Identifying Interaction Clusters for MiRNA and MRNA Pairs in TCGA Network.
Algorithms
Carcinoma, Hepatocellular
/ genetics
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Genome, Human
Genomics
/ methods
Guanine Nucleotide Exchange Factors
/ genetics
Humans
Liver Neoplasms
/ genetics
MicroRNAs
/ genetics
Phosphatidylinositol 3-Kinases
/ genetics
RNA, Messenger
/ genetics
Receptor, Platelet-Derived Growth Factor beta
/ genetics
Receptors, Lysophosphatidic Acid
/ genetics
Receptors, Prostaglandin
/ genetics
The Cancer Genome Atlas
clustering algorithm
gene regulation
liver hepatocellular carcinoma
mRNA
miRNA
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
11 09 2019
11 09 2019
Historique:
received:
14
08
2019
accepted:
06
09
2019
entrez:
14
9
2019
pubmed:
14
9
2019
medline:
17
1
2020
Statut:
epublish
Résumé
Existing methods often fail to recognize the conversions for the biological roles of the pairs of genes and microRNAs (miRNAs) between the tumor and normal samples. We have developed a novel cluster scoring method to identify messenger RNA (mRNA) and miRNA interaction pairs and clusters while considering tumor and normal samples jointly. Our method has identified 54 significant clusters for 15 cancer types selected from The Cancer Genome Atlas project. We also determined the shared clusters across tumor types and/or subtypes. In addition, we compared gene and miRNA overlap between lists identified in our liver hepatocellular carcinoma (LIHC) study and regulatory relationships reported from human and rat nonalcoholic fatty liver disease studies (NAFLD). Finally, we analyzed biological functions for the single significant cluster in LIHC and uncovered a significantly enriched pathway (phospholipase D signaling pathway) with six genes represented in the cluster, symbols:
Identifiants
pubmed: 31514484
pii: genes10090702
doi: 10.3390/genes10090702
pmc: PMC6770970
pii:
doi:
Substances chimiques
Guanine Nucleotide Exchange Factors
0
LPAR2 protein, human
0
MicroRNAs
0
RAPGEF3 protein, human
0
RNA, Messenger
0
Receptors, Lysophosphatidic Acid
0
Receptors, Prostaglandin
0
prostaglandin F2alpha receptor
0
PIK3R3 protein, human
EC 2.7.1.137
PDGFRB protein, human
EC 2.7.10.1
Receptor, Platelet-Derived Growth Factor beta
EC 2.7.10.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Déclaration de conflit d'intérêts
The authors declare that they have no competing interests.
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