scholarly journals Identification and functional characterization of the miRNA-gene regulatory network in chronic myeloid leukemia lineage negative cells

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
S. Agatheeswaran ◽  
N. C. Pattnayak ◽  
S. Chakraborty
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Myeloid Leukemia ◽  
Functional Characterization ◽  
Mirna Gene ◽  
Gene Regulatory

scholarly journals BCL2 and hsa-miR-181a-5p are potential biomarkers associated with papillary thyroid cancer based on bioinformatics analysis

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Cong Zhang ◽  
Chunrui Bo ◽  
Lunhua Guo ◽  
Pingyang Yu ◽  
Susheng Miao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Gene Regulatory Network ◽  
Papillary Thyroid Cancer ◽  
Regulatory Network ◽  
Mirna Gene ◽  
Cancer Type ◽  
Papillary Thyroid ◽  
Ppi Network ◽  
Gene Regulatory

Abstract Background The morbidity of thyroid carcinoma has been rising worldwide and increasing faster than any other cancer type. The most common subtype with the best prognosis is papillary thyroid cancer (PTC); however, the exact molecular pathogenesis of PTC is still not completely understood. Methods In the current study, 3 gene expression datasets (GSE3678, GSE3467, and GSE33630) and 2 miRNA expression datasets (GSE113629 and GSE73182) of PTC were selected from the Gene Expression Omnibus (GEO) database and were further used to identify differentially expressed genes (DEGs) and deregulated miRNAs between normal thyroid tissue samples and PTC samples. Then, Gene Ontology (GO) and pathway enrichment analyses were conducted, and a protein-protein interaction (PPI) network was constructed to explore the potential mechanism of PTC carcinogenesis. The hub gene detection was performed using the CentiScaPe v2.0 plugin, and significant modules were discovered using the MCODE plugin for Cytoscape. In addition, a miRNA-gene regulatory network in PTC was constructed using common deregulated miRNAs and DEGs. Results A total of 263 common DEGs and 12 common deregulated miRNAs were identified. Then, 6 significant KEGG pathways (P < 0.05) and 82 significant GO terms were found to be enriched, indicating that PTC was closely related to amino acid metabolism, development, immune system, and endocrine system. In addition, by constructing a PPI network and miRNA-gene regulatory network, we found that hsa-miR-181a-5p regulated the most DEGs, while BCL2 was targeted by the most miRNAs. Conclusions The results of this study suggested that hsa-miR-181a-5p and BCL2 and their regulatory networks may play important roles in the pathogenesis of PTC.

758 Functional Characterization of NK- and T-cells in IFN-a Monotherapy Treated Chronic Myeloid Leukemia (CML) Patients

2012 ◽  
Vol 48 ◽  
pp. S179-S180
Author(s):  
M. Ilander ◽  
A. Kreutzman ◽  
P. Rohon ◽  
T. Melo ◽  
J. Vakkila ◽  
...  
Keyword(s):  
T Cells ◽  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Functional Characterization

Characterization of a gene regulatory network underlying astringency loss in persimmon fruit

Planta ◽  
2017 ◽  
Vol 247 (3) ◽  
pp. 733-743 ◽  
Author(s):  
Soichiro Nishiyama ◽  
Noriyuki Onoue ◽  
Atsushi Kono ◽  
Akihiko Sato ◽  
Keizo Yonemori ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Persimmon Fruit ◽  
Gene Regulatory

scholarly journals Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development

