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CAGEライブラリー／解析結果HDDは、平日に到着するように発送致しますが、不測の事態が起きた場合には、休日に到着する可能性があることをご了承下さい。大量にご注文の際は発送方法が変更になる場合がございます。

論文

手法に関する論文

1. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Hirabayashi S et al,Nat Genet.2019; 51(9), 1369-1379.
2. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Haberle V et al,Nucleic Acids Res.2015; 43(8), e51.
3. RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). Ohmiya H et al,BMC Genomics.2014; 15, 269.
4. Detecting expressed genes using CAGE. Murata M et al,Methods Mol Biol.2014; 1164, 67-85.

ヒト・マウス以外でCAGEを用いた論文（抜粋）

CAGEを使用した論文一覧

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2022


1. Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension. Dahale S et al, Life Sci Alliance. 2022-04 Apr; 5(4):e202101234.
2. Insights regarding sirtuin-dependent gene regulation during white koji production. Futagami T et al, Commun Integr Biol. 2022-12-31 Dec; (1)15:92-95.
3. Suppression of human trophoblast syncytialization by human cytomegalovirus infection. Mimura N et al, Placenta. 2022; 117, 200-208.
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Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Guerrini M et al, Semin Immunopathol. 2022 Jan; 44(1), 127-136
Cytoplasmic localization of connexin 26 suppresses transition of β‐catenin into the nucleus in intestinal‐ and mix‐type gastric cancer. Nakazawa N et al, Ann Gastroenterol Surg. 2022-02-20 Feb; :ags3.12552.
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2021


1. Genome wide analysis of bovine enhancers and promoters across developmental stages in liver. Forutan M et al, Proc Assoc Advmt Anim Breed Genet. 2021; 24, 126-130.
2. Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes. Chiba Y et al, J Dent Res. 2021; 220345211049785.
3. CAGE-Seq Reveals that HIV-1 Latent Infection Does Not Trigger Unique Cellular Responses in a Jurkat T Cell Model. Matsui H et al, J Virol. 2021; 95(8), e02394-20.
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Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm. Sun Y et al, Nat Commun. 2021; 12(1), 1361.
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Abugessaisa I et al, Nucleic Acids Res. 2021; 49(D1), D892-D898.
IL-4i1 Regulation of Immune Protection During Mycobacterium tuberculosis Infection. Hlaka L et al, J Infect Dis. 2021; 224, 2170-2180.
Spontaneous pulmonary emphysema in mice lacking all three nitric oxide synthase isoforms. Kato K et al, Sci Rep. 2021; 11(1), 22088.
Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle. Deviatiiarov R et al, Commun Biol. 2021; 4(1), 1290.
Runt-related transcription factor-2 (Runx2) is required for bone matrix protein gene expression in committed osteoblasts in mice. Qin X et al, J Bone Miner Res. 2021; 36(10), 2081-2095.
The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. Ducoli L et al, BMC Genom Data. 2021; 22(1), 33.
Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin. Bäckdahl J et al, Cell Metab. 2021; 33(9), 1869-1882.e6.
Transcription start site‐level expression of thyroid transcription factor 1 isoforms in lung adenocarcinoma and its clinicopathological significance. Sano K et al, J Pathol: Clin Res. 2021; 7(4), 361-374.
Genome-Wide Atlas of Promoter Expression Reveals Contribution of Transcribed Regulatory Elements to Genetic Control of Disuse-Mediated Atrophy of Skeletal Muscle. Pintus S et al, Biology. 2021; 10(6), 557.
WWOX Loses the Ability to Regulate Oncogenic AP-2γ and Synergizes with Tumor Suppressor AP-2α in High-Grade Bladder Cancer. Kołat D et al, Cancers. 2021; 13(12), 2957.
Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus. Forutan M et al, Commun Biol. 2021; 4(1), 829.
Both murine and human sperm contain intact large RNAs. Wang Z et al, Biol Reprod. 2021; 104(6), 1184-1186.
Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11. Tokumoto S et al, Int J Mol Sci. 2021; 22(11), 5798.
Titanium nanoparticles potentially affect gingival tissue through IL-13α2 receptor expression. Ishikawa T et al, J Oral Sci. 2021; 63(3), 263-266.
eNEMAL, an enhancer RNA transcribed from a distal MALAT1 enhancer, promotes NEAT1 long isoform expression. Stone J et al, PLoS One. 2021; 16(5), e0251515.
Development of p53 knockout U87MG cell line for unbiased drug delivery testing system using CRISPR-Cas9 and transcriptomic analysis. Kwon A et al, J Biotech. 2021; 332, 72-82.
Identification of candidate PAX2-regulated genes implicated in human kidney development. Yamamura Y et al, Sci Rep. 2021; 11(1), 9123.
Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State. Mileti E et al, Diabetes. 2021; 70(7), 1486-1497.
Cancer‐associated fibroblast migration in non‐small cell lung cancers is modulated by increased integrin α11 expression. Iwai M et al, Mol Oncol. 2021; 15(5), 1507-1527.
Conophylline inhibits hepatocellular carcinoma by inhibiting activated cancer-associated fibroblasts through suppression of G Protein-Coupled Receptor 68. Yamanaka T et al, Mol Cancer Ther. 2021; 20(6), 1019-1028.
Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. Khor J et al, Genome Res. 2021; 31(9), 1680-1692.
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2020


1. TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage. Yu C et al, Nat Commun. 2020; 11(1), 6439.
2. Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages. Taguch A et al, scientific reports. 2020; 10(1), 17991.
3. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Ho J et al, Cell. 2020; 181(7), 1502-1517. E23.
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Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Morioka M et al, Bioinformatics for Cancer Immunotherapy: Methods and Protocols. 2020; 277-301.
Recounting the FANTOM CAGE-Associated Transcriptome. Imada E et al, Genome Res. 2020; 30(7), 1073-1081.
Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation. Zhang H et al, RNA Biol. 2020; 18(11), 1642-1652.
Heat shock induces the nuclear accumulation of YAP1 via SRC. Jiang X et al, Exp Cell Res. 2020; 399(1), 112439.
A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants. Efremova L et al, Genes. 2020; 11(12), 1407.
Deep phenotyping of myalgic encephalomyelitis/chronic fatigue syndrome in Japanese population. Kitami T et al, Sci Rep. 2020; 10(1), 19933.
The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs. Wei G et al, iScience. 2020; 23(11), 101741.
Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). Salavati M et al, Front Genet. 2020; 11, 580580.
Long Non-coding RNAs Diversity in Form and Function: From Microbes to Humans. Toomer G et al, The Chemical Biology of Long Noncoding RNAs. 2020; 1-57.
Experimental glioma with high bHLH expression harbor increased replicative stress and are sensitive toward ATR inhibition. Koch M et al, Neuro-oncol adv. 2020; 2(1), vdaa115.
Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart. Gacita A et al, Circ Heart Fail. 2020; 13(10), 467-480.
Circadian clock mechanism driving mammalian photoperiodism. Wood S et al, Nat Commun. 2020; 11(1), 1-15.
CAGE-seq analysis of osteoblast derived from cleidocranial dysplasia human induced pluripotent stem cells. Ooki A et al, Bone. 2020; 141, 115582.
Amplification of autocrine motility factor and its receptor in multiple myeloma and other musculoskeletal tumors. Nakajima K, Raz A A, J Bone Oncol. 2020; 23, 100308.
Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion. Kohno S et al, Oncogene. 2020; 39(34), 5690-5707.
Functional annotation of human long noncoding RNAs via molecular phenotyping. Ramilowski J et al, Genome Res. 2020; 30(7), 1060-1072.
The RNA exosome shapes the expression of key protein-coding genes. Wu M et al, Nucleic Acids Res. 2020; 48(15), 8509-8528.
The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1. Gažová I et al, Front Cell Dev Biol. 2020; 8, 498.
Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Wragg J et al, Nucleic Acids Res. 2020; 48(15), 8374-8392.
The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts. Beckedorff F et al, Cell Rep. 2020; 32(3), 107917.
Mac-2-binding protein glycan isomer enhances the aggressiveness of hepatocellular carcinoma by activating mTOR signaling. Dolgormaa G et al, Br J Cancer. 2020; 123(7), 1145-1153.
Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. Lewis S et al, PLoS Genet. 2020; 16(6), e1008864.
Epigenetic regulation of spurious transcription initiation in Arabidopsis. Le N et al, Nat Commun. 2020; 11(1), 3224.
Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences. Clohisey S et al, J Virol. 2020; 94(10), e01720-19.
The African Swine Fever Virus Transcriptome. Cackett G et al, J Virol. 2020; 94(9), e00119-20.
Sirtuin SirD is involved in α-amylase activity and citric acid production in Aspergillus luchuensis mut. kawachii during a solid-state fermentation process. Miyamoto A et al, ‎J Biosci Bioeng. 2020; 129(4), 454-466.
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways. Thieffry A et al, Plant Cell. 2020; 32(6), 1845-1867.
Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer Cells. Chen R et al, Front Oncol. 2020; 10, 316.
PD-1 imposes qualitative control of cellular transcriptomes in response to T cell activation. Shimizu K et al, Mol Cell. 2020; 77(5), 937-950.e6.
microRNA-875-5p plays critical role for mesenchymal condensation in epithelial-mesenchymal interaction during tooth development. Funada K et al, Sci Rep. 2020; 10(1), 4918.
PLAG1 enhances the stemness profiles of acinar cells in normal human salivary glands in a cell type-specific manner. Goto Y et al, J Oral Biosci. 2020; 62(1), 99-106.
RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Bonetti A et al, Nat Commun. 2020; 11(1), 1-14.
Belinostat resolves skin barrier defects in atopic dermatitis by targeting the dysregulated miR-335: SOX6 axis. Liew W et al, J Allergy Clin Immunol. 2020; 146(3), 606-620.e12.
Metabolite/phytohormone–gene regulatory networks in soybean organs under dehydration conditions revealed by integration analysis. Maruyama K et al, Plant J. 2020; 103(1), 197-211.
LaeA controls citric acid production through regulation of the citrate exporter-encoding cexA gene in Aspergillus luchuensis mut. kawachii. Kadooka C et al, Appl Environ Microbiol. 2020; 86(5), e01950-19.
Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Montgomery S et al, Curr Biol. 2020; 30(4), 573-588.e7.
Dual role of Jam3b in early hematopoietic and vascular development. Kobayashi I et al, Development. 2020; 147(1), dev181040.
Expression of a Constitutively Active Form of Hck in Chondrocytes Activates Wnt and Hedgehog Signaling Pathways, and Induces Chondrocyte Proliferation in Mice. Matsuura V et al, Int J Mol Sci. 2020; 21(8), 2682.
Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nepal C et al, Nat Commun. 2020; 11(1), 168.
Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements. Lu D et al, Genes Dev. 2020; 34(9-10), 663-677.
Genome-Wide Analysis of Transcription Start Sites and Core Promoter Elements in Hevea brasiliensis. Makita Y et al, The Rubbe Tree Genome. 2020; 81-91.
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2019


1. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Hirabayashi S et al, Nat Genet. 2019; 51(9), 1369-1379.
2. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. Ha T J et al, BMC Genomics. 2019; 20(1), 718.
3. CXCL4/PF4 is a predictive biomarker of cardiac differentiation potential of human induced pluripotent stem cells. Ohashi F et al, Sci Rep. 2019; 9(1), 4638.
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Transcription Start Site Mapping Using Super-low Input Carrier-CAGE. Cvetesic N et al, J Vis Exp. 2019; (148), e59805.
Mesenchymal stem cells cultured under hypoxic conditions had a greater therapeutic effect on mice with liver cirrhosis compared to those cultured under normal oxygen conditions. Kojima Y et al, Regen Ther. 2019; 11, 269-281.
HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP. Miyazato P et al, Retrovirology. 2019; 16(1), 38.
CAGEfightR: analysis of 5'-end data using R/Bioconductor. Thodberg M et al, BMC Bioinformatics. 2019; 20(1), 487.
The WWOX Gene Influences Cellular Pathways in the Neuronal Differentiation of Human Neural Front Cell. Kośla K et al, Front Cell Neurosci. 2019; 13, 391.
An impaired intrinsic microglial clock system induces neuroinflammatory alterations in the early stage of amyloid precursor protein knock-in mouse brain. Ni J et al, J Neuroinflammation. 2019; 16(1), 173.
Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis. Zhou X et al, Cell Mol Life Sci. 2019; 76(11), 2185-2198.
A step-by-step guide to analyzing CAGE data using R/Bioconductor. Thodberg M et al, F1000Res. 2019; 8, 886.
Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. Lu Z, Lin Z Z, Genome Res. 2019; 29(7), 1198-1210.
Identification of hypothalamic genes in associating with food intake during incubation behavior in domestic chicken. Takeda M et al, Anim Sci J. 2019; 90(9), 1293-1302.
Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68. O’Grady T et al, Cell Rep. 2019; 27(13), 3988-4002.e5.
Intra- and interspecies comparison of EYS transcripts highlights its characteristics in the eye. Takita S et al, FASEB J. 2019; 33(8), 9422-9433.
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions. Hardwick SA et al, Front Genet. 2019; 10, 309.
Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson's Disease. Valentine MNZ et al, Sci Data. 2019; 6(1), 20.
Specific Features of Fibrotic Lung Fibroblasts Highly Sensitive to Fibrotic Processes Mediated via TGF-β-ERK5 Interaction. Kadoya K et al, Cell Physiol Biochem. 2019; 52(4), 822-837.
Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. Zucchelli et al, Mol Neurobiol. 2019; 56, 5392-5415.
Comprehensive analysis of chromatin signature and transcriptome uncovers functional lncRNAs expressed in nephron progenitor cells. Nishikawa M et al, Biochim Biophys Acta Gene Regul Mech. 2019; 1862(1), 58-70.
YeasTSS: an integrative web database of yeast transcription start sites. McMillan J et al, Database. 2019; baz048.
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2018


1. Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β. Alhendi AMN et al, Sci Rep. 2018; 8(1), 13164.
2. Genome-Wide TSS Identification in Maize. Mejia-Guerra MK et al, Methods Mol Biol. 2018; 1830, 239-256.
3. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Reyes A et al, Nucleic Acids Res. 2018; 46(2), 582-592.
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SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Cvetesic N et al, Genome Res. 2018; 28(12), 1943-1956.
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Lizio M et al, Nucleic Acids Res. 2018; 47(Database issue), D752-D758.
NanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing. Ivanchenko MG et al, Methods Mol Biol. 2018; 1830, 225-237.
Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Adiconis X et al, Nat Methods. 2018; 15(7), 505-511.
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. Börlin CS et al, FEMS Yeast Res. 2018; 19(2), foy128.
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. Thodberg M et al, Nucleic Acids Res. 2018; 47(4), 1671-1691.
Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity. Sakaue S et al, Nucleic Acids Res. 2018; 46(22), 11898-11909.
Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. Vacca A et al, Open Biol. 2018; 8(8), 180011.
CAGE-seq analysis of Epstein-Barr virus lytic gene transcription: 3 kinetic classes from 2 mechanisms. Djavadian R et al, PLoS Pathog. 2018; 14(6), e1007114.
Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Roy S et al, Sci Rep. 2018; 8(1), 6758.
Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9. Sakaguchi Y et al, Sci Rep. 2018; 8(1), 7504.
Characterization of the human RFX transcription factor family by regulatory and target geneanalysis. Sugiaman-Trapman D et al, BMC Genomics. 2018; 19(1), 181.
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. Baillie JK et al, PLoS Comput Biol. 2018; 14(3), e1005934.
Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate. Danks GB,et al, BMC Genomics. 2018; 19(1), 164.
Correction to: Relatively frequent switching of transcription start sites during cerebellar development. Zhang P et al, BMC Genomics. 2018; 19(1), 39.
TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts. Horie M et al, Am J Physiol Lung Cell Mol Physiol. 2018; 314(1), L177-L191.
Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors. Daskalakis M et al, Cell Cycle. 2018; 17(7), 811-822.
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2017


1. An atlas of human long non-coding RNAs with accurate 5' ends. Hon CC et al, Nature. 2017; 543(7644), 199-204.
2. Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. Francescatto M et al, Sci Data. 2017; 4, 170163.
3. Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis. Yoshida E et al, Sci Rep. 2017; 7(1), 14160.
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Linking FANTOM5 CAGE peaks to annotations with CAGEscan. Bertin N,et al, Sci Data. 2017; 4, 170147.
The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types. Kawaji H et al, Sci Data. 2017; 4, 170113.
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. Abugessaisa I et al, Sci Data. 2017; 4, 170107.
FANTOM5 CAGE profiles of human and mouse samples. Noguchi S et al, Sci Data. 2017; 4, 170112.
TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct. Izumi Y et al, PLoS One. 2017; 12(8), e0184185.
The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers. Abugessaisa I et al, Methods Mol Biol. 2017; 1611, 199-217.
Deep Cap Analysis of Gene Expression (CAGE): Genome-Wide Identification of Promoters, Quantification of Their Activity, and Transcriptional Network Inference. Fort A et al, Methods Mol Biol. 2017; 1543, 111-126.
NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes. Poulain S et al, Methods Mol Biol. 2017; 1543, 57-109.
Monitoring transcription initiation activities in rat and dog. Lizio M et al, Sci Data. 2017; 4, 170173.
Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas. Yoshihara M et al, EBioMedicine. 2017; 25, 175-186.
Genome-wide profiling of transcribed enhancers during macrophage activation. Denisenko E et al, Epigenetics Chromatin. 2017; 10(1), 50.
Arabidopsis thaliana cold-regulated 47 gene 5'-untranslated region enables stable high-level expression of transgenes. Yamasaki S et al, J Biosci Bioeng. 2017; 125(1), 124-130.
Systematic analysis of transcription start sites in avian development. Lizio M et al, PLoS Biol. 2017; 15(9), e2002887.
An integrated expression atlas of miRNAs and their promoters in human and mouse. de Rie D et al, Nat Biotechnol. 2017; 35(9), 872-878.
Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain. Liu S et al, Genome Res. 2017; 27(9), 1608-1620.
Application of a CAGE Method to an Avian Development Study. Deviatiiarov R et al, Methods Mol Biol. 2017; 1650, 101-109.
High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor. Yoshihara M et al, Sci Rep. 2017; 7(1), 2845.
A high-quality annotated transcriptome of swine peripheral blood. Liu H et al, BMC Genomics. 2017; 18(1), 479.
Correlation of EGFR or KRAS mutation status with 18F-FDG uptake on PET-CT scan in lung adenocarcinoma. Takamochi K et al, PLoS One. 2017; 12(4), e0175622.
Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. Baillie JK et al, PLoS Genet. 2017; 13(3), e1006641.
A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny. Sugiyama D et al, Stem Cells Dev. 2017; 26(5), 314-327.
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Lizio M et al, Nucleic Acids Res. 2017; 45(D1), D737-D743.
Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution. Ehrlund A et al, Diabetes. 2017; 66(1), 218-230.
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2016


1. Cap Analysis of Gene Expression (CAGE) Sequencing Reveals Alterations of the Transcriptional Signatures of FLT3-ITD with Secondary D835 TKD Mutations in Acute Myeloid Leukemia. Tabe Y et al, Blood. 2016; 128(22), 1530.
2. Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases. Murakawa Y et al, Trends Genet. 2016; 32(2), 76-88.
3. Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers. Kaczkowski B et al, Cancer Res. 2016; 76(2), 216-226.
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FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. Abugessaisa I et al, Database. 2016; baw105.
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Chen CY et al, Sci Rep. 2016; 6, 37324.
Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma. Altinel K et al, J Virol. 2016; 90(23), 10811-10822.
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Alam T et al, Nucleic Acids Res. 2016; 45(5), 2838-2848.
Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Kleftogiannis D et al, Nucleic Acids Res. 2016; 45(4), e25.
Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. Raborn RT et al, Genetics. 2016; 204(2), 593-612.
Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis. Horie M et al, Sci Rep. 2016; 6, 33666.
Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung. Takamochi K et al, BMC Cancer. 2016; 16(1), 760.
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Lau NS et al, Sci Rep. 2016; 6, 28594.
Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. Radzisheuskaya A et al, Nucleic Acids Res. 2016; 44(18), e141.
Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe. Blauwendraat C et al, Genome Med. 2016; 8, 65.
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. Arenillas DJ et al, Bioinformatics. 2016; 32(18), 2858-2860.
DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C. Klein S et al, J Cell Sci. 2016; 129(13), 2573-2585.
Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis. Yamaguchi K et al, Sci Rep. 2016; 6, 26011.
nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs. Gandin V et al, Genome Res. 2016; 26(5), 636-648.
The emerging role of noncoding RNA in prostate cancer progression and its implication on diagnosis and treatment. Takayama K et al, Brief Funct Genomics. 2016; 15(3), 257-265.
Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment. Romano O et al, Sci Rep. 2016; 6, 24724.
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. St Laurent G et al, Nucleic Acids Res. 2016; 44(7), 3233-3252.
C9orf72 is differentially expressed in the central nervous system and myeloid cells and consistently reduced in C9orf72, MAPT and GRN mutation carriers. Rizzu P et al, Acta Neuropathol Commun. 2016; 4(1), 37.
A predictive computational framework for direct reprogramming between human cell types. Rackham OJ et al, Nat Genet. 2016; 48(3), 331-335.
Large-scale profiling of signalling pathways reveals an asthma specific signature in bronchial smooth muscle cells. Alexandrova E et al, Oncotarget. 2016; 7, 25150-25161.
Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine. Nguyen Q et al, Curr Top Microbiol Immunol. 2016; 394, 237-258.
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2015


1. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner E et al, Science. 2015; 347(6225), 1010-1014.
2. CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors. Hashimoto K et al, Genome Res. 2015; 25(12), 1812-1824.
3. Coexpression networks identify brain region-specific enhancer RNAs in the human brain. Yao P et al, Nat Neurosci. 2015; 18(8), 1168-1174.
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CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Haberle V et al, Nucleic Acids Res. 2015; 43(8), e51.
Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Fraser J et al, Mol Syst Biol. 2015; 11(12), 852.
The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. Hurst LD et al, PLoS Biol. 2015; 13(12), e1002315.
Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Lennartsson A et al, Epigenetics Chromatin. 2015; 8, 55.
Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. Mejía-Guerra MK et al, Plant Cell. 2015; 27(12), 3309-3320.
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. Carbajo D et al, PLoS One. 2015; 10(12), e0144176.
Tor Signaling Regulates Transcription of Amino Acid Permeases through a GATA Transcription Factor Gaf1 in Fission Yeast. Yan M et al, PLoS One. 2015; 10(12), e0144677.
Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome. Robert C et al, BMC Genomics. 2015; 16(1), 970.
DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium. Dieterich LC et al, Cell Rep. 2015; 13(7), 1493-1504.
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line. Lizio M et al, Front Genet. 2015; 6, 331.
The frequent evolutionary birth and death of functional promoters in mouse and human. Young RS et al, Genome Res. 2015; 25(10), 1546-1557.
Paradigm shifts in genomics through the FANTOM projects. de Hoon M et al, Mamm Genome. 2015; 26(9-10), 391-402.
Targeting Batf2 for infectious diseases and cancer. Guler R et al, Oncotarget. 2015; 6(29), 26575-26582.
Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Roy S et al, Nucleic Acids Res. 2015; 43(14), 6969-6982.
NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites. Cumbie JS et al, BMC Genomics. 2015; 16, 597.
Expression of mouse Dab2ip transcript variants and gene methylation during brain development. Salami F et al, Gene. 2015; 568(1), 19-24.
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Yu NY et al, Nucleic Acids Res. 2015; 43(14), 6787-6798.
EpiFactors: a comprehensive database of human epigenetic factors and complexes. Medvedeva YA et al, Database. 2015; bav067.
Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells. Mina M et al, Sci Rep. 2015; 5, 11999.
A draft network of ligand-receptor-mediated multicellular signalling in human. Ramilowski JA et al, Nat Commun. 2015; 6, 7866.
Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells. Joshi A et al, J Leukoc Biol. 2015; 97(5), 985-995.
Retinoic acid potentiates inflammatory cytokines in human mast cells: identification of mast cells as prominent constituents of the skin retinoid network. Babina M et al, Mol Cell Endocrinol. 2015; 406, 49-59.
ElemeNT: a computational tool for detecting core promoter elements. Sloutskin A et al, Transcription. 2015; 6(3), 41-50.
Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease. Carrieri C et al, Front Cell Neurosci. 2015; 9, 114.
Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. Aitken S et al, PLoS Comput Biol. 2015; 11(4), e1004217.
Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions. Sokol M et al, Retrovirology. 2015; 12, 32.
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. Yoshihara M et al, PLoS One. 2015; 10(3), e0117581.
Transcription factor, promoter, and enhancer utilization in human myeloid cells. Joshi A et al, J Leukoc Biol. 2015; 97(5), 985-995.
piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. Han BW et al, Bioinformatics. 2015; 31(4), 593-595.
Characterization of Novel Transcripts of Human Papillomavirus Type 16 Using Cap Analysis Gene Expression Technology. Taguchi A et al, Journal of Virology. 2015; 89(4), 2448-2452.
Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify noncoding loci resistant to reprogramming. Fort A et al, Cell Cycle. 2015; 14(8), 1148-1155.
The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Liang C et al, Nat Commun. 2015; 6, 6066.
Gateways to the FANTOM5 promoter level mammalian expression atlas. Lizio M et al, Genome Biol. 2015; 16, 22.
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2014


1. An atlas of active enhancers across human cell types and tissues. Andersson R et al, Nature. 2014; 507(7493), 455-461.
2. A promoter level mammalian expression atlas. FANTOM Consortium et al, Nature. 2014; 507(7493), 462-470.
3. Two independent transcription initiation codes overlap on vertebrate core promoters. Haberle V et al, Nature. 2014; 507(7492), 381-385.
    and more


