@article {1225,
	title = {The pan-cancer pathological regulatory landscape.},
	journal = {Scientific reports},
	volume = {6},
	year = {2016},
	month = {2016 Dec 21},
	pages = {39709},
	abstract = {Dysregulation of the normal gene expression program is the cause of a broad range of diseases, including cancer. Detecting the specific perturbed regulators that have an effect on the generation and the development of the disease is crucial for understanding the disease mechanism and for taking decisions on efficient preventive and curative therapies. Moreover, detecting such perturbations at the patient level is even more important from the perspective of personalized medicine. We applied the Transcription Factor Target Enrichment Analysis, a method that detects the activity of transcription factors based on the quantification of the collective transcriptional activation of their targets, to a large collection of 5607 cancer samples covering eleven cancer types. We produced for the first time a comprehensive catalogue of altered transcription factor activities in cancer, a considerable number of them significantly associated to patient{\textquoteright}s survival. Moreover, we described several interesting TFs whose activity do not change substantially in the cancer with respect to the normal tissue but ultimately play an important role in patient prognostic determination, which suggest they might be promising therapeutic targets. An additional advantage of this method is that it allows obtaining personalized TF activity estimations for individual patients.},
	issn = {2045-2322},
	doi = {10.1038/srep39709},
	url = {http://www.nature.com/articles/srep39709},
	author = {Falco, Matias M and Bleda, Marta and Carbonell-Caballero, Jos{\'e} and Joaqu{\'\i}n Dopazo}
}
@article {435,
	title = {The pan-cancer pathological regulatory landscape},
	journal = {Scientific Reports},
	volume = {6},
	year = {2016},
	month = {Jan-12-2016},
	doi = {10.1038/srep39709},
	url = {http://www.nature.com/articles/srep39709http://www.nature.com/articles/srep39709.pdfhttp://www.nature.com/articles/srep39709.pdfhttp://www.nature.com/articles/srep39709},
	author = {Falco, Matias M. and Bleda, Marta and Carbonell-Caballero, Jos{\'e} and Dopazo, Joaquin}
}
@article {1033,
	title = {Pathways systematically associated to Hirschsprung{\textquoteright}s disease.},
	journal = {Orphanet journal of rare diseases},
	volume = {8},
	year = {2013},
	month = {2013 Dec 2},
	pages = {187},
	abstract = {Despite it has been reported that several loci are involved in Hirschsprung{\textquoteright}s disease, the molecular basis of the disease remains yet essentially unknown. The study of collective properties of modules of functionally-related genes provides an efficient and sensitive statistical framework that can overcome sample size limitations in the study of rare diseases. Here, we present the extension of a previous study of a Spanish series of HSCR trios to an international cohort of 162 HSCR trios to validate the generality of the underlying functional basis of the Hirschsprung{\textquoteright}s disease mechanisms previously found. The Pathway-Based Analysis (PBA) confirms a strong association of gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other processes related to the disease. In addition, network analysis recovers sub-networks significantly associated to the disease, which contain genes related to the same functionalities, thus providing an independent validation of these findings. The functional profiles of association obtained for patients populations from different countries were compared to each other. While gene associations were different at each series, the main functional associations were identical in all the five populations. These observations would also explain the reported low reproducibility of associations of individual disease genes across populations.},
	keywords = {GWAS, Hirschprung, network analysis, Pathway Based Analysis},
	issn = {1750-1172},
	doi = {10.1186/1750-1172-8-187},
	url = {http://www.ojrd.com/content/8/1/187/abstract},
	author = {Fern{\'a}ndez, Raquel M and Bleda, Marta and Luz{\'o}n-Toro, Berta and Garc{\'\i}a-Alonso, Luz and Arnold, Stacey and Sribudiani, Yunia and Besmond, Claude and Lantieri, Francesca and Doan, Betty and Ceccherini, Isabella and Lyonnet, Stanislas and Hofstra, Robert Mw and Chakravarti, Aravinda and Anti{\v n}olo, Guillermo and Joaqu{\'\i}n Dopazo and Borrego, Salud}
}
@article {495,
	title = {Pathways systematically associated to Hirschsprung{\textquoteright}s disease.},
	journal = {Orphanet J Rare Dis},
	volume = {8},
	year = {2013},
	month = {2013 Dec 02},
	pages = {187},
	abstract = {<p>Despite it has been reported that several loci are involved in Hirschsprung{\textquoteright}s disease, the molecular basis of the disease remains yet essentially unknown. The study of collective properties of modules of functionally-related genes provides an efficient and sensitive statistical framework that can overcome sample size limitations in the study of rare diseases. Here, we present the extension of a previous study of a Spanish series of HSCR trios to an international cohort of 162 HSCR trios to validate the generality of the underlying functional basis of the Hirschsprung{\textquoteright}s disease mechanisms previously found. The Pathway-Based Analysis (PBA) confirms a strong association of gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other processes related to the disease. In addition, network analysis recovers sub-networks significantly associated to the disease, which contain genes related to the same functionalities, thus providing an independent validation of these findings. The functional profiles of association obtained for patients populations from different countries were compared to each other. While gene associations were different at each series, the main functional associations were identical in all the five populations. These observations would also explain the reported low reproducibility of associations of individual disease genes across populations. </p>},
	keywords = {Female, Genetic Predisposition to Disease, Genotype, Hirschsprung Disease, Humans, Male, Polymorphism, Single Nucleotide},
	issn = {1750-1172},
	doi = {10.1186/1750-1172-8-187},
	author = {Fern{\'a}ndez, Raquel M and Bleda, Marta and Luz{\'o}n-Toro, Berta and Garc{\'\i}a-Alonso, Luz and Arnold, Stacey and Sribudiani, Yunia and Besmond, Claude and Lantieri, Francesca and Doan, Betty and Ceccherini, Isabella and Lyonnet, Stanislas and Hofstra, Robert Mw and Chakravarti, Aravinda and Anti{\v n}olo, Guillermo and Dopazo, Joaquin and Borrego, Salud}
}
