Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.

Autor: Andrew T Kwon, Alice Yi Chou, David J Arenillas, Wyeth W Wasserman

Publikováno v: PLoS Computational Biology, Vol 7, Iss 12, p e1002256 (2011)

We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for

Externí odkaz: https://doaj.org/article/6c9a710453c5402face97518a5837cbf

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Autor: Jayson Harshbarger, Imad Abugessaisa, Julian Gough, Takeya Kasukawa, Andreas Lennartsson, Hiromasa Ono, Jordan A. Ramilowski, Alistair R. R. Forrest, Atsushi Kondo, Hans-Ioan Ienasescu, Shuei Noguchi, Jessica Severin, David J. Arenillas, Anthony Mathelier, Piero Carninci, Marina Lizio, Hidemasa Bono, Yoshihide Hayashizaki, Yulia A. Medvedeva, Finn Drabløs, Albin Sandelin, Robin Andersson, Hideya Kawaji, Owen J. L. Rackham, Christopher J. Mungall

Publikováno v: Nucleic Acids Research
D737-D743
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Lizio, M, Harshbarger, J, Abugessaisa, I, Noguchi, S, Kondo, A, Severin, J, Mungall, C, Arenillas, D, Mathelier, A, Medvedeva, Y A, Lennartsson, A, Drabløs, F, Ramilowski, J A, Rackham, O, Gough, J, Andersson, R, Sandelin, A G, Ienasescu, H-I, Ono, H, Bono, H, Hayashizaki, Y, Carninci, P, Forrest, A R R, Kasukawa, T & Kawaji, H 2017, ' Update of the FANTOM web resource : high resolution transcriptome of diverse cell types in mammals ', Nucleic Acids Research, vol. 45, no. D1, pp. D737-D743 . https://doi.org/10.1093/nar/gkw995
Lizio, M; Harshbarger, J; Abugessaisa, I; Noguchi, S; Kondo, A; Severin, J; et al.(2017). Update of the FANTOM web resource: High resolution transcriptome of diverse cell types in mammals. Nucleic Acids Research, 45(D1), D737-D743. doi: 10.1093/nar/gkw995. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/29z4n735
Nucleic acids research, vol 45, iss D1

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f456181615d598f37b606fb6fb396d21
http://europepmc.org/articles/PMC5210666

GeneYenta: A Phenotype­Based Rare Disease Case Matching Tool Based on Online Dating Algorithms for the Acceleration of Exome Interpretation

Autor: Millan S. Patel, Wyeth W. Wasserman, Maja Tarailo­Graovac, Zachary D. Maurer, David J. Arenillas, Michael Gottlieb, Clara D.M. van Karnebeek, Linlea Armstrong, Savanie Maithripala

Publikováno v: Human Mutation. 36:432-438

Advances in next-generation sequencing (NGS) technologies have helped reveal causal variants for genetic diseases. In order to establish causality, it is often necessary to compare genomes of unrelated individuals with similar disease phenotypes to i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0719351708f0c20f3eb6deb94ce60632
https://doi.org/10.1002/humu.22772

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Autor: Oriol Fornes, Anthony Mathelier, Benoit Ballester, Jeanne Chèneby, Marius Gheorghe, Arnaud Stigliani, Ge Tan, François Parcy, Aziz Khan, David J. Arenillas, Robin van der Lee, Wyeth W. Wasserman, Klaas Vandepoele, Jaime A. Castro-Mondragon, Damir Baranasic, Albin Sandelin, Shubhada Rajabhau Kulkarni, Boris Lenhard, Adrien Bessy

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2018, 46 (D1), pp.D260-D266. ⟨10.1093/nar/gkx1126⟩
Nucleic Acids Research, Oxford University Press, 2018, 46 (D1), pp.D1284-D1284. ⟨10.1093/nar/gkx1188⟩
Nucleic Acids Research D1 (46), D260-D266. (2018)
Nucleic Acids Research, 2018, 46 (D1), pp.D260-D266. ⟨10.1093/nar/gkx1126⟩
Khan, A, Fornes, O, Stigliani, A, Gheorghe, M, Castro-Mondragon, J A, van der Lee, R, Bessy, A, Chèneby, J, Kulkarni, S R, Tan, G, Baranasic, D, Arenillas, D J, Sandelin, A G, Vandepoele, K, Lenhard, B, Ballester, B, Wasserman, W W, Parcy, F & Mathelier, A 2018, ' JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework ', Nucleic Acids Research, vol. 46, no. D1, gkx1126, pp. D260-D266 . https://doi.org/10.1093/nar/gkx1126
NUCLEIC ACIDS RESEARCH
Nucleic Acids Research, 2018, 46 (D1), pp.D1284-D1284. ⟨10.1093/nar/gkx1188⟩
D1284
D266
D260

International audience; JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across mult

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2c1285884bec05a5f9afa4fefd8186a8
https://pubmed.ncbi.nlm.nih.gov/29140473

A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses

Autor: David J. Arenillas, Alistair R. R. Forrest, Chih-Yu Chen, Yifeng Li, Anthony Mathelier, Wenqiang Shi, Yoshihide Hayashizaki, Carolyn J. Brown, Wyeth W. Wasserman, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji, Piero Carninci, Allison Matthews

Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. Such differences

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf75ea3f611a5cb64d9b2f717154cc42
https://doi.org/10.1101/044172