Detecting expressed genes using CAGE. Murata M et al, Methods Mol Biol. 2014; 1164, 67-85.
RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). Ohmiya H et al, BMC Genomics. 2014; 15, 269.
Understanding Epistatic Interactions between Genes Targeted by Non-coding Regulatory Elements in Complex Diseases. Sung MK et al, Genomics Inform. 2014; 12(4), 181-186.
CAGE-defined promoter regions of the genes implicated in Rett Syndrome. Vitezic M et al, BMC Genomics. 2014; 15, 1177.
Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Verardo R et al, Stem Cells. 2014; 32(11), 2998-3011.
Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury. Yasuda M et al, BMC Genomics. 2014; 15, 982.
Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. Grison A et al, BMC Genomics. 2014; 15, 729.
Mast cell transcriptome elucidation: what are the implications for allergic disease in the clinic and where do we go next? Babina M et al, Expert Rev Clin Immunol. 2014; 10(8), 977-980.
Integrating epigenetic marks for identification of transcriptionally active miRNAs. Xiao Y et al, Genomics. 2014; 104(2), 70-78.
A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Tomaru Y et al, Nucleic Acids Res. 2014; 42(14), 8905-8913.
A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Hurst LD et al, Genome Biol. 2014; 15(7), 413.
CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Hasegawa Y et al, Sci Rep. 2014; 4, 5228.
The evolution of human cells in terms of protein innovation. Sardar AJ et al, Mol Biol Evol. 2014; 31(6), 1364-1374.
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Fort A et al, Nat Genet. 2014; 46(6), 558-566.
Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping. Yamaga R et al, Biochem Biophys Res Commun. 2014; 447(3), 531-536.
MOIRAI: a compact workflow system for CAGE analysis. Hasegawa A et al, BMC Bioinformatics. 2014; 15, 144.
Genomics: a catalogue of human gene activity. Lokody I et al, Nat Rev Genet. 2014; 15(5), 290.
Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Davis MR et al, Mol Gen Metab. 2014; 112(1), 73-83.
Transcription and enhancer profiling in human monocyte subsets. Schmidl C et al, Blood. 2014; 123(17), e90-99.
The enhancer and promoter landscape of human regulatory and conventional T cell subpopulations. Schmidl C et al, Blood. 2014; 123(17), e68-e78.
Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Motakis E et al, Blood. 2014; 123(17), e58-e67.
High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Prasad P et al, Blood. 2014; 123(17), e46-e57.
Explaining the correlations among properties of mammalian promoters. Frith MC et al, Nucleic Acids Res. 2014; 42(8), 4823-4832.
Deep sequencing blood transcriptomes. Forrest AR et al, Blood. 2014; 123(17), 2595-2596.
Comparison of CAGE and RNA-seq transcriptome profiling using a clonally amplified and single molecule next generation sequencing. Kawaji H et al, Genome Res. 2014; 24(4), 708-717.
Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Rönnerblad M et al, Blood. 2014; 123(17), e79-e89.
Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Morikawa H et al, Proc Natl Acad Sci U S A. 2014; 111(14), 5289-5294.
Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. Arner E et al, PLoS One. 2014; 9(3), e80274.
Effects of cytosine methylation on transcription factor binding sites. Medvedeva YA et al, BMC Genomics. 2014; 15, 119.
Interactive visualization and analysis of large-scale NGS data-sets using ZENBU. Severin J et al, Nat Biotechnol. 2014; 32(3), 217-219.
Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. Rye M et al, BMC Genomics. 2014; 15, 120.
CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. Dimont E et al, Bioinformatics. 2014; 30(8), 1183-1184.
NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Pascarella G et al, Front Cell Neurosci. 2014; 8, 41.
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2013


2013
1. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Tang DT et al, Nucleic Acids Res. 2013; 41(3), e44.
2. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Nepal C et al, Genome Res. 2013; 23(11), 1938-1950.
3. A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. Sompallae R et al, Front Genet. 2013; 4, 209.
4. Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation. Harbers M et al, BMC Genomics. 2013; 14, 665.
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2012


2012
1. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Carrieri C et al, Nature. 2012; 491(7424), 454-457.
2. Landscape of transcription in human cells. Djebali S et al, Nature. 2012; 489(7414), 101-108.
3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium, Nature. 2012; 489(7414), 57-74.
4. CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Takahashi H et al, Methods Mol Biol. 2012; 786, 181-200.
5. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H et al, Nat Protoc. 2012; 7(3), 542-561.
6. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer. Itoh M et al, PLoS One. 2012; 7(1), e30809.
7. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Derrien T et al, Genome Res. 2012; 22(9), 1775-1789.
8. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Schroder K et al, Proc Natl Acad Sci U S A. 2012; 109(16), E944-E953.
9. Promoter architecture of mouse olfactory receptor genes. Plessy C et al, Genome Res. 2012; 22(3), 486-497.
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2011


2011
1. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Salimullah M et al, Cold Spring Harb Protoc. 2011; 2011(1), pdb.prot5559.
2. Discovery of the "RNA continent" through a contrarian's research strategy. Hayashizaki Y et al, Genes Genet Syst. 2011; 86(4), 221-229.
3. Macrophages.com: an on-line community resource for innate immunity research. Robert C et al, Immunobiology. 2011; 216(11), 1203-1211.
4. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Chien CH et al, Nucleic Acids Res. 2011; 39(21), 9345-9356.
5. Systematic clustering of transcription start site landscapes. Zhao X et al, PLoS One. 2011; 6(8), e23409.
6. Unamplified cap analysis of gene expression on a single-molecule sequencer. Kanamori-Katayama M et al, Genome Res. 2011; 21(7), 1150-1159.
7. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Hoskins RA et al, Genome Res. 2011; 21(2), 182-192.
8. Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Kawaji H et al, Nucleic Acids Res. 2011; 39(Database issue), D856-D860.
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2010


2010
1. Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. Vitezic M et al, Nucleic Acids Res. 2010; 38(22), 8141-8148.
2. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Plessy C et al, Nat Methods. 2010; 7(7), 528-534.
3. An atlas of combinatorial transcriptional regulation in mouse and man. Ravasi T et al, Cell. 2010; 140(5), 744-752.
4. High sensitivity TSS prediction: estimates of locations where TSS cannot occur. Schaefer U et al, PLoS One. 2010; 5(11), e13934.
5. Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies. Hestand MS et al, Nucleic Acids Res. 2010; 38(16), e165.
6. The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Kubosaki A et al, Mol Immunol. 2010; 47(14), 2295-2302.
7. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Atanur SS et al, Genome Res. 2010; 20(6), 791-803.
8. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. Kratz A et al, BMC Genomics. 2010; 11, 257.
9. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. de Hoon MJ et al, Genome Res. 2010; 20(2), 257-264.
10. Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation. Forrest AR et al, Leukemia. 2010; 24(2), 460-466.
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2009


