当前位置： SCI文献检索 > GENOME BIOLOGY期刊下所有文献 > Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

Abstract：

BACKGROUND:RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering the relative abundances of different transcripts from the same gene. RESULTS:Here we show that, in a given condition, most protein coding genes have one major transcript expressed at significantly higher level than others, that in human tissues the major transcripts contribute almost 85 percent to the total mRNA from protein coding loci, and that often the same major transcript is expressed in many tissues. We detect a high degree of overlap between the set of major transcripts and a recently published set of alternatively spliced transcripts that are predicted to be translated utilizing proteomic data. Thus, we hypothesize that although some minor transcripts may play a functional role, the major ones are likely to be the main contributors to the proteome. However, we still detect a non-negligible fraction of protein coding genes for which the major transcript does not code a protein. CONCLUSIONS:Overall, our findings suggest that the transcriptome from protein coding loci is dominated by one transcript per gene and that not all the transcripts that contribute to transcriptome diversity are equally likely to contribute to protein diversity. This observation can help to prioritize candidate targets in proteomics research and to predict the functional impact of the detected changes in variation studies.

journal_name

Genome Biol

journal_title

Genome biology

authors

Gonzàlez-Porta M,Frankish A,Rung J,Harrow J,Brazma A

doi

10.1186/gb-2013-14-7-r70

subject

Has Abstract

pub_date

2013-07-01 00:00:00

pages

R70

issue

7

eissn

1474-7596

issn

1474-760X

pii

gb-2013-14-7-r70

journal_volume

14

pub_type

杂志文章

相关文献

GENOME BIOLOGY文献大全
  • Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs.

    abstract：BACKGROUND:Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammali...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2006-7-10-r91

    authors： Cardone MF,Alonso A,Pazienza M,Ventura M,Montemurro G,Carbone L,de Jong PJ,Stanyon R,D'Addabbo P,Archidiacono N,She X,Eichler EE,Warburton PE,Rocchi M

    更新日期：2006-01-01 00:00:00

  • Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6.

    abstract：BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1457-6

    authors： Prins BP,Mead TJ,Brody JA,Sveinbjornsson G,Ntalla I,Bihlmeyer NA,van den Berg M,Bork-Jensen J,Cappellani S,Van Duijvenboden S,Klena NT,Gabriel GC,Liu X,Gulec C,Grarup N,Haessler J,Hall LM,Iorio A,Isaacs A,Li-Gao R,

    更新日期：2018-07-17 00:00:00

  • New tricks for old NODs.

    abstract：:Recent work has identified the human NOD-like receptor NLRX1 as a negative regulator of intracellular signaling leading to type I interferon production. Here we discuss these findings and the questions and implications they raise regarding the function of NOD-like receptors in the antiviral response. ...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2008-9-4-217

    authors： Pietras EM,Cheng G

    更新日期：2008-04-25 00:00:00

  • Decreasing miRNA sequencing bias using a single adapter and circularization approach.

    abstract：:The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1488-z

    authors： Barberán-Soler S,Vo JM,Hogans RE,Dallas A,Johnston BH,Kazakov SA

    更新日期：2018-09-03 00:00:00

  • Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells.

    abstract：BACKGROUND:While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS:We systematically compare five different...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1445-x

    authors： Wang Y,Liu KI,Sutrisnoh NB,Srinivasan H,Zhang J,Li J,Zhang F,Lalith CRJ,Xing H,Shanmugam R,Foo JN,Yeo HT,Ooi KH,Bleckwehl T,Par YYR,Lee SM,Ismail NNB,Sanwari NAB,Lee STV,Lew J,Tan MH

    更新日期：2018-05-29 00:00:00

  • The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

    abstract：BACKGROUND:The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functio...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0780-4

    authors： Chung O,Jin S,Cho YS,Lim J,Kim H,Jho S,Kim HM,Jun J,Lee H,Chon A,Ko J,Edwards J,Weber JA,Han K,O'Brien SJ,Manica A,Bhak J,Paek WK

    更新日期：2015-10-21 00:00:00

  • Correction to: DNA copy number evolution in Drosophila cell lines.

    abstract：:Following publication of the original article [1], the authors reported the following errors. ...

    journal_title：Genome biology

    pub_type： 杂志文章,已发布勘误

    doi：10.1186/s13059-019-1668-5

    authors： Lee H,McManus CJ,Cho DY,Eaton M,Renda F,Somma MP,Cherbas L,May G,Powell S,Zhang D,Zhan L,Resch A,Andrews J,Celniker SE,Cherbas P,Przytycka TM,Gatti M,Oliver B,Graveley B,MacAlpine D

    更新日期：2019-03-11 00:00:00

  • Supervised harvesting of expression trees.

    abstract：BACKGROUND:We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2001-2-1-research0003

    authors： Hastie T,Tibshirani R,Botstein D,Brown P

    更新日期：2001-01-01 00:00:00

  • The evolution of relapse of adult T cell acute lymphoblastic leukemia.

    abstract：BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-02192-z

    authors： Sentís I,Gonzalez S,Genescà E,García-Hernández V,Muiños F,Gonzalez C,López-Arribillaga E,Gonzalez J,Fernandez-Ibarrondo L,Mularoni L,Espinosa L,Bellosillo B,Ribera JM,Bigas A,Gonzalez-Perez A,Lopez-Bigas N

