Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways

Hamid Hamzeiy; Rabia Suluyayla; Christoph Brinkrolf; Sebastian Jan Janowski; Ralf Hofestädt; Jens Allmer

doi:10.3233/978-1-61499-896-9-183

Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways

Hamid Hamzeiy
, Rabia Suluyayla
, Christoph Brinkrolf
, Sebastian Jan Janowski
, Ralf Hofestädt
, Jens Allmer^*

^*Corresponding author for this work

BIOS Applied Bioinformatics

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic › peer-review

10 Citations (Scopus)

Abstract

MicroRNAs (miRNAs), approximately 22 nucleotides long, posttranscriptionally active gene expression regulators, play active roles in modulating cellular processes. Gene regulation and miRNA regulation are intertwined and the main aim of this study is to facilitate the analysis of miRNAs within gene regulatory pathways. VANESA enables the reconstruction of biological pathways and supports visualization and simulation. To support integrative miRNA and gene pathway analyses, a custom database of experimentally proven miRNAs, integrating data from miRBase, TarBase and miRTarBase, was added to DAWIS-M.D., which is the main data source for VANESA. Analysis of human KEGG pathways within DAWIS-M.D. showed that 661 miRNAs (~1/3 recorded human miRNAs) lead to 65,474 interactions. hsa-miR-335-5p targets most genes in our system (2,544); while the most targeted gene (with 71 miRNAs) is NUFIP2 (Nuclear Fragile X Mental Retardation Protein Interacting Protein 2). Amyotrophic Lateral Sclerosis (ALS), a complex neurodegenerative disease, was chosen as a proof of concept model. Using our system, it was possible to reduce the initially several hundred genes and miRNAs associated with ALS to eight genes, 19 miRNAs and 31 interactions. This highlights the effectiveness of the implemented system to distill important information from otherwise hard to access, highly convoluted and vast regulatory networks.

Original language	English
Title of host publication	German Medical Data Sciences
Subtitle of host publication	A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.), GMDS 2018
Editors	Ursula Hubner, Ulrich Sax, Hans-Ulrich Prokosch, Bernhard Breil, Harald Binder, Antonia Zap, Brigitte Strahwald, Tim Beissbarth, Niels Grabe, Anke Scholer
Publisher	IOS Press
Pages	183-187
Number of pages	5
Volume	253
ISBN (Electronic)	9781614998952
DOIs	https://doi.org/10.3233/978-1-61499-896-9-183
Publication status	Published - 2018
Event	63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology, GMDS 2018 - Osnabruck, Germany Duration: 2 Sept 2018 → 6 Sept 2018

Publication series

Name	Studies in Health Technology and Informatics
Volume	253
ISSN (Print)	0926-9630
ISSN (Electronic)	1879-8365

Conference/symposium

Conference/symposium	63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology, GMDS 2018
Country/Territory	Germany
City	Osnabruck
Period	2/09/18 → 6/09/18

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

amyotrophic lateral sclerosis
gene expression regulation
KEGG
metabolic networks and pathways
microRNAs
miRBase
miRTarBase

Access to Document

10.3233/978-1-61499-896-9-183Licence: CC BY-NC

https://edepot.wur.nl/581853Licence: CC BY-NC

Cite this

Hamzeiy, H., Suluyayla, R., Brinkrolf, C., Janowski, S. J., Hofestädt, R., & Allmer, J. (2018). Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. In U. Hubner, U. Sax, H.-U. Prokosch, B. Breil, H. Binder, A. Zap, B. Strahwald, T. Beissbarth, N. Grabe, & A. Scholer (Eds.), German Medical Data Sciences: A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.), GMDS 2018 (Vol. 253, pp. 183-187). (Studies in Health Technology and Informatics; Vol. 253). IOS Press. https://doi.org/10.3233/978-1-61499-896-9-183

Hamzeiy, Hamid ; Suluyayla, Rabia ; Brinkrolf, Christoph et al. / Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. German Medical Data Sciences: A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.), GMDS 2018. editor / Ursula Hubner ; Ulrich Sax ; Hans-Ulrich Prokosch ; Bernhard Breil ; Harald Binder ; Antonia Zap ; Brigitte Strahwald ; Tim Beissbarth ; Niels Grabe ; Anke Scholer. Vol. 253 IOS Press, 2018. pp. 183-187 (Studies in Health Technology and Informatics).

