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Item type: Item , The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape [supplementary information](Universitat Pompeu Fabra, 2018-04-27) Dobon, Begoña; Hassan, Hisham Y.; Laayouni, Hafid, 1968-; Luisi, Pierre, 1985-; Ricaño Ponce, Isis; Zhernakova, Alexandra; Wijmenga, Cisca; Tahir, Hanan; Comas, David, 1969-; Netea, Mihai G; Bertranpetit, Jaume, 1952-Item type: Item , Quantitative predictions of protein interactions with long noncoding RNAs(Universitat Pompeu Fabra, 2016) Cirillo, DavideLong noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions. Here we introduce Global Score as a tool to predict protein interactions with lncRNAs (http://service.tartaglialab.com/new_submission/globalscore). We used enhanced CLIP (eCLIP) to test the binding of the lncRNA Xist to the RBPs HnrnpK (Global Score of 0.99), Ptbp1 (0.99), Lbr (0.79), HnrnpU (Saf-A) (0.66), Spen (Sharp) (0.59) and negative control Dkc1 (0.01). Global Score prediction correlates with the eCLIP binding profile (Pearson correlation = 0.93). As for the binding sites, Spen and HnrnpK, Ptbp1, and Lbr interact respectively with Xist A, B, and E repeats and adjacent regions, while HnrnpU binds across the whole transcript, and Dkc1 does not interact with Xist.Item type: Item , Performance of low-cost monitors to assess household air pollution [dataset](Universitat Pompeu Fabra, 2016-02-22) Curto Tirado, Ariadna, 1987-; Donaire González, David; Barrera Gómez, Jose; Marshall, Julian D.; Nieuwenhuijsen, Mark J.; Wellenius, Gregory A.; Tonne, CathrynRaw data of PM2.5 and CO from an indoor wood-combustion experiment. We evaluated the performance of two low-cost sensors measuring fine particulate matter (PM2.5) (HAPEX Nano, Climate Solutions Consulting, and TZOA-R Model RD02, MyTZOA) and one measuring carbon monoxide (CO) (EL-USB-CO, Lascar Electronics Ltd.) in a real-world wood-combustion experiment. PM2.5 devices were compared against a DustTrak (Model 8534, TSI Inc.) and a BGI pump (BGI4004, BGI Inc.) and the EL-USB-CO data-logger was compared against a Q-Trak (Model 7575, TSI Inc.). Sampling was conducted in a single-family house in Terrassa (Spain) during five non-consecutive days. All devices were co-located 1 meter away from an indoor fireplace and 0.6 meters above the ground. Fire was set once per day with hardwood logs and kept burning for 12 hours including a minimum of 2 hours with an opened window. The data provided is the raw output from all the devices tested for the 5 sampling days aiming interested researchers to play with the data and reproduce our findings.Item type: Item , Intogen - Catalog of driver mutations(Universitat Pompeu Fabra, 2016-10) Tamborero Noguera, David; Rubio Pérez, Carlota; Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; Vivancos Prellezo, Ana; Rovira Guerín, Ana; Tusquets, Ignasi; Albanell Mestres, Joan; Tabernero Cartula, Josep; Dienstman, Rodrigo; González-Pérez, Abel; López Bigas, NúriaThis database contains the results of the driver analysis performed by the Cancer Genome Interpreter across 6,792 exomes of a pan-cancer cohort of 28 tumor types. Validated oncogenic mutations are identified according to the state-of-the-art clinical and experimental data, whereas the effect of the mutations of unknown significance is predicted by the OncodriveMUT method.Item type: Item , TCGI prescription(Universitat Pompeu Fabra, 2016-10) Tamborero Noguera, David; Rubio Pérez, Carlota; Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; Vivancos Prellezo, Ana; Rovira Guerín, Ana; Tusquets, Ignasi; Albanell Mestres, Joan; Rodon, Jordi; Tabernero Cartula, Josep; Dienstman, Rodrigo; González-Pérez, Abel; López Bigas, NúriaCGI drug prescription assigns targeted drugs to a tumor, based on its genomic alterations, according different levels of evidence (from pre-clinical assays to clinical guidelines).Item type: Item , OncodriveMUT(Universitat Pompeu Fabra, 2016-01) Tamborero Noguera, David; Rubio Pérez, Carlota; Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; Vivancos Prellezo, Ana; Rovira Guerín, Ana; Tusquets, Ignasi; Albanell Mestres, Joan; Rodon, Jordi; Tabernero Cartula, Josep; Dienstman, Rodrigo; González-Pérez, Abel; López Bigas, NúriaBioinformatics method to identify individual driver