    更新日期：2020-11-23 00:00:00

  • Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.

    abstract：BACKGROUND:Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS:We use high throughput single-cell RNA-seq...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1426-0

    authors： Han X,Chen H,Huang D,Chen H,Fei L,Cheng C,Huang H,Yuan GC,Guo G

    更新日期：2018-04-05 00:00:00

  • Quantifying the mechanisms of domain gain in animal proteins.

    abstract：BACKGROUND:Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechan...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2010-11-7-r74

    authors： Buljan M,Frankish A,Bateman A

    更新日期：2010-01-01 00:00:00

  • The sequence of human chromosome 21 and implications for research into Down syndrome.

    abstract：:The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2000-1-2-reviews0002

    authors： Gardiner K,Davisson M

    更新日期：2000-01-01 00:00:00

  • Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.

    abstract：BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2007-8-9-r180

    authors： Clark TG,Andrew T,Cooper GM,Margulies EH,Mullikin JC,Balding DJ

    更新日期：2007-01-01 00:00:00

  • The greatest catch: big game fishing for mRNA-bound proteins.

    abstract：:Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/gb4030

    authors： Sibley CR,Attig J,Ule J

    更新日期：2012-07-17 00:00:00

  • Reduced selection leads to accelerated gene loss in Shigella.

    abstract：BACKGROUND:Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given t...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2007-8-8-r164

    authors： Hershberg R,Tang H,Petrov DA

    更新日期：2007-01-01 00:00:00

  • A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology.

    abstract：:A report on the Cold Spring Harbor Asia conference on Genome Assisted Biology of Crops and Model Plant Systems Meeting, held in Suzhou, China, April 21-25, 2014. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/gb4176

    authors： Lee I

    更新日期：2014-05-23 00:00:00

  • A prediction-based resampling method for estimating the number of clusters in a dataset.

    abstract：BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2002-3-7-research0036

    authors： Dudoit S,Fridlyand J

    更新日期：2002-06-25 00:00:00

  • quantro: a data-driven approach to guide the choice of an appropriate normalization method.

    abstract：:Normalization is an essential step in the analysis of high-throughput data. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation. However, these methods rely on the assumption that observed global changes across samples are due to unwanted...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0679-0

    authors： Hicks SC,Irizarry RA

    更新日期：2015-06-04 00:00:00

  • In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.

    abstract：BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-02236-4

    authors： Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y

    更新日期：2021-01-04 00:00:00

  • Alternative splicing links histone modifications to stem cell fate decision.

    abstract：BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-018-1512-3

    authors： Xu Y,Zhao W,Olson SD,Prabhakara KS,Zhou X

    更新日期：2018-09-14 00:00:00

  • Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

    abstract：BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0644-y

    authors： Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

    更新日期：2015-04-16 00:00:00

  • Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca.

    abstract：BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-02080-6

    authors： Fan R,Gu Z,Guang X,Marín JC,Varas V,González BA,Wheeler JC,Hu Y,Li E,Sun X,Yang X,Zhang C,Gao W,He J,Munch K,Corbett-Detig R,Barbato M,Pan S,Zhan X,Bruford MW,Dong C

    更新日期：2020-07-02 00:00:00

  • Domain atrophy creates rare cases of functional partial protein domains.

    abstract：BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-015-0655-8

    authors： Prakash A,Bateman A

    更新日期：2015-04-30 00:00:00

  • Studying the microbiology of the indoor environment.

    abstract：:The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2013-14-2-202

    authors： Kelley ST,Gilbert JA

    更新日期：2013-02-28 00:00:00

  • An improved method for detecting and delineating genomic regions with altered gene expression in cancer.

    abstract：:Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method c...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2008-9-1-r13

    authors： Nilsson B,Johansson M,Heyden A,Nelander S,Fioretos T

    更新日期：2008-01-21 00:00:00

  • ReMixT: clone-specific genomic structure estimation in cancer.

    abstract：:Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complic...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-017-1267-2

    authors： McPherson AW,Roth A,Ha G,Chauve C,Steif A,de Souza CPE,Eirew P,Bouchard-Côté A,Aparicio S,Sahinalp SC,Shah SP

    更新日期：2017-07-27 00:00:00

  • Survey of human mitochondrial diseases using new genomic/proteomic tools.

    abstract：BACKGROUND:We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein mutations that give rise to human mitochondrial diseases. (Bayesian priors are conditional probabilit...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2001-2-6-research0021

    authors： Plasterer TN,Smith TF,Mohr SC

    更新日期：2001-01-01 00:00:00

  • Large-scale assignment of orthology: back to phylogenetics?

    abstract：:Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2008-9-10-235

    authors： Gabaldón T

    更新日期：2008-10-30 00:00:00

  • In silico meets in vivo.

    abstract：:A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/gb-2008-9-2-302

    authors： Weng Z,Guigó R

    更新日期：2008-01-01 00:00:00

  • Organizing knowledge to enable personalization of medicine in cancer.

    abstract：:Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-014-0438-7

    authors： Good BM,Ainscough BJ,McMichael JF,Su AI,Griffith OL

    更新日期：2014-08-27 00:00:00