively studying a specific gene locus. Heat shock transcription factor (HSF) and the promoter heat shock element (HSE) are among the most highly conserved transcriptional regulatory elements in nature.HSF mediates the transcriptional response of eukaryotic cells to heat, infection and inflammation, pharmacological agents, and other stresses.A physical interaction of TFs, chromatin-modifying enzymes (histone acetyl/methyltransferases and deacetylases/demethylases) and other accessory proteins with DNA is needed to modulate transcription dynamics, determining cell fate (Atkinson and Halfon, 2014). Ch IP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Local chromatin states and epigenetic modifications can limit, or promote, TF occupancies at specific loci. doi: 10.1038/nbt.1630 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Mc Leay, R. Genome-wide in silico prediction of gene expression. doi: 10.1093/bioinformatics/bts529 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Ouyang, Z., Zhou, Q., and Wong, W.
We also highlight the lack of data benchmarks and the need to develop tools for data integration from a statistical viewpoint, designed in the spirit of reproducible research.