mutations.Item type: Item , iDGP(Universitat Pompeu Fabra, 2006-07) Furney, Simon J.; Albà Soler, Mar; López Bigas, NúriaDatabase of human genes prioritized for their probability of involvement in dominant or recessive hereditary diseases.Item type: Item , Evolvavility(Universitat Pompeu Fabra, 2007-10) López Bigas, Núria; De, Subhajyoti; Teichmann, Sarah A.Mutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642Item type: Item , funcSTAR(Universitat Pompeu Fabra, 2007-10) Shikhagaie, Medya; López Bigas, NúriaWeb tool for the selection of SNPs from the STAR project with potential functional effect.Item type: Item , CGProp(Universitat Pompeu Fabra, 2007-12) Furney, Simon J.; Madden, Stephen F.; Kisiel, Tomasz A.; Higgins, Desmond G.; López Bigas, NúriaCancer gene properties.Item type: Item , RBP2(Universitat Pompeu Fabra, 2008-09) López Bigas, Núria; Kisiel, Tomasz A.; DeWaal, Dannielle C.; Holmes, Katherine B.; Volkert, Tom L.; Gupta, Sumeet; Love, Jennifer; Murray, Heather L.; Young, Richard A.; Benevolenskaya, Elizaveta V.Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.Item type: Item , IntOGen - Arrays(Universitat Pompeu Fabra, 2010-02) Gundem, Gunes; Pérez Llamas, Christian, 1976-; Jené i Sanz, Alba, 1984-; Kedzierska, Anna; Islam, Abul, 1978-; Déu Pons, Jordi; Furney, Simon J.; López Bigas, NúriaGenes and pathways affected by expression and copy number changes in tumors across projects and cancer types.Item type: Item , p27(Universitat Pompeu Fabra, 2011-12) Pippa, Raffaella; Espinosa Blay, Lluís; Gundem, Gunes; Garcia Escudero, Ramon; Dominguez, Ana; Orlando, Serena; Gallastegui, E.; Saiz, Cristina; Besson, Arnaud; Pujol Sobrevía, María Jesús; López Bigas, Núria; Paramio, Jesus M.; Bigas Salvans, Anna; Bachs Valldeneu, OriolThe cyclin-cdk (cyclin-dependent kinase) inhibitor p27(Kip1) (p27) has a crucial negative role on cell cycle progression. In addition to its classical role as a cyclin-cdk inhibitor, it also performs cyclin-cdk-independent functions as the regulation of cytoskeleton rearrangements and cell motility. p27 deficiency has been associated with tumor aggressiveness and poor clinical outcome, although the mechanisms underlying this participation still remain elusive. We report here a new cellular function of p27 as a transcriptional regulator in association with p130/E2F4 complexes that could be relevant for tumorigenesis. We observed that p27 associates with specific promoters of genes involved in important cellular functions as processing and splicing of RNA, mitochondrial organization and respiration, translation and cell cycle. On these promoters p27 co-localizes with p130, E2F4 and co-repressors as histone deacetylases (HDACs) and mSIN3A. p27 co-immunoprecipitates with these proteins and by affinity chromatography, we demonstrated a direct interaction of p27 with p130 and E2F4 through its carboxyl-half. We have also shown that p130 recruits p27 on the promoters, and there p27 is needed for the subsequent recruitment of HDACs and mSIN3A. Expression microarrays and luciferase assays revealed that p27 behaves as transcriptional repressor of these p27-target genes (p27-TGs). Finally, in human tumors, we established a correlation with overexpression of p27-TGs and poor survival. Thus, this new function of p27 as a transcriptional repressor could have a role in the major aggressiveness of tumors with low levels of p27.Item type: Item , SVGMap(Universitat Pompeu Fabra, 2012-01) Rafael-Palou, Xavier; Schroeder, Michael Philipp, 1986-; López Bigas, NúriaThe aim of SVGMap is helping in the visualisation of experimental data which are associated with some graphical representation. Thus SVGMap browser allows to generate images with colored areas corresponding to the chosen data and color scale./nThe data is represented as a table and is searchable. All data as well as the generated images/figures can be exported easily through the interface./nAdditionally the tool allows to manage (add, edit or delete) experiments and configure the front-end user search appearance such as the number of images to be displayed, the scale types to use and more.Item type: Item , Oncodrive-CIS(Universitat Pompeu Fabra, 2013-02) Tamborero Noguera, David; López Bigas, Núria; González-Pérez, AbelOncodrive-CIS is a method aimed to identify