@inproceedings{68cf38519e4d4aac8572e9280f235e2d,

title = "Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways",

abstract = "MicroRNAs (miRNAs), approximately 22 nucleotides long, posttranscriptionally active gene expression regulators, play active roles in modulating cellular processes. Gene regulation and miRNA regulation are intertwined and the main aim of this study is to facilitate the analysis of miRNAs within gene regulatory pathways. VANESA enables the reconstruction of biological pathways and supports visualization and simulation. To support integrative miRNA and gene pathway analyses, a custom database of experimentally proven miRNAs, integrating data from miRBase, TarBase and miRTarBase, was added to DAWIS-M.D., which is the main data source for VANESA. Analysis of human KEGG pathways within DAWIS-M.D. showed that 661 miRNAs (\textasciitilde{}1/3 recorded human miRNAs) lead to 65,474 interactions. hsa-miR-335-5p targets most genes in our system (2,544); while the most targeted gene (with 71 miRNAs) is NUFIP2 (Nuclear Fragile X Mental Retardation Protein Interacting Protein 2). Amyotrophic Lateral Sclerosis (ALS), a complex neurodegenerative disease, was chosen as a proof of concept model. Using our system, it was possible to reduce the initially several hundred genes and miRNAs associated with ALS to eight genes, 19 miRNAs and 31 interactions. This highlights the effectiveness of the implemented system to distill important information from otherwise hard to access, highly convoluted and vast regulatory networks.",

keywords = "amyotrophic lateral sclerosis, gene expression regulation, KEGG, metabolic networks and pathways, microRNAs, miRBase, miRTarBase",

author = "Hamid Hamzeiy and Rabia Suluyayla and Christoph Brinkrolf and Janowski, \{Sebastian Jan\} and Ralf Hofest{\"a}dt and Jens Allmer",

year = "2018",

doi = "10.3233/978-1-61499-896-9-183",

language = "English",

volume = "253",

series = "Studies in Health Technology and Informatics",

publisher = "IOS Press",

pages = "183--187",

editor = "Ursula Hubner and Ulrich Sax and Hans-Ulrich Prokosch and Bernhard Breil and Harald Binder and Antonia Zap and Brigitte Strahwald and Tim Beissbarth and Niels Grabe and Anke Scholer",

booktitle = "German Medical Data Sciences",

address = "Netherlands",

note = "63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology, GMDS 2018 ; Conference date: 02-09-2018 Through 06-09-2018",

}

Hamzeiy, H, Suluyayla, R, Brinkrolf, C, Janowski, SJ, Hofestädt, R & Allmer, J 2018, Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. in U Hubner, U Sax, H-U Prokosch, B Breil, H Binder, A Zap, B Strahwald, T Beissbarth, N Grabe & A Scholer (eds), German Medical Data Sciences: A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.), GMDS 2018. vol. 253, Studies in Health Technology and Informatics, vol. 253, IOS Press, pp. 183-187, 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology, GMDS 2018, Osnabruck, Germany, 2/09/18. https://doi.org/10.3233/978-1-61499-896-9-183

Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. / Hamzeiy, Hamid; Suluyayla, Rabia; Brinkrolf, Christoph et al.
German Medical Data Sciences: A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.), GMDS 2018. ed. / Ursula Hubner; Ulrich Sax; Hans-Ulrich Prokosch; Bernhard Breil; Harald Binder; Antonia Zap; Brigitte Strahwald; Tim Beissbarth; Niels Grabe; Anke Scholer. Vol. 253 IOS Press, 2018. p. 183-187 (Studies in Health Technology and Informatics; Vol. 253).

