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Tissue-based map of the human proteome

Published on Jan 23, 2015in Science41.04
· DOI :10.1126/science.1260419
Mathias Uhlén90
Estimated H-index: 90
(KTH: Royal Institute of Technology),
Linn Fagerberg21
Estimated H-index: 21
(KTH: Royal Institute of Technology)
+ 33 AuthorsFredrik Pontén54
Estimated H-index: 54
(Science for Life Laboratory)
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Abstract
Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map ...
  • References (52)
  • Citations (2312)
Cite
References52
Newest
Published on Jan 1, 2015in Journal of Gastroenterology5.13
Gabriela Gremel6
Estimated H-index: 6
(Uppsala University),
Alkwin Wanders19
Estimated H-index: 19
(Uppsala University)
+ 6 AuthorsFredrik Pontén54
Estimated H-index: 54
(Uppsala University)
Background The gastrointestinal tract (GIT) is subdivided into different anatomical organs with many shared functions and characteristics, but also distinct differences. We have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to describe the gene and protein expression patterns that define the human GIT.
Published on Nov 15, 2014in Human Molecular Genetics4.54
Iakes Ezkurdia17
Estimated H-index: 17
,
David A. Juan2
Estimated H-index: 2
+ 6 AuthorsMichael L. Tress26
Estimated H-index: 26
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and...
Published on Jul 1, 2014in The FASEB Journal5.39
Caroline Kampf29
Estimated H-index: 29
(Science for Life Laboratory),
Adil Mardinoglu27
Estimated H-index: 27
(Chalmers University of Technology)
+ 6 AuthorsMathias Uhlén90
Estimated H-index: 90
(KTH: Royal Institute of Technology)
Human liver physiology and the genetic etiology of the liver diseases can potentially be elucidated through the identification of proteins with enriched expression in the liver. Here, we combined data from RNA sequencing (RNA-Seq) and antibody-based immunohistochemistry across all major human tissues to explore the human liver proteome with enriched expression, as well as the cell type-enriched expression in hepatocyte and bile duct cells. We identified in total 477 protein-coding genes with ele...
Published on Jun 1, 2014in Molecular Human Reproduction3.40
Dijana Djureinovic8
Estimated H-index: 8
(Uppsala University),
Linn Fagerberg21
Estimated H-index: 21
(KTH: Royal Institute of Technology)
+ 4 AuthorsFredrik Pontén54
Estimated H-index: 54
(Uppsala University)
The testis' function is to produce haploid germ cells necessary for reproduction. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to c ...
Published on May 1, 2014in Nature Communications11.88
Adil Mardinoglu27
Estimated H-index: 27
,
Rasmus Agren13
Estimated H-index: 13
+ 3 AuthorsJens B. Nielsen84
Estimated H-index: 84
(Chalmers University of Technology)
Several liver disorders result from perturbations in the metabolism of hepatocytes, and their underlying mechanisms can be outlined through the use of genome-scale metabolic models (GEMs). Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an extensive description of lipid metabolism. We build iHepatocytes2322 using Human Metabolic Reaction 2.0 database and proteomics data in Human Protein Atlas, which experimentally val...
Published on May 1, 2014in Nature43.07
Min-Sik Kim40
Estimated H-index: 40
(Johns Hopkins University),
Sneha M. Pinto18
Estimated H-index: 18
+ 69 AuthorsAkhilesh Pandey83
Estimated H-index: 83
A draft map of the human proteome is presented here, accounting for over 80% of the annotated protein-coding genes in humans; some novel protein-coding regions, including translated pseudogenes, non-coding RNAs and upstream open reading frames, are identified.
Published on May 1, 2014in Nature43.07
Mathias Wilhelm11
Estimated H-index: 11
,
Judith Schlegl6
Estimated H-index: 6
+ 19 AuthorsBernhard Kuster50
Estimated H-index: 50
A mass-spectrometry-based draft of the human proteome and a public database for analysis of proteome data are presented; assembled information is used to estimate the size of the protein-coding genome, to identify organ-specific proteins, proteins predicting drug resistance or sensitivity, and many translated long intergenic non-coding RNAs, and to reveal conserved control of protein abundance.
Published on Mar 28, 2014in Molecular Systems Biology9.80
Rasmus Agren13
Estimated H-index: 13
(Chalmers University of Technology),
Adil Mardinoglu27
Estimated H-index: 27
(Chalmers University of Technology)
+ 3 AuthorsJens Nielsen17
Estimated H-index: 17
(Chalmers University of Technology)
Genome-scale metabolic models (GEMs) have proven useful as scaffolds for the integration of omics data for understanding the genotype–phenotype relationship in a mechanistic manner. Here, we evaluated the presence/absence of proteins encoded by 15,841 genes in 27 hepatocellular carcinoma (HCC) patients using immunohistochemistry. We used this information to reconstruct personalized GEMs for six HCC patients based on the proteomics data, HMR 2.0, and a task-driven model reconstruction algorithm (...
Published on Feb 1, 2014in Molecular & Cellular Proteomics4.83
Linn Fagerberg21
Estimated H-index: 21
(KTH: Royal Institute of Technology),
Björn M. Hallström23
Estimated H-index: 23
(KTH: Royal Institute of Technology)
+ 31 AuthorsKarolina Edlund23
Estimated H-index: 23
(Uppsala University)
Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative ...
