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
N1 - Publisher Copyright:
© 2018 The authors and IOS Press.
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 -