2018 ◽  
Vol 23 (4) ◽  
pp. 557-569.e9 ◽  
Author(s):  
Christa Geeke Toenhake ◽  
Sabine Anne-Kristin Fraschka ◽  
Mahalingam Shanmugiah Vijayabaskar ◽  
David Robert Westhead ◽  
Simon Jan van Heeringen ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Chromatin Accessibility ◽  
Blood Stage ◽  
Stage Development ◽  
Gene Regulatory

scholarly journals Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

2014 ◽  
Vol 25 (1) ◽  
pp. 41-56 ◽  
Author(s):  
Juan L. Mateo ◽  
Debbie L.C. van den Berg ◽  
Maximilian Haeussler ◽  
Daniela Drechsel ◽  
Zachary B. Gaber ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Regulatory Network ◽  
Neural Stem Cell ◽  
Regulatory Network ◽  
Self Renewal ◽  
Gene Regulatory ◽  
Cell Gene ◽  
Stem Cell Gene

scholarly journals Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

2017 ◽  
Vol 27 (12) ◽  
pp. 2129-2129
Author(s):  
Juan L. Mateo ◽  
Debbie L.C. van den Berg ◽  
Maximilian Haeussler ◽  
Daniela Drechsel ◽  
Zachary B. Gaber ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Regulatory Network ◽  
Neural Stem Cell ◽  
Regulatory Network ◽  
Self Renewal ◽  
Gene Regulatory ◽  
Cell Gene ◽  
Stem Cell Gene

Analysis of Hypoxiamir-Gene Regulatory Network Identifies Critical MiRNAs Influencing Cell-Cycle Regulation Under Hypoxic Conditions

MicroRNA ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 223-236 ◽  
Author(s):  
Apoorv Gupta ◽  
Sugadev Ragumani ◽  
Yogendra Kumar Sharma ◽  
Yasmin Ahmad ◽  
Pankaj Khurana
Keyword(s):  
Cell Cycle ◽  
Gene Regulatory Network ◽  
Stress Responses ◽  
Regulatory Network ◽  
Topological Analysis ◽  
Functional Characterization ◽  
Cell Cycle Checkpoint ◽  
Hypoxic Stress ◽  
Pathway Enrichment ◽  
Gene Regulatory

Background: Hypoxia is a pathophysiological condition which arises due to low oxygen concentration in conditions like cardiovascular diseases, inflammation, ascent to higher altitude, malignancies, deep sea diving, prenatal birth, etc. A number of microRNAs (miRNAs), Transcription Factors (TFs) and genes have been studied separately for their role in hypoxic adaptation and controlling cell-cycle progression and apoptosis during this stress. Objective: We hypothesize that miRNAs and TFs may act in conjunction to regulate a multitude of genes and play a crucial and combinatorial role during hypoxia-stress-responses and associated cellcycle control mechanisms. Method: We collected a comprehensive and non-redundant list of human hypoxia-responsive miRNAs (also known as hypoxiamiRs). Their experimentally validated gene-targets were retrieved from various databases and a comprehensive hypoxiamiR-gene regulatory network was built. Results: Functional characterization and pathway enrichment of genes identified phospho-proteins as enriched nodes. The phospho-proteins which were localized both in the nucleus and cytoplasm and could potentially play important role as signaling molecules were selected; and further pathway enrichment revealed that most of them were involved in NFkB signaling. Topological analysis identified several critical hypoxiamiRs and network perturbations confirmed their importance in the network. Feed Forward Loops (FFLs) were identified in the subnetwork of enriched genes, miRNAs and TFs. Statistically significant FFLs consisted of four miRNAs (hsa-miR-182-5p, hsa- miR-146b-5p, hsa-miR-96, hsa-miR-20a) and three TFs (SMAD4, FOXO1, HIF1A) both regulating two genes (NFkB1A and CDKN1A). Conclusion: Detailed BioCarta pathway analysis identified that these miRNAs and TFs together play a critical and combinatorial role in regulating cell-cycle under hypoxia, by controlling mechanisms that activate cell-cycle checkpoint protein, CDKN1A. These modules work synergistically to regulate cell-proliferation, cell-growth, cell-differentiation and apoptosis during hypoxia. A detailed mechanistic molecular model of how these co-regulatory FFLs may regulate the cell-cycle transitions during hypoxic stress conditions is also put forth. These biomolecules may play a crucial and deterministic role in deciding the fate of the cell under hypoxic-stress.

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