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic › peer-review

TY - GEN

T1 - Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways

AU - Hamzeiy, Hamid

AU - Suluyayla, Rabia

AU - Brinkrolf, Christoph

AU - Janowski, Sebastian Jan

AU - Hofestädt, Ralf

AU - Allmer, Jens

PY - 2018

Y1 - 2018

N2 - MicroRNAs (miRNAs), approximately 22 nucleotides long, posttranscriptionally active gene expression regulators, play active roles in modulating cellular processes. Gene regulation and miRNA regulation are intertwined and the main aim of this study is to facilitate the analysis of miRNAs within gene regulatory pathways. VANESA enables the reconstruction of biological pathways and supports visualization and simulation. To support integrative miRNA and gene pathway analyses, a custom database of experimentally proven miRNAs, integrating data from miRBase, TarBase and miRTarBase, was added to DAWIS-M.D., which is the main data source for VANESA. Analysis of human KEGG pathways within DAWIS-M.D. showed that 661 miRNAs (~1/3 recorded human miRNAs) lead to 65,474 interactions. hsa-miR-335-5p targets most genes in our system (2,544); while the most targeted gene (with 71 miRNAs) is NUFIP2 (Nuclear Fragile X Mental Retardation Protein Interacting Protein 2). Amyotrophic Lateral Sclerosis (ALS), a complex neurodegenerative disease, was chosen as a proof of concept model. Using our system, it was possible to reduce the initially several hundred genes and miRNAs associated with ALS to eight genes, 19 miRNAs and 31 interactions. This highlights the effectiveness of the implemented system to distill important information from otherwise hard to access, highly convoluted and vast regulatory networks.

AB - MicroRNAs (miRNAs), approximately 22 nucleotides long, posttranscriptionally active gene expression regulators, play active roles in modulating cellular processes. Gene regulation and miRNA regulation are intertwined and the main aim of this study is to facilitate the analysis of miRNAs within gene regulatory pathways. VANESA enables the reconstruction of biological pathways and supports visualization and simulation. To support integrative miRNA and gene pathway analyses, a custom database of experimentally proven miRNAs, integrating data from miRBase, TarBase and miRTarBase, was added to DAWIS-M.D., which is the main data source for VANESA. Analysis of human KEGG pathways within DAWIS-M.D. showed that 661 miRNAs (~1/3 recorded human miRNAs) lead to 65,474 interactions. hsa-miR-335-5p targets most genes in our system (2,544); while the most targeted gene (with 71 miRNAs) is NUFIP2 (Nuclear Fragile X Mental Retardation Protein Interacting Protein 2). Amyotrophic Lateral Sclerosis (ALS), a complex neurodegenerative disease, was chosen as a proof of concept model. Using our system, it was possible to reduce the initially several hundred genes and miRNAs associated with ALS to eight genes, 19 miRNAs and 31 interactions. This highlights the effectiveness of the implemented system to distill important information from otherwise hard to access, highly convoluted and vast regulatory networks.

KW - amyotrophic lateral sclerosis

KW - gene expression regulation

KW - KEGG

KW - metabolic networks and pathways

KW - microRNAs

KW - miRBase

KW - miRTarBase

U2 - 10.3233/978-1-61499-896-9-183

DO - 10.3233/978-1-61499-896-9-183

M3 - Conference paper

C2 - 30147069

AN - SCOPUS:85056274164

VL - 253

T3 - Studies in Health Technology and Informatics

SP - 183

EP - 187

BT - German Medical Data Sciences

A2 - Hubner, Ursula

A2 - Sax, Ulrich

A2 - Prokosch, Hans-Ulrich

A2 - Breil, Bernhard

A2 - Binder, Harald

A2 - Zap, Antonia

A2 - Strahwald, Brigitte

A2 - Beissbarth, Tim

A2 - Grabe, Niels

A2 - Scholer, Anke

PB - IOS Press

T2 - 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology, GMDS 2018

Y2 - 2 September 2018 through 6 September 2018

ER -

Hamzeiy H, Suluyayla R, Brinkrolf C, Janowski SJ, Hofestädt R, Allmer J. Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. In Hubner U, Sax U, Prokosch HU, Breil B, Binder H, Zap A, Strahwald B, Beissbarth T, Grabe N, Scholer A, editors, German Medical Data Sciences: A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.), GMDS 2018. Vol. 253. IOS Press. 2018. p. 183-187. (Studies in Health Technology and Informatics). doi: 10.3233/978-1-61499-896-9-183

Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways

Abstract

Publication series

Conference/symposium

UN SDGs

Keywords

Access to Document

Fingerprint

Cite this