STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data

Research output: Contribution to journalJournal articlepeer-review

Standard

STITCH 5 : augmenting protein-chemical interaction networks with tissue and affinity data. / Szklarczyk, Damian; Santos Delgado, Alberto; von Mering, Christian; Jensen, Lars Juhl; Bork, Peer; Kuhn, Michael.

In: Nucleic Acids Research, Vol. 44, No. D1, 2016, p. D380-84.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Szklarczyk, D, Santos Delgado, A, von Mering, C, Jensen, LJ, Bork, P & Kuhn, M 2016, 'STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data', Nucleic Acids Research, vol. 44, no. D1, pp. D380-84. https://doi.org/10.1093/nar/gkv1277

APA

Szklarczyk, D., Santos Delgado, A., von Mering, C., Jensen, L. J., Bork, P., & Kuhn, M. (2016). STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 44(D1), D380-84. https://doi.org/10.1093/nar/gkv1277

Vancouver

Szklarczyk D, Santos Delgado A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research. 2016;44(D1):D380-84. https://doi.org/10.1093/nar/gkv1277

Author

Szklarczyk, Damian ; Santos Delgado, Alberto ; von Mering, Christian ; Jensen, Lars Juhl ; Bork, Peer ; Kuhn, Michael. / STITCH 5 : augmenting protein-chemical interaction networks with tissue and affinity data. In: Nucleic Acids Research. 2016 ; Vol. 44, No. D1. pp. D380-84.

Bibtex

@article{d97cfb900b104b9690a5e17e7b22430d,
title = "STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data",
abstract = "Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH ('Search Tool for Interacting Chemicals') that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.",
author = "Damian Szklarczyk and {Santos Delgado}, Alberto and {von Mering}, Christian and Jensen, {Lars Juhl} and Peer Bork and Michael Kuhn",
note = "{\textcopyright} The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.",
year = "2016",
doi = "10.1093/nar/gkv1277",
language = "English",
volume = "44",
pages = "D380--84",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

RIS

TY - JOUR

T1 - STITCH 5

T2 - augmenting protein-chemical interaction networks with tissue and affinity data

AU - Szklarczyk, Damian

AU - Santos Delgado, Alberto

AU - von Mering, Christian

AU - Jensen, Lars Juhl

AU - Bork, Peer

AU - Kuhn, Michael

N1 - © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2016

Y1 - 2016

N2 - Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH ('Search Tool for Interacting Chemicals') that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.

AB - Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH ('Search Tool for Interacting Chemicals') that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.

U2 - 10.1093/nar/gkv1277

DO - 10.1093/nar/gkv1277

M3 - Journal article

C2 - 26590256

VL - 44

SP - D380-84

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -

ID: 152246474