2009
1. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Kawaji H et al, Genome Biol. 2009; 10(4), R40.
2. Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. Schmeier S et al, BMC Genomics. 2009; 10, 595.
3. Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential. Hoat TX et al, BMC Cell Biol. 2009; 10, 69.
4. MiR-107 and MiR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines. Takahashi Y et al, PLoS One. 2009; 4(8), e6677.
5. High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line. Adati N et al, BMC Res Notes. 2009; 2, 153.
6. Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis. Tomaru Y et al, Genome Biol. 2009; 10(11), R121.
7. SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes. Kawaji H et al, BMC Bioinformatics. 2009; 10, 133.
8. Tiny RNAs associated with transcription start sites in animals. Taft RJ et al, Nat Genet. 2009; 41(5), 572-578.
9. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. FANTOM Consortium et al, Nat Genet. 2009; 41(5), 553-562.
10. The regulated retrotransposon transcriptome of mammalian cells. Faulkner GJ et al, Nat Genet. 2009; 41(5), 563-571.
11. Data-driven normalization strategies for high-throughput quantitative RT-PCR. Mar JC et al, BMC Bioinformatics. 2009; 10, 110.
12. A transcription factor affinity-based code for mammalian transcription initiation. Megraw M et al, Genome Res. 2009; 19(4), 644-656.
13. Chromatin conformation signatures of cellular differentiation. Fraser J et al, Genome Biol. 2009; 10(4), R37.
14. Transcriptional features of genomic regulatory blocks. Akalin A et al, Genome Biol. 2009; 10(4), R38.
15. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Severin J et al, Genome Biol. 2009; 10(4), R39.
16. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Valen E et al, Genome Res. 2009; 19(2), 255-265.
17. Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation. Kubosaki A et al, Genome Biol. 2009; 10(4), R41.
18. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Balwierz PJ et al, Genome Biol. 2009; 10(7), R79.
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2008


2008
1. Genome-wide analysis of cancer/testis gene expression. Hofmann O et al, Proc Natl Acad Sci U S A. 2008; 105(51), 20422-20427.
2. Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation. Tochitani S et al, Biochem Biophys Res Commun. 2008; 372(4), 691-696.
3. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Maeda N et al, Biotechniques. 2008; 45(1), 95-97.
4. The Ewing sarcoma protein (EWS) binds directly to the proximal elements of the macrophage-specific promoter of the CSF-1 receptor (csf1r) gene. Hume DA et al, J Immunol. 2008; 180(10), 6733-6742.
5. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Faulkner GJ et al, Genomics. 2008; 91(3), 281-288.
6. The RNA continent. Yasuda J et al, Adv Cancer Res. 2008; 99, 77-112.
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2007


2007
1. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. ENCODE Project Consortium et al, Nature. 2007; 447(7146), 799-816.
2. Large-scale clustering of CAGE tag expression data. Shimokawa K et al, BMC Bioinformatics. 2007; 8, 161.
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2006


2006
1. CAGE: cap analysis of gene expression. Kodzius R et al, Nat Methods. 2006; 3(3), 211-222.
2. The complexity of the mammalian transcriptome. Gustincich S et al, J Physiol. 2006; 575(Pt2), 321-332.
3. Tagging mammalian transcription complexity. Carninci P et al, Trends Genet. 2006; 22(9), 501-510.
4. Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Ajioka I et al, Keio J Med. 2006; 55(3), 107-110.
5. Transcriptional network dynamics in macrophage activation. Nilsson R et al, Genomics. 2006; 88(2), 133-142.
6. Genome-wide analysis of mammalian promoter architecture and evolution. Carninci P et al, Nat Genet. 2006; 38(6), 626-635.
7. Dynamic usage of transcription start sites within core promoters. Kawaji H et al, Genome Biol. 2006; 7(12), R118.
8. Subcellular localization of mammalian type II membrane proteins. Aturaliya RN et al, Traffic. 2006; 7(5), 613-625.
9. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. Maeda N et al, PLoS Genet. 2006; 2(4), e62.
10. The abundance of short proteins in the mammalian proteome. Frith MC et al, PLoS Genet. 2006; 2(4), e52.
11. Pseudo-messenger RNA: phantoms of the transcriptome. Frith MC et al, PLoS Genet. 2006; 2(4), e23.
12. Mice and men: their promoter properties. Bajic VB et al, PLoS Genet. 2006; 2(4), e54.
13. Heterotachy in mammalian promoter evolution. Taylor MS et al, PLoS Genet. 2006; 2(4), e30.
14. Genome Network and FANTOM3: assessing the complexity of the transcriptome. Hayashizaki Y et al, PLoS Genet. 2006; 2(4), e63.
15. Distinguishing protein-coding from non-coding RNAs through support vector machines. Liu J et al, PLoS Genet. 2006; 2(4), e29.
16. Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. Davis MJ et al, PLoS Genet. 2006; 2(4), e46.
17. Complex Loci in human and mouse genomes. Engström PG et al, PLoS Genet. 2006; 2(4), e47.
18. Clusters of internally primed transcripts reveal novel long noncoding RNAs. Furuno M et al, PLoS Genet. 2006; 2(4), e37.
19. A simple physical model predicts small exon length variations. Chern TM et al, PLoS Genet. 2006; 2(4), e45.
20. A method for similarity search of genomic positional expression using CAGE. Seno S et al, PLoS Genet. 2006; 2(4), e44.
21. Discrimination of non-protein-coding transcripts from protein-coding mRNA. Frith MC et al, RNA Biol. 2006; 3(1), 40-48.
22. CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Kawaji H et al, Nucleic Acids Res. 2006; 34(Database issue), D632-D636.
23. Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Forrest AR et al, Genome Biol. 2006; 7(1), R5.
24. Alternate transcription of the Toll-like receptor signaling cascade. Wells CA et al, Genome Biol. 2006; 7(2), R10.
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2005


2005
1. The transcriptional landscape of the mammalian genome. Carninci P et al, Science. 2005; 309(5740), 1559-1563.
2. Fewer Genes, More Noncoding RNA. Claverie JM, Science. 2005; 309(5740), 1529-1530.
3. Antisense transcription in the mammalian transcriptome. Katayama S et al, Science. 2005; 309(5740), 1564-1566.
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2004


