Kawaura Kanako, Mochida Keiichi, Enju Akiko, Totoki Yasushi, Toyoda Atsushi, Sakaki Yoshiyuki, ...
Abstract Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs) for wheat is becoming particularly important for...
Hidden layers of human small RNAs (2008)
Kawaji Hideya, Nakamura Mari, Takahashi Yukari, Sandelin Albin, Katayama Shintaro, Fukuda Shiro, ...
Abstract Background Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the...
Forrest Alistair, Taylor Darrin, Fink J Lynn, Gongora M Milena, Flegg Cameron, Teasdale Rohan, ...
Abstract Background Protein kinases and protein phosphatases are the fundamental components of phosphorylation dependent protein regulatory systems. We have created a database for the protein...
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. (2006)
Maeda Norihiro, Kasukawa Takeya, Oyama Rieko, Gough Julian, Frith Martin, Engström Pär G, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Mice and men: their promoter properties. (2006)
Bajic Vladimir B, Tan Sin Lam, Christoffels Alan, Schönbach Christian, Lipovich Leonard, Yang Liang, ...
Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe...
The abundance of short proteins in the mammalian proteome. (2006)
Frith Martin C, Forrest Alistair R, Nourbakhsh Ehsan, Pang Ken C, Kai Chikatoshi, Kawai Jun, ...
Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual...
Complex Loci in human and mouse genomes. (2006)
Engström Pär G, Suzuki Harukazu, Ninomiya Noriko, Akalin Altuna, Sessa Luca, Lavorgna Giovanni, ...
Mammalian genomes harbor a larger than expected number of complex loci, in which multiple genes are coupled by shared transcribed regions in antisense orientation and/or by bidirectional core...
Davis Melissa J, Hanson Kelly A, Clark Francis, Fink J Lynn, Zhang Fasheng, Kasukawa Takeya, ...
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two...
A simple physical model predicts small exon length variations. (2006)
Chern Tzu-Ming, Van Nimwegen Erik, Kai Chikatoshi, Kawai Jun, Carninci Piero, Hayashizaki Yoshihide, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
A method for similarity search of genomic positional expression using CAGE. (2006)
Seno Shigeto, Takenaka Yoichi, Kai Chikatoshi, Kawai Jun, Carninci Piero, Hayashizaki Yoshihide, ...
With the advancement of genome research, it is becoming clear that genes are not distributed on the genome in random order. Clusters of genes distributed at localized genome positions have been...
Clusters of internally primed transcripts reveal novel long noncoding RNAs. (2006)
Furuno Masaaki, Pang Ken C, Ninomiya Noriko, Fukuda Shiro, Frith Martin C, Bult Carol, ...
Non-protein-coding RNAs (ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several...
Heterotachy in mammalian promoter evolution. (2006)
Taylor Martin S, Kai Chikatoshi, Kawai Jun, Carninci Piero, Hayashizaki Yoshihide
We have surveyed the evolutionary trends of mammalian promoters and upstream sequences, utilising large sets of experimentally supported transcription start sites (TSSs). With 30,969 well-defined...
Pseudo-messenger RNA: phantoms of the transcriptome. (2006)
Frith Martin C, Wilming Laurens G, Forrest Alistair, Kawaji Hideya, Tan Sin Lam, Wahlestedt Claes, ...
The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble...
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes (2006)
Brahmachary Manisha, Schönbach Christian, Yang Liang, Huang Enli, Tan Sin, Chowdhary Rajesh, ...
Abstract Background Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition...