Abstract:
:Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yu NY,Hallström BM,Fagerberg L,Ponten F,Kawaji H,Carninci P,Forrest AR,Fantom Consortium.,Hayashizaki Y,Uhlén M,Daub COdoi
10.1093/nar/gkv608subject
Has Abstractpub_date
2015-08-18 00:00:00pages
6787-98issue
14eissn
0305-1048issn
1362-4962pii
gkv608journal_volume
43pub_type
杂志文章abstract::We previously reported the isolation of PRP28, a gene in Saccharomyces cerevisiae whose activity is required for the first step of nuclear mRNA splicing in vivo. Sequence analysis revealed that PRP28 is included in the 'DEAD-box' gene family, members of which are thought to function as ATP-dependent RNA helicases. Gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3187
更新日期:1994-08-11 00:00:00
abstract::The transcripts of a 6Kbp region of the mitochondrial genome of S. cerevisiae, localized in the 21S rRNA-OXI1 span and including 12 tRNA genes (from tRNA(thr) to tRNA(ala)) and several G+C clusters, have been studied by analysis of in vitro capped primary transcripts and by fine mapping of the 5' ends of transcripts. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.16.6387
更新日期:1987-08-25 00:00:00
abstract::Bcg I and Bcg I-like restriction endonucleases cleave double stranded DNA specifically on both sides of their asymmetric recognition sequences which are interrupted by several ambiguous base pairs. Their heterosubunit structure, bifunctionality and stimulation by AdoMet make them different from other classified restri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.22.4444
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abstract::Bulk replicative DNA synthesis in eukaryotes is highly accurate and efficient, primarily because of two DNA polymerases (Pols): Pols δ and ε. The high fidelity of these enzymes is due to their intrinsic base selectivity and proofreading exonuclease activity which, when coupled with post-replication mismatch repair, he...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1034
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.731
更新日期:1987-01-26 00:00:00
abstract::Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.21.5937
更新日期:1991-11-11 00:00:00
abstract::Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.3039
更新日期:1988-04-11 00:00:00
abstract::The delivery of site-specific post-translational modifications to histones generates an epigenetic regulatory network that directs fundamental DNA-mediated processes and governs key stages in development. Methylation of histone H4 lysine-20 has been implicated in DNA repair, transcriptional silencing, genomic stabilit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt776
更新日期:2014-01-01 00:00:00
abstract::We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of micro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.12.3237
更新日期:1991-06-25 00:00:00
abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9861
更新日期:1987-12-10 00:00:00
abstract::The structure in solution of an RNA fragment (218 nucleotides long) containing part of E. coli 16S rRNA domain 2 has been studied using the intrinsic photoaffinity probe 4-thiouridine (s4U). In vitro transcription with T7 polymerase, in the presence of s4U triphosphate yielded complete RNA molecules. An affinity elect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.13.3653
更新日期:1991-07-11 00:00:00
abstract::To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the fi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki071
更新日期:2005-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1152
更新日期:2015-01-01 00:00:00
abstract::A novel approach for the amplification of cDNA ends is described. It requires only minimal amounts of material, a simple cDNA synthesis reaction and a single PCR reaction to amplify the desired 5'- or 3'-ends of a certain cDNA of interest. It combines the so called CapFinder approach with solid phase cDNA synthesis, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.22.e96
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abstract::SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1277
更新日期:2017-04-20 00:00:00
abstract::An open reading frame upstream from nifHDK operon of Klebsiella pneumoniae had been described. The orientation of this open reading frame is opposite to that of nifHDK and sequence homology was found between the open reading frame promoter and the promoter of nifHDK operon. A recombinant plasmid carrying the promoter ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.12.4241
更新日期:1983-06-25 00:00:00
abstract::Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase acti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki640
更新日期:2005-06-08 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp281
更新日期:2009-07-01 00:00:00
abstract::Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa874
更新日期:2020-11-18 00:00:00
abstract::The mouse is widely used as system to study human genetic mechanisms. However, extensive rewiring of transcriptional regulatory networks often confounds translation of findings between human and mouse. Site-specific gain and loss of individual transcription factor binding sites (TFBS) has caused functional divergence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2018-02-28 00:00:00
abstract::In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) ret...
journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.12.2302
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abstract::Members of the HMG-I(Y) family of mammalian nonhistone proteins are of importance because they have been demonstrated to bind specifically to the minor groove of A.T-rich sequences both in vitro and in vivo and to function as gene transcriptional regulatory proteins in vivo. Here we report the cloning, sequencing, cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.18.4259
更新日期:1993-09-11 00:00:00
abstract::In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...
journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.7.e23
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2003-09-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::Transposition of Saccharomyces cerevisiae Ty1 retroelements has been shown to involve reverse transcription in intracytoplasmic virus-like particles (Ty-VLPs). Ty DNA present in the particles specified by Ty1-H3 element was found to consist of the full-length genomic DNA as well as incomplete cDNAs mainly of plus pola...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.15.3513
更新日期:1993-07-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.5.1151
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abstract::The human prothrombin G20210A polymorphism located at the 3' cleavage site of the mRNA results in elevated plasma prothrombin levels and increased risk of venous thrombosis. This polymorphism has been shown to directly influence a variety of processes related to prothrombin mRNA metabolism. We have constructed plasmid...
journal_title:Nucleic acids research
pub_type: 杂志文章
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