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H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational

J.-i. Takeda, Y. Suzuki, M. Nakao, T. Kuroda, S. Sugano, T. Gojobori, T. Imanishi
2007 Nucleic Acids Research  
In this database, each of the alternative splicing (AS) variants corresponds to a completely sequenced and carefully annotated human full-length cDNA, one of those collected for the H-Invitational humantranscriptome  ...  The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts.  ...  Habara, H. Nakaoka, F. Todokoro, Y. Imamizu, M. Ogawa and C. Yamasaki for genome mapping, ORF prediction and functional annotation of the H-Invitational cDNA dataset.  ... 
doi:10.1093/nar/gkl854 pmid:17130147 pmcid:PMC1716722 fatcat:6hkvbl4vmbeklmwekqv7ynwc4m

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery

Jun-ichi Takeda, Chisato Yamasaki, Katsuhiko Murakami, Yoko Nagai, Miho Sera, Yuichiro Hara, Nobuo Obi, Takuya Habara, Takashi Gojobori, Tadashi Imanishi
2012 Nucleic Acids Research  
In our analysis, 19 309 annotated genes were specific to H-InvDB and not found in RefSeq and Ensembl.  ...  In the latest version, H-InvDB 8.0, a total of 244 709 human complementary DNA was mapped onto the hg19 reference genome and 43 829 gene loci, including nonprotein-coding ones, were identified.  ...  ACKNOWLEDGEMENTS The authors acknowledge all the members of the H-Invitational consortium and the Genome Information Integration Project (GIIP) for participating in the annotation work of human full-length  ... 
doi:10.1093/nar/gks1245 pmid:23197657 pmcid:PMC3531145 fatcat:7r3vwzepiraw5juff6lm7sf6ia

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs

Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi
2008 Nucleic Acids Research  
Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice.  ...  To exclude the possibility that the full-length human cDNAs used in the present study, especially those with retained introns, were cloning artefacts or prematurely spliced transcripts, we experimentally  ...  Wakaguri for their technical support during the computational analysis and are grateful to all who annotated the full-length human cDNAs at the H-Inv and H-Inv 2 conferences.  ... 
doi:10.1093/nar/gkn677 pmid:18838389 pmcid:PMC2582632 fatcat:4wfphimgnrfkjfwg7haptrtdy4

Splice-mediated Variants of Proteins (SpliVaP) – data and characterization of changes in signatures among protein isoforms due to alternative splicing

Matteo Floris, Massimiliano Orsini, Thangavel Thanaraj
2008 BMC Genomics  
Conclusion: (i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms.  ...  (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences.  ...  Acknowledgements The authors thank Professor Anna Tramontano for her support and encouragement. Ricardo Medda is acknowledged for his help with accessing and mining data from OMIM entries.  ... 
doi:10.1186/1471-2164-9-453 pmid:18831736 pmcid:PMC2573899 fatcat:2uvxwmyfgvdb3byhuhf6j2n344

Function of alternative splicing

Olga Kelemen, Paolo Convertini, Zhaiyi Zhang, Yuan Wen, Manli Shen, Marina Falaleeva, Stefan Stamm
2013 Gene  
However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system.  ...  Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes.  ...  Acknowledgments This work is supported by NIH RO1 GM083187 and an Endowment of the Universty of Kentucky. We thank Eva R. McEnrue for editorial help.  ... 
doi:10.1016/j.gene.2012.07.083 pmid:22909801 pmcid:PMC5632952 fatcat:4t6cozxi2vffnnkhm6difvwhnu

Methods for transcript variant discovery and alternative expression analysis : application to the study of fluorouracil resistance in colorectal cancer

Malachi Griffith
2010
For example, the approach was insensitive to isoforms with small differences in sequence content and limited by both the transcriptome annotations and the number of microarray features available at design  ...  Several studies have suggested that many genes are alternatively expressed to produced multiple mRNA isoforms and many of these remain undiscovered.  ...  Full-length sequencing of cDNA libraries As the cost of Sanger sequencing and primer synthesis has gone down it has become more practical to conduct full length sequencing of cDNA clones representing complete  ... 
doi:10.14288/1.0068972 fatcat:atrxurgcgjhizfcjvkzo4gsemq

Information theoretical prediction of alternative splicing with application to type-2 Diabetes Mellitus [article]

Axel Rasche, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2010
For the detection of alternative splicing a new method based on an information theoretic concept is introduced to the field of gene expression analysis.  ...  In the course of my work I have developed a software pipeline for the analysis of alternative splicing and differential gene expression.  ...  Not only he offered me a motivating topic, but competently lead me into computational biology, a dynamic field of science at the interface between mathematics, biology and computer science.  ... 
doi:10.17169/refubium-14074 fatcat:2ewta4zwjnfkffiawob57s52ay