Integration and visualization of non-coding RNA and protein interaction networks

Alexander Junge; Jan Christian Refsgaard; Christian Garde; Xiaoyong Pan; Alberto Santos Delgado; Christian Anthon; Ferhat Alkan; Christian von Mering; Christopher Workman; Lars Juhl Jensen; Jan Gorodkin

Integration and visualization of non-coding RNA and protein interaction networks

Alexander Junge, Jan Christian Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos Delgado, Christian Anthon, Ferhat Alkan, Christian von Mering, Christopher Workman, Lars Juhl Jensen, Jan Gorodkin

Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

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Abstract

Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By integrating ncRNA and protein networks, RAIN provides a more complete picture of the cell’s complex interaction network. RAIN aggregates associations and (predicted) interactions of a vast collection of ncRNA classes, including microRNAs and long ncRNAs, collected from a wide range of resources: a) curated knowledge, b) experimentally supported interactions, c) predicted microRNA-target interactions, and d) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain

Original language	English
Publication date	2015
Number of pages	1
Publication status	Published - 2015
Event	First Annual Danish Bioinformatics Conference - Odense, Denmark Duration: 27 Aug 2015 → 27 Nov 2015

Conference

Conference	First Annual Danish Bioinformatics Conference
Country/Territory	Denmark
City	Odense
Period	27/08/2015 → 27/11/2015

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Junge, Alexander ; Refsgaard, Jan Christian ; Garde, Christian ; Pan, Xiaoyong ; Santos Delgado, Alberto ; Anthon, Christian ; Alkan, Ferhat ; von Mering, Christian ; Workman, Christopher ; Jensen, Lars Juhl ; Gorodkin, Jan. / Integration and visualization of non-coding RNA and protein interaction networks. Abstract from First Annual Danish Bioinformatics Conference, Odense, Denmark.1 p.

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title = "Integration and visualization of non-coding RNA and protein interaction networks",

abstract = "Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By integrating ncRNA and protein networks, RAIN provides a more complete picture of the cell{\textquoteright}s complex interaction network. RAIN aggregates associations and (predicted) interactions of a vast collection of ncRNA classes, including microRNAs and long ncRNAs, collected from a wide range of resources: a) curated knowledge, b) experimentally supported interactions, c) predicted microRNA-target interactions, and d) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain",

author = "Alexander Junge and Refsgaard, {Jan Christian} and Christian Garde and Xiaoyong Pan and {Santos Delgado}, Alberto and Christian Anthon and Ferhat Alkan and {von Mering}, Christian and Christopher Workman and Jensen, {Lars Juhl} and Jan Gorodkin",

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Integration and visualization of non-coding RNA and protein interaction networks. / Junge, Alexander; Refsgaard, Jan Christian; Garde, Christian; Pan, Xiaoyong; Santos Delgado, Alberto; Anthon, Christian; Alkan, Ferhat; von Mering, Christian; Workman, Christopher; Jensen, Lars Juhl; Gorodkin, Jan.

2015. Abstract from First Annual Danish Bioinformatics Conference, Odense, Denmark.

Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

TY - ABST

T1 - Integration and visualization of non-coding RNA and protein interaction networks

AU - Junge, Alexander

AU - Refsgaard, Jan Christian

AU - Garde, Christian

AU - Pan, Xiaoyong

AU - Santos Delgado, Alberto

AU - Anthon, Christian

AU - Alkan, Ferhat

AU - von Mering, Christian

AU - Workman, Christopher

AU - Jensen, Lars Juhl

AU - Gorodkin, Jan

PY - 2015

Y1 - 2015

N2 - Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By integrating ncRNA and protein networks, RAIN provides a more complete picture of the cell’s complex interaction network. RAIN aggregates associations and (predicted) interactions of a vast collection of ncRNA classes, including microRNAs and long ncRNAs, collected from a wide range of resources: a) curated knowledge, b) experimentally supported interactions, c) predicted microRNA-target interactions, and d) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain

AB - Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By integrating ncRNA and protein networks, RAIN provides a more complete picture of the cell’s complex interaction network. RAIN aggregates associations and (predicted) interactions of a vast collection of ncRNA classes, including microRNAs and long ncRNAs, collected from a wide range of resources: a) curated knowledge, b) experimentally supported interactions, c) predicted microRNA-target interactions, and d) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain

M3 - Conference abstract for conference

T2 - First Annual Danish Bioinformatics Conference

Y2 - 27 August 2015 through 27 November 2015

ER -

Integration and visualization of non-coding RNA and protein interaction networks

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