Limits...
Comprehensive comparison of large-scale tissue expression datasets.

Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ - PeerJ (2015)

Bottom Line: Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated.We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining.We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen , Denmark.

ABSTRACT
For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface.

No MeSH data available.


TISSUES: all data accessible in a single resource.The TISSUES web resource integrates all the data compared in this study, quantifies the reliability of each gene–tissue association, and thereby makes associations from different sources comparable. When searching for a human protein, the user is presented with a body map that provides a complete overview of where the protein is likely expressed by coloring the 21 major tissues according to the confidence of the protein–tissue association. The body map is interactive and allows the user to see which sources of evidence support expression in a given tissue. The TISSUES web resource is available at http://tissues.jensenlab.org.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4493645&req=5

fig-7: TISSUES: all data accessible in a single resource.The TISSUES web resource integrates all the data compared in this study, quantifies the reliability of each gene–tissue association, and thereby makes associations from different sources comparable. When searching for a human protein, the user is presented with a body map that provides a complete overview of where the protein is likely expressed by coloring the 21 major tissues according to the confidence of the protein–tissue association. The body map is interactive and allows the user to see which sources of evidence support expression in a given tissue. The TISSUES web resource is available at http://tissues.jensenlab.org.

Mentions: The web interface allows the user to search for a human gene and get a complete overview of where it may be expressed. To provide an at-a-glance overview, we show a body map with each the 21 major tissues colored according to the confidence that the gene of interest is expressed there (Fig. 7). The figure also allows the user to see which sources of evidence support expression in a given tissue. Three interactive tables below the body map provide the user with more detailed information for the evidence from UniProtKB, high-throughput experiments, and text mining. This includes information on additional tissues, linkout to the source of the evidence whenever possible, and a unified confidence score ranging from 1 to 5 stars (see ‘Methods’).


Comprehensive comparison of large-scale tissue expression datasets.

Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ - PeerJ (2015)

TISSUES: all data accessible in a single resource.The TISSUES web resource integrates all the data compared in this study, quantifies the reliability of each gene–tissue association, and thereby makes associations from different sources comparable. When searching for a human protein, the user is presented with a body map that provides a complete overview of where the protein is likely expressed by coloring the 21 major tissues according to the confidence of the protein–tissue association. The body map is interactive and allows the user to see which sources of evidence support expression in a given tissue. The TISSUES web resource is available at http://tissues.jensenlab.org.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493645&req=5

fig-7: TISSUES: all data accessible in a single resource.The TISSUES web resource integrates all the data compared in this study, quantifies the reliability of each gene–tissue association, and thereby makes associations from different sources comparable. When searching for a human protein, the user is presented with a body map that provides a complete overview of where the protein is likely expressed by coloring the 21 major tissues according to the confidence of the protein–tissue association. The body map is interactive and allows the user to see which sources of evidence support expression in a given tissue. The TISSUES web resource is available at http://tissues.jensenlab.org.
Mentions: The web interface allows the user to search for a human gene and get a complete overview of where it may be expressed. To provide an at-a-glance overview, we show a body map with each the 21 major tissues colored according to the confidence that the gene of interest is expressed there (Fig. 7). The figure also allows the user to see which sources of evidence support expression in a given tissue. Three interactive tables below the body map provide the user with more detailed information for the evidence from UniProtKB, high-throughput experiments, and text mining. This includes information on additional tissues, linkout to the source of the evidence whenever possible, and a unified confidence score ranging from 1 to 5 stars (see ‘Methods’).

Bottom Line: Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated.We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining.We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen , Denmark.

ABSTRACT
For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface.

No MeSH data available.