Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

Noemí Del-Toro; Margaret J. Duesbury; Maximilian Koch; Livia Perfetto; A. R Shrivastava; David Ochoa; Omar Wagih; Janet Piñero; Max Kotlyar; Chiara Pastrello; Pedro Beltrão; Laura Inés Furlong; Igor Jurisica; Henning Hermjakob; Sandra E. Orchard; Pablo Porras; Jyoti Khadake; Birgit H.M. Meldal; Simona Panni; David Thorneycroft; Kim Van Roey; Sara Abbani; Lukasz Salwínski; Matteo Pellegrini; Marta Iannuccelli; Luana Licata; Gianni Cesareni; Bernd Roechert; Alan James Bridge; Mais G. Ammari; Fiona M. McCarthy; Fiona C. Broackes-Carter; Nancy H. Campbell; Anna N. Melidoni; Milagros Rodriguez-Lopez; Ruth C. Lovering; Sruthi Jagannathan; Carol Chen; David J. Lynn; Sylvie Ricard-Blum; Usha Mahadevan; Arathi Raghunath

doi:10.1038/s41467-018-07709-6

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

Noemí Del-Toro, Margaret J. Duesbury, Maximilian Koch, Livia Perfetto, A. R Shrivastava, David Ochoa, Omar Wagih, Janet Piñero, Max Kotlyar, Chiara Pastrello, Pedro Beltrão, Laura Inés Furlong, Igor Jurisica, Henning Hermjakob, Sandra E. Orchard, Pablo Porras, Jyoti Khadake, Birgit H.M. Meldal, Simona Panni, David ThorneycroftKim Van Roey, Sara Abbani, Lukasz Salwínski, Matteo Pellegrini, Marta Iannuccelli, Luana Licata, Gianni Cesareni, Bernd Roechert, Alan James Bridge, Mais G. Ammari, Fiona M. McCarthy, Fiona C. Broackes-Carter, Nancy H. Campbell, Anna N. Melidoni, Milagros Rodriguez-Lopez, Ruth C. Lovering, Sruthi Jagannathan, Carol Chen, David J. Lynn, Sylvie Ricard-Blum, Usha Mahadevan, Arathi Raghunath

Research output: Contribution to journal › Article › peer-review

56 Citations (Scopus)

Abstract

The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

Original language	English
Article number	10
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-07709-6
Publication status	Published - 2019

Access to Document

10.1038/s41467-018-07709-6

Cite this

Del-Toro, N., Duesbury, M. J., Koch, M., Perfetto, L., Shrivastava, A. R., Ochoa, D., Wagih, O., Piñero, J., Kotlyar, M., Pastrello, C., Beltrão, P., Furlong, L. I., Jurisica, I., Hermjakob, H., Orchard, S. E., Porras, P., Khadake, J., Meldal, B. H. M., Panni, S., ... Raghunath, A. (2019). Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications, 10(1), Article 10. https://doi.org/10.1038/s41467-018-07709-6

@article{420329116a594af590e534305e100a2a,

title = "Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set",

abstract = "The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule{\textquoteright}s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.",

author = "Noem{\'i} Del-Toro and Duesbury, {Margaret J.} and Maximilian Koch and Livia Perfetto and Shrivastava, {A. R} and David Ochoa and Omar Wagih and Janet Pi{\~n}ero and Max Kotlyar and Chiara Pastrello and Pedro Beltr{\~a}o and Furlong, {Laura In{\'e}s} and Igor Jurisica and Henning Hermjakob and Orchard, {Sandra E.} and Pablo Porras and Jyoti Khadake and Meldal, {Birgit H.M.} and Simona Panni and David Thorneycroft and {Van Roey}, Kim and Sara Abbani and Lukasz Salw{\'i}nski and Matteo Pellegrini and Marta Iannuccelli and Luana Licata and Gianni Cesareni and Bernd Roechert and Bridge, {Alan James} and Ammari, {Mais G.} and McCarthy, {Fiona M.} and Broackes-Carter, {Fiona C.} and Campbell, {Nancy H.} and Melidoni, {Anna N.} and Milagros Rodriguez-Lopez and Lovering, {Ruth C.} and Sruthi Jagannathan and Carol Chen and Lynn, {David J.} and Sylvie Ricard-Blum and Usha Mahadevan and Arathi Raghunath",

year = "2019",

doi = "10.1038/s41467-018-07709-6",

language = "English",

volume = "10",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature",

number = "1",

}

Del-Toro, N, Duesbury, MJ, Koch, M, Perfetto, L, Shrivastava, AR, Ochoa, D, Wagih, O, Piñero, J, Kotlyar, M, Pastrello, C, Beltrão, P, Furlong, LI, Jurisica, I, Hermjakob, H, Orchard, SE, Porras, P, Khadake, J, Meldal, BHM, Panni, S, Thorneycroft, D, Van Roey, K, Abbani, S, Salwínski, L, Pellegrini, M, Iannuccelli, M, Licata, L, Cesareni, G, Roechert, B, Bridge, AJ, Ammari, MG, McCarthy, FM, Broackes-Carter, FC, Campbell, NH, Melidoni, AN, Rodriguez-Lopez, M, Lovering, RC, Jagannathan, S, Chen, C, Lynn, DJ, Ricard-Blum, S, Mahadevan, U & Raghunath, A 2019, 'Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set', Nature Communications, vol. 10, no. 1, 10. https://doi.org/10.1038/s41467-018-07709-6

TY - JOUR

T1 - Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

AU - Del-Toro, Noemí

AU - Duesbury, Margaret J.

AU - Koch, Maximilian

AU - Perfetto, Livia

AU - Shrivastava, A. R

AU - Ochoa, David

AU - Wagih, Omar

AU - Piñero, Janet

AU - Kotlyar, Max

AU - Pastrello, Chiara

AU - Beltrão, Pedro

AU - Furlong, Laura Inés

AU - Jurisica, Igor

AU - Hermjakob, Henning

AU - Orchard, Sandra E.

AU - Porras, Pablo

AU - Khadake, Jyoti

AU - Meldal, Birgit H.M.

AU - Panni, Simona

AU - Thorneycroft, David

AU - Van Roey, Kim

AU - Abbani, Sara

AU - Salwínski, Lukasz

AU - Pellegrini, Matteo

AU - Iannuccelli, Marta

AU - Licata, Luana

AU - Cesareni, Gianni

AU - Roechert, Bernd

AU - Bridge, Alan James

AU - Ammari, Mais G.

AU - McCarthy, Fiona M.

AU - Broackes-Carter, Fiona C.

AU - Campbell, Nancy H.

AU - Melidoni, Anna N.

AU - Rodriguez-Lopez, Milagros

AU - Lovering, Ruth C.

AU - Jagannathan, Sruthi

AU - Chen, Carol

AU - Lynn, David J.

AU - Ricard-Blum, Sylvie

AU - Mahadevan, Usha

AU - Raghunath, Arathi

PY - 2019

Y1 - 2019

N2 - The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

AB - The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

UR - http://www.scopus.com/inward/record.url?scp=85059496699&partnerID=8YFLogxK

U2 - 10.1038/s41467-018-07709-6

DO - 10.1038/s41467-018-07709-6

M3 - Article

SN - 2041-1723

VL - 10

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 10

ER -

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

Abstract

Access to Document

Other files and links

Fingerprint

Cite this