2004
1. Integrated analysis of the genome and the transcriptome by FANTOM. Katayama S et al, Brief Bioinform. 2004; 5(3), 249-258.
2. FREP: a database of functional repeats in mouse cDNAs. Nagashima T et al, Nucleic Acids Res. 2004; 32(Database issue), D471-D475.
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2003


2003
1. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Shiraki T et al, Proc Natl Acad Sci U S A. 2003; 100(26), 15776-15781.
2. Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts. Hirozane-Kishikawa T et al, Biotechniques. 2003; 35(3), 510-6, 518.
3. The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Grimmond SM et al, Genome Res. 2003; 13(6B), 1350-1359.
4. The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer. Suzuki H et al, Genome Res. 2003; 13(6B), 1534-1541.
5. The comparative proteomics of ubiquitination in mouse. Semple CA et al, Genome Res. 2003; 13(6B), 1389-1394.
6. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Carninci P et al, Genome Res. 2003; 13(6B), 1273-1289.
7. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Bono H et al, Genome Res. 2003; 13(6B), 1318-1323.
8. Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Ravasi T et al, Genome Res. 2003; 13(6B), 1430-1442.
9. Phosphoregulators: protein kinases and protein phosphatases of mouse. Forrest AR et al, Genome Res. 2003; 13(6B), 1443-1454.
10. Mouse proteome analysis. Kanapin A et al, Genome Res. 2003; 13(6B), 1335-1344.
11. Kinesin superfamily proteins (KIFs) in the mouse transcriptome. Miki H et al, Genome Res. 2003; 13(6B), 1455-1465.
12. Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS. Nagashima T et al, Genome Res. 2003; 13(6B), 1520-1533.
13. Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome. Zavolan M et al, Genome Res. 2003; 13(6B), 1290-1300.
14. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Numata K et al, Genome Res. 2003; 13(6B), 1301-1306.
15. Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. Tajul-Arifin K et al, Genome Res. 2003; 13(6B), 1416-1429.
16. Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set. Schriml LM et al, Genome Res. 2003; 13(6B), 1496-1500.
17. GeneLynx mouse: integrated portal to the mouse genome. Lenhard B et al, Genome Res. 2003; 13(6B), 1501-1504.
18. Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set. Forrest AR et al, Genome Res. 2003; 13(6B), 1366-1375.
19. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Nikaido I et al, Genome Res. 2003; 13(6B), 1402-1409.
20. Development and evaluation of an automated annotation pipeline and cDNA annotation system. Kasukawa T et al, Genome Res. 2003; 13(6B), 1542-1551.
21. Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set. Brusic V et al, Genome Res. 2003; 13(6B), 1307-1317.
22. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Wells CA et al, Genome Res. 2003; 13(6B), 1360-1365.
23. Connecting sequence and biology in the laboratory mouse. Baldarelli RM et al, Genome Res. 2003; 13(6B), 1505-1519.
24. Comprehensive analysis of the mouse metabolome based on the transcriptome. Bono H et al, Genome Res. 2003; 13(6B), 1345-1349.
25. Comparative analysis of apoptosis and inflammation genes of mice and humans. Reed JC et al, Genome Res. 2003; 13(6B), 1376-1388.
26. CDS annotation in full-length cDNA sequence. Furuno M et al, Genome Res. 2003; 13(6B), 1478-1487.
27. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Kiyosawa H et al, Genome Res. 2003; 13(6B), 1324-1334.
28. Analysis of the mouse transcriptome for genes involved in the function of the nervous system. Gustincich S et al, Genome Res. 2003; 13(6B), 1395-1401.
29. A comprehensive transcript map of the mouse Gnas imprinted complex. Holmes R et al, Genome Res. 2003; 13(6B), 1410-1415.
30. G protein-coupled receptor genes in the FANTOM2 database. Kawasawa Y et al, Genome Res. 2003; 13(6B), 1466-1477.
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2002


2002
1. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y et al, Nature. 2002; 420(6915), 563-573.
2. FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. Bono H et al, Nucleic Acids Res. 2002; 30(1), 116-118.
3. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Carninci P et al, Biotechniques. 2002; 33(2), 306-309.
4. Extra-long first-strand cDNA synthesis. Carninci P et al, Biotechniques. 2002; 32(5), 984-985.
5. Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes. Ravasi T et al, J Immunol. 2002; 168(1), 44-50.
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2001


2001
1. Functional annotation of a full-length mouse cDNA collection. Kawai J et al, Nature. 2001; 409(6821), 685-690.
2. Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing. Shibata Y et al, Biotechniques. 2001; 31(5), 1042 1044 1048-9.
3. Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Carninci P et al, Genomics. 2001; 77(1-2), 79-90.
4. Cloning Full-Length, Cap-Trapper-Selected cDNAs by Using the Single-Strand Linker Ligation Method. Shibata Y et al, Biotechniques. 2001; 30(6), 1250-1254.
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2000


2000
1. Viva la revolution! A report from the FANTOM meeting. Quackenbush J et al, Nat Genet. 2000; 26(3), 255-256.
2. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Carninci P et al, Genome Res. 2000; 10(10), 1617-1630.
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1999


1999
1. High-efficiency full-length cDNA cloning. Carninci P et al, Methods Enzymol. 1999; 303, 19-44.
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1998


1998
1. Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA. Carninci P et al, Proc Natl Acad Sci U S A. 1998; 95(2), 520-524.
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1997


1997
1. High efficiency selection of full-length cDNA by improved biotinylated cap trapper. Carninci P et al, DNA Res. 1997; 4(1), 61-66.
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1996


1996
1. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Carninci P et al, Genomics. 1996; 37(3), 327-336.
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