those copy number alterations (CNAs) leading to larger in cis expression changes that may be useful in elucidating the role of these aberrations in cancer. This is based on the hypothesis that a gene driving oncogenesis through copy number changes is more prone to bias towards overexpression (or underexpression) as compared to bystanders. The effect of the gene dosage is assessed by observing expression changes not only among tumors but also taking into account normal samples data, when available./nOncodrive-CIS has several potential benefits: first, it did not examine the frequency of the CNAs across samples and therefore the detection of low-recurrent driver alterations was not impaired. Second, amplifications and deletions were evaluated separately to obtain a fair ranking of genes, because the expression change measured in deletions was lower than the one obtained from multi-copy amplifications. Third, the expression of genes in tumor samples was analyzed according to the copy number status but was also compared to normal samples, thus better revealing the gene misregulation role of CNAs in cancer cells. And finally, it should be emphasized that the relationship between expression changes and their functional impact is complex, thus Oncodrive-CIS is proposed as a method to elucidate the role of CNAs in cancer which may be complementary to analyses based on other criteria.Item type: Item , IntOGen - Cancer driver database (2013)(Universitat Pompeu Fabra, 2013-05) González-Pérez, Abel; Pérez Llamas, Christian, 1976-; Déu Pons, Jordi; Tamborero Noguera, David; Schroeder, Michael Philipp, 1986-; Jené i Sanz, Alba, 1984-; Santos, Alberto; López Bigas, NúriaMutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642Item type: Item , IntOGen - TCGA pan-cancer12 high confidence drivers(Universitat Pompeu Fabra, 2013-10) Tamborero Noguera, David; González-Pérez, Abel; Pérez Llamas, Christian, 1976-; Déu Pons, Jordi; Kandoth, Cyriac; Reimand, Jüri; Lawrence, Michael S.; Getz, Gad; Bader, Gary D.; Ding, Li; López Bigas, NúriaThis file lists the High Confidence Drivers identified as part of the pan-cancer12 initiative, published in the paper Comprehensive identification of mutational cancer driver genes across 12 tumor types" Scientific Reports 3:2650, 2013, doi:10.1038/srep02650Item type: Item , IntOGen - Cancer Drivers Actionability Database(Universitat Pompeu Fabra, 2015-03) Rubio Pérez, Carlota; Tamborero Noguera, David; Schroeder, Michael Philipp, 1986-; Antolín Hernández, Albert, 1984-; Déu Pons, Jordi; Pérez Llamas, Christian, 1976-; Mestres i López, Jordi; González-Pérez, Abel; López Bigas, NúriaThis database contains data on the interactions with therapeutic agents an driver genes contained in Cancer Drivers Database (2014.12). It characterizes the interacting therapeutic agents in terms of clinical phase and cancer prescription, among other features. Additionally, it contains ancillary information on specific genomic alterations associated to drug effectiveness which are FDA approved or clinically being tested together with data on other genomic alterations known to be responsible of drug primary resistance.Item type: Item , IntOGen - Cancer Drivers Database (2014)(Universitat Pompeu Fabra, 2015-03) Rubio Pérez, Carlota; Tamborero Noguera, David; Schroeder, Michael Philipp, 1986-; Antolín Hernández, Albert, 1984-; Déu Pons, Jordi; Pérez Llamas, Christian, 1976-; Mestres i López, Jordi; González-Pérez, Abel; López Bigas, NúriaThis database contains information on the genes identified as drivers in Rubio-Perez and Tamborero et al. (2015). It contains information on driver identification at mutational, CNA and gene fusion level. Additional ancillary information about the role and major clonality of drivers is also included. A table is also provided with the list of datasets used for mutational driver identification.Item type: Item , C10-HDAC7(Universitat Pompeu Fabra, 2013-05) Barneda Zahonero, Bruna; Román González, Lidia; Collazo, Olga; Rafati, Haleh; Islam, Abul, 1978-; Bussmann, Lars; Di Tullio, Alessandro, 1982-; Andrés, Luisa De; Graf, T. (Thomas); López Bigas, Núria; Mahmoudi, Tokameh; Parra, MaribelHDAC7 is a repressor of myeloid genes whose downregulation in pre-B cells is required for transdifferentiation into macrophages.