Published on Jan 1, 2014in Nucleic Acids Research11.15
Vivian Law3
Estimated H-index: 3
(National Institute for Nanotechnology),
Craig Knox24
Estimated H-index: 24
(National Institute for Nanotechnology)
+ 15 AuthorsVanessa Neveu13
Estimated H-index: 13
(National Institute for Nanotechnology)
DrugBank (http://www.drugbank.ca) is a comprehensive online database containing extensive biochemical and pharmacological information about drugs, their mechanisms and their targets. Since it was first described in 2006, DrugBank has rapidly evolved, both in response to user requests and in response to changing trends in drug research and development. Previous versions of DrugBank have been widely used to facilitate drug and in silico drug target discovery. The latest update, DrugBank 4.0, has b...
Cited By2312
Newest
Published on Jan 1, 2020
Matthew K. Breitenstein3
Estimated H-index: 3
(UPenn: University of Pennsylvania),
Erin L. Crowgey (Wilmington University)
This chapter introduces fundamental concepts of pharmacogenomics, including drug metabolism, and provides an informatics workflow-based perspective inspired by a learning healthcare system framework. Our intent is that the reader sees pharmacogenomics as a foundation of precision medicine, which is reliant upon informatics to deliver actionable patient-tailored knowledge at the point of care. Further, pharmacogenomics knowledge is poised to be further developed so as to be amenable to multi-drug...
Published on Dec 1, 2019in Cancer Cell International3.44
Jinhui Liu3
Estimated H-index: 3
(Nanjing Medical University),
Shulin Zhou3
Estimated H-index: 3
(Nanjing Medical University)
+ 4 AuthorsWenjun Cheng3
Estimated H-index: 3
(Nanjing Medical University)
Background Endometrial cancer (EC) is one of the female malignant tumors. Endometrial cancer predominately affects post-menopausal women. Bioinformatics analysis has been widely applied to screen and analyze genes in linkage to various types of cancer progression.
Published on Feb 8, 2019in World Journal of Surgical Oncology1.97
Dingyuan Hu2
Estimated H-index: 2
,
Daniel Ansari19
Estimated H-index: 19
+ 3 AuthorsRoland Andersson53
Estimated H-index: 53
Background Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extremely dense stroma, which has a fundamental role in tumor progression. Fibronectin (FN1) is the main constituent of the tumor stroma in pancreatic cancer. This study aimed to explore the association between FN1 and clinicopathological characteristics and disease survival.
Published on Dec 1, 2019in Genome Biology14.03
Antonin Morillon12
Estimated H-index: 12
(Curie Institute),
Daniel Gautheret40
Estimated H-index: 40
(Université Paris-Saclay)
Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation revealed by massively parallel sequencing. Much may be missed by ignoring this unreferenced RNA diversity. There is plentiful evidence for non-reference transcripts with important p...
Published on 2019in Scientific Reports4.01
Sara Brin Rosenthal3
Estimated H-index: 3
(UCSD: University of California, San Diego),
Kevin T. Bush37
Estimated H-index: 37
(UCSD: University of California, San Diego),
Sanjay K. Nigam53
Estimated H-index: 53
(UCSD: University of California, San Diego)
Genes central to drug absorption, distribution, metabolism and elimination (ADME) also regulate numerous endogenous molecules. The Remote Sensing and Signaling Hypothesis argues that an ADME gene-centered network—including SLC and ABC “drug” transporters, “drug” metabolizing enzymes (DMEs), and regulatory genes—is essential for inter-organ communication via metabolites, signaling molecules, antioxidants, gut microbiome products, uremic solutes, and uremic toxins. By cross-tissue co-expression ne...
Published on Dec 1, 2019
Alexandre Paix12
Estimated H-index: 12
(JHUSOM: Johns Hopkins University School of Medicine),
Dominique Rasoloson5
Estimated H-index: 5
(JHUSOM: Johns Hopkins University School of Medicine)
+ 1 AuthorsGeraldine Seydoux48
Estimated H-index: 48
(JHUSOM: Johns Hopkins University School of Medicine)
Published on Dec 1, 2019in Scientific Reports4.01
John E. Nielsen (UCPH: University of Copenhagen), Antoine D. Rolland5
Estimated H-index: 5
(French Institute of Health and Medical Research)
+ 8 AuthorsBernard Jégou50
Estimated H-index: 50
(French Institute of Health and Medical Research)
Heavy use of cannabis (marijuana) has been associated with decreased semen quality, which may reflect disruption of the endocannabinoid system (ECS) in the male reproductive tract by exogenous cannabinoids. Components of ECS have been previously described in human spermatozoa and in the rodent testis but there is little information on the ECS expression within the human testis. In this study we characterised the main components of the ECS by immunohistochemistry (IHC) on archived testis tissue s...
Published on Dec 1, 2019in Breast Cancer Research5.68
Kevin D. Wright3
Estimated H-index: 3
(MCW: Medical College of Wisconsin),
Bradley Miller6
Estimated H-index: 6
(MCW: Medical College of Wisconsin)
+ 9 AuthorsHallgeir Rui44
Estimated H-index: 44
(MCW: Medical College of Wisconsin)
Background SHC1 proteins (also called SHCA) exist in three functionally distinct isoforms (p46SHC, p52SHC, and p66SHC) that serve as intracellular adaptors for several key signaling pathways in breast cancer. Despite the broad evidence implicating SHC1 gene products as a central mediator of breast cancer, testing the isoform-specific roles of SHC1 proteins have been inaccessible due to the lack of isoform-specific inhibitors or gene knockout models.
Published on Dec 1, 2019in Genome Biology14.03
Dimitra Repana ('KCL': King's College London), Joel Nulsen ('KCL': King's College London)+ 6 AuthorsFrancesca D. Ciccarelli27
Estimated H-index: 27
('KCL': King's College London)
The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites. This represents a more than 1.5-fold content increase compared to the previous version. NCG also annotates properties of cancer genes,...
View next paperThe Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans