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...
A rescue strategy for multimapping short sequence tags of transcriptional activity by CAGE (2008)
Faulkner, Geoffrey J., Forrest, Alistair Raymond Russell, Chalk, Alistair Morgan, Schroder, Kate, Hayashizaki, Yoshihide, Carninci, Piero, ...
Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription...
A rescue strategy for multimapping short sequence tags of transcriptional activity by CAGE (2008)
Faulkner, Geoffrey J., Forrest, Alistair Raymond Russell, Chalk, Alistair Morgan, Schroder, Kate, Hayashizaki, Yoshihide, Carninci, Piero, ...
Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription...
Simplified ontologies allowing comparison of developmental mammalian gene expression (2007)
Kruger, Adele, Hofmann, Oliver, Carninci, Piero, Hayashizaki, Yoshihide, Hide, Winston
Abstract Model organisms represent an important resource for understanding the fundamental aspects of mammalian biology. Mapping of biological phenomena between model organisms is complex and if it...
Large-scale clustering of CAGE tag expression data (2007)
Shimokawa, Kazuro, Okamura-Oho, Yuko, Kurita, Takio, Frith, Martin C, Kawai, Jun, Carninci, Piero, ...
Abstract Background Recent analyses have suggested that many genes possess multiple transcription start sites (TSSs) that are differentially utilized in different tissues and cell lines. We have...
Katayama, Shintaro, Kanamori-Katayama, Mutsumi, Yamaguchi, Kazumi, Carninci, Piero, Hayashizaki, Yoshihide
Abstract Cap analysis gene expression (CAGE) technology has revealed numerous transcription start sites (TSSs) in mammals and has suggested complex promoter-based patterns of regulation. We developed...
Genomic organization of transcriptomes in mammals: coregulation and cofunctionality (2007)
Purmann, Antje, Toedling, Joern, Schueler, Markus, Carninci, Piero, Lehrach, Hans, Hayashizaki, Yoshihide, ...
In studies of their transcriptional activity, genomes have shown a high order of organization. We assessed the question of how genomically neighboring genes are transcriptionally coupled across...
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...
Dynamic usage of transcription start sites within core promoters (2006)
Kawaji, Hideya, Frith, Martin C, Katayama, Shintaro, Sandelin, Albin, Kai, Chikatoshi, Kawai, Jun, ...
Abstract Background Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously...
Ponjavic, Jasmina, Lenhard, Boris, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
Abstract Background The TATA box, one of the most well studied core promoter elements, is associated with induced, context-specific expression. The lack of precise transcription start site (TSS)...
Evolutionary turnover of mammalian transcription start sites (2006)
Frith, Martin C., Ponjavic, Jasmina, Fredman, David, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, ...
Alignments of homologous genomic sequences are widely used to identify functional genetic elements and study their evolution. Most studies tacitly equate homology of functional elements with sequence...
Complex Loci in Human and Mouse Genomes (2006)
Engström, Pär G., Suzuki, Harukazu, Ninomiya, Norika, 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...
Pseudo–Messenger RNA: Phantoms of the Transcriptome (2006)
Martin C. Frith, Laurens G. Wilming, Alistair Forrest, Hideya Kawaji, Sin Lam Tan, Claes Wahlestedt, ...
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...
Heterotachy in Mammalian Promoter Evolution (2006)
Martin S. Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
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...
Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs (2006)
Masaaki Furuno, Ken C. Pang, Noriko Ninomiya, Shiro Fukuda, Martin C. Frith, Carol Bult, ...
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...
A Method for Similarity Search of Genomic Positional Expression Using CAGE (2006)
Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, ...
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...
A Simple Physical Model Predicts Small Exon Length Variations (2006)
Tzu-Ming Chern, Erik Van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, ...
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...
Melissa J. Davis, Kelly A. Hanson, Francis Clark, J. Lynn Fink, Fasheng Zhang, Takeya Kasukawa, ...
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...
