Delineating developmental and metabolic pathways<i>in vivo</i>by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

Miki, Rika; Kadota, Koji; Bono, Hidemasa; Mizuno, Yosuke; Tomaru, Yuji; Carninci, Piero; Itoh, Masayoshi; Shibata, Kazuhiro; Kawai, Jun; Konno, Hiroyuki; Watanabe, Sachihiko; Sato, Kenjiro; Tokusumi, Yumiko; Kikuchi, Noriko; Ishii, Yoshiyuki; Hamaguchi, Yohei; Nishizuka, Itaru; Gotō, Hitoshi; Nitanda, Hiroyuki; Satoh, Susumu; Yoshiki, Atsushi; Kusakabe, Moriaki; DeRisi, Joseph L.; Eisen, Michael B.; Iyer, Vishwanath R.; Brown, Patrick O.; Muramatsu, Masami; Shimada, Hiroshi; Okazaki, Yasushi; Hayashizaki, Yoshihide

doi:10.1073/pnas.041605498

Cited by 192 publications

(154 citation statements)

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“…go.jp/READ/) (Miki et al 2001;Bono et al 2003). Correlating expression analysis by sequencing subtracted libraries, microarray, and other methods such as SAGE will present further computational challenges.…”

Section: Tissue Cdna Encyclopediamentioning

confidence: 99%

“…A TU is computationally defined to be a group of transcripts that contain a common core of genetic information having the same orientation, which does not necessarily correspond to proteincoding regions . From this collection, 60,770 fully sequenced cDNA clones have been function annotated Okazaki et al 2002) and used for genetics studies, expression profiling (Miki et al 2001), protein-protein interaction studies (Suzuki et al 2003), and alternative splicing (Kochiwa et al 2002). The analysis of polyadenylation signals also suggests that a majority of the 3Ј ends are likely to be true ends.…”

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confidence: 99%

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Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Carninci¹,

Waki²,

Shiraki³

et al. 2003

Genome Res.

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156

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We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3Ј-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by genome.cshlp.org Downloaded from annotated in the FANTOM-2 annotation. We have also produced 547,149 5Ј end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, 5Ј-end clusters identify regions that are potential promoters for 8637 known genes and 5Ј-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.[Supplemental material available online at www.genome.org.]One of the primary goals of genome sequencing projects is to identify the genome sequences that are transcribed into functional mRNAs, so that full-length cDNAs can be isolated to allow further downstream biology, and functional and structural genomics. The limitations of a priori genome annotation dictate that the transcriptome needs to be identified experimentally via cDNA cloning and sequencing. Although expressed sequence tags (ESTs) (Adams et al. 1991(Adams et al. , 1995Hillier et al. 1996;Marra et al. 1999;Kargul et al. 2001) and ORESTES (Camargo et al. 2001) have been extremely valuable for new gene discovery, these approaches have not allowed highthroughput recovering of full-length cDNA clones nor definition of protein sequence derived from actual cDNA clones. To overcome such problems, we undertook from the year 1995, a strategic project aimed at the comprehensive collection of at least one full-length cDNA derived from each mouse gene, a strategy that is recently becoming useful in similar projects to collect full-length gene collections (Stapleton et al. 2002;Strausberg et al. 2002).Because of the limited processivity of reverse transcriptase and other limitations, standard cDNA libraries generally contain a majority of truncated transcripts. The introductio...

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Section: Tissue Cdna Encyclopediamentioning

confidence: 99%

mentioning

confidence: 99%

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Carninci¹,

Waki²,

Shiraki³

et al. 2003

Genome Res.

Self Cite

156

132

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show abstract

“…We have constructed such a resource by profiling 46 human and 45 mouse tissues from diverse tissue origins. Whereas several recent studies have also described high-throughput gene expression measurements on diverse tissue sets (7)(8)(9), previous analyses of physiological gene function have been limited to identification of housekeeping genes, and clustering of genes involved in metabolic pathways and development of the central nervous system. The analysis of the data described in the current work has a significantly different and expanded scope.…”

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confidence: 99%

Large-scale analysis of the human and mouse transcriptomes

Cooke

Ching

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http:͞͞ expression.gnf.org) that integrates data visualization and curation of current gene annotations.

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“…Clustering analysis of gene expression patterns of isolated mouse macrophages and 49 mouse tissues (13,19) demonstrated that macrophage samples clustered independently from these tissues. Macrophages clustered closest to hemopoietic tissues such as the spleen, but were clearly distinct from the rest of the tissues.…”

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confidence: 99%

Gpnmb Is Induced in Macrophages by IFN-γ and Lipopolysaccharide and Acts as a Feedback Regulator of Proinflammatory Responses

Ripoll

Irvine

Ravasi

et al. 2007

The Journal of Immunology

202

187

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The process of inflammation requires the selective expression of a suite of genes in cells of the macrophage lineage. To identify candidate regulators of inflammation, we used cDNA microarrays to compare the transcriptome of inflammatory macrophages (thioglycolate-elicited peritoneal macrophages), bone marrow-derived macrophages, nonadherent spleen cells, and fibroblasts. We identified genes that were macrophage restricted and further elevated in inflammatory macrophages, and characterized the function of one such gene, gpnmb. Gpnmb mRNA expression was enriched in myelomonocytic cell lines and macrophage-related tissues and strongly up-regulated during macrophage differentiation. Epitope-tagged GPNMB expressed in RAW264.7 cells exhibited a perinuclear distribution and colocalized with the Golgi marker coat protein β. Upon activation of macrophages with IFN-γ and LPS, GPNMB translocated from the Golgi apparatus to vesicular compartments scattered toward the periphery. Gpnmb overexpression in RAW264.7 cells caused a 2-fold reduction in the production of the cytokines IL-6 and IL-12p40 and the inflammatory mediator NO in response to LPS. DBA mice, which have an inactivating point mutation in the gpnmb gene, exhibited reduced numbers of myeloid cells, elevated numbers of thioglycolate-elicited peritoneal macrophages, and higher levels of proinflammatory cytokines in response to LPS. Thus, GPNMB acts as a negative regulator of macrophage inflammatory responses.

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Delineating developmental and metabolic pathwaysin vivoby expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

Cited by 192 publications

References 15 publications

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Large-scale analysis of the human and mouse transcriptomes

Gpnmb Is Induced in Macrophages by IFN-γ and Lipopolysaccharide and Acts as a Feedback Regulator of Proinflammatory Responses

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