Complex Loci in Human and Mouse Genomes (2006)
Pär G. Engström, Harukazu Suzuki, Noriko Ninomiya, Altuna Akalin, Luca Sessa, Giovanni Lavorgna, ...
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...
Mice and Men: Their Promoter Properties (2006)
Vladimir B. Bajic, Sin Lam Tan, Alan Christoffels, Christian Schönbach, Leonard Lipovich, Liang Yang, ...
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)
Martin C. Frith, Alistair R. Forrest, Ehsan Nourbakhsh, Ken C. Pang, Chikatoshi Kai, Jun Kawai, ...
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...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G. Engström, ...
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...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Abstract Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair RR, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nic J, Kolle, Gabriel, ...
Abstract Background Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We...
Wada, Kazuhiro, Howard, Jason T., McConnell, Patrick, Whitney, Osceola, Lints, Thierry, Rivas, Miriam V., ...
Songbirds have one of the most accessible neural systems for the study of brain mechanisms of behavior. However, neuroethological studies in songbirds have been limited by the lack of high-throughput...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine, Chalk, Alistair Morgan, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
BACKGROUND : Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair RR, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nick J, Kolle, Gabriel, ...
Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine, Chalk, Alistair Morgan, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
BACKGROUND : Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair RR, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nick J, Kolle, Gabriel, ...
Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par 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...
Complex Loci in Human and Mouse Genomes (2006)
Engstrom, Par G., Suzuki, Harukazu, Ninomiya, Noriko, Alkalin, 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...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par 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...
Complex Loci in Human and Mouse Genomes (2006)
Engstrom, Par G., Suzuki, Harukazu, Ninomiya, Noriko, Alkalin, 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...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine, Chalk, Alistair Morgan, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
BACKGROUND : Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair RR, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nick J, Kolle, Gabriel, ...
Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par 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...
Complex Loci in Human and Mouse Genomes (2006)
Engstrom, Par G., Suzuki, Harukazu, Ninomiya, Noriko, Alkalin, 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...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Frith, Martin C., Forrest, Alistair R. R., Ravasi, Timothy, ...
Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a welldefined site, and more plastic, broad and evolvable CpG-rich promoters. We have...
Mice and men: Their promoter properties (2006)
Bajic, Vladimir B., Tan, Sin Lam, Christoffels, Alan, Schonbach, Christian, Lilpovich, 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...
LOCATE: a mouse protein subcellular localization database (2006)
Fink, J. Lynn, Aturaliya, Rajith N., Davis, Melissa J., Zhang, Fasheng, Hanson, Kelly, Teasdale, Melvena S., ...
We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence...
Subcellular localization of mammalian type II membrane proteins (2006)
Aturaliya,Rajith N., Fink, J. Lynn, Davis, Melissa J., Hanson, Kelly A., Miranda,Kevin C., Forrest,Alistair R. R., ...
Application of a computational membrane organization prediction pipeline, MemO, identified putative type II membrane proteins as proteins predicted to encode a single alpha-helical transmembrane...
Transcriptional network dynamics in macrophage activation (2006)
Nilsson, Roland, Bajic, Vladimir B., Suzuki,Harukazu, Bernardo,Diego D., Bjorkegren,Johan, Katayama, Shintaro, ...
Transcriptional regulatory networks govern cell differentiation and the cellular response to external stimuli. However, mammalian model systems have not yet been accessible for network analysis....
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair Raymond Russell, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nic J, Kolle, Gabriel, ...
Background Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair Raymond Russell, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known...
The Abundance of Short Proteins in the Mammalian Proteome (2006)
Frith, Martin C., Forrest, Alistair Raymond Russell, 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...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair Raymond Russell, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nic J, Kolle, Gabriel, ...
Background Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair Raymond Russell, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known...
The Abundance of Short Proteins in the Mammalian Proteome (2006)
Frith, Martin C., Forrest, Alistair Raymond Russell, 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...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (2006)
Forrest, Alistair Raymond Russell, Taylor, Darrin F, Crowe, Mark L, Chalk, Alistair M, Waddell, Nic J, Kolle, Gabriel, ...
Background Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook...