Underlying functional genomics of fat deposition in adipose tissue

Bakhtiarizadeh, Mohammad Reza; Moradi-Shahrbabak, Mohammad; Ebrahimie, Esmaeil

doi:10.1016/j.gene.2013.03.045

Cited by 62 publications

(42 citation statements)

References 48 publications

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“…Genome-wide analysis using Expressed Sequence Tags (ESTs) and available genomic sequences offer new possibilities in global genome analysis and detection of AS events [16]. ESTs represent the functional transcripts expressed from active genes in the cells, tissues or conditions investigated and generally give an overview of the developmental and physiological processes that function in these conditions [19][20][21][22][23]. Homology based-mapping of ESTs against genomic sequences acts as a corner stone approach to discover and delineate AS variants [24].…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

et al. 2015

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a b s t r a c tIn this study, using homology mapping of assembled expressed sequence tags against the genomic data, we identified alternative splicing events in barley. Results demonstrated that intron retention is frequently associated with specific abiotic stresses. Network analysis resulted in discovery of some specific sub-networks between miRNAs and transcription factors in genes with high number of alternative splicing, such as cross talk between SPL2, SPL10 and SPL11 regulated by miR156 and miR157 families. To confirm the alternative splicing events, elongation factor protein (MLOC_3412) was selected followed by experimental verification of the predicted splice variants by Semi quantitative Reverse Transcription PCR (qRT-PCR). Our novel integrative approach opens a new avenue for functional annotation of alternative splicing through regulatory-based network discovery.

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Section: Introductionmentioning

confidence: 99%

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

et al. 2015

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“…FABP4 is a fatty acid binding protein specific to mammalian adipose tissue [62, 63]. No significant difference was observed between induced ASCs treated with ST and non-treated control cells.…”

Section: Resultsmentioning

confidence: 99%

SalmonellaEnhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells

Foutouhi¹,

Mohamad‐Fauzi²,

Storey³

et al. 2019

Preprint

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22 and interpretation; DB: Study design, Provision of study material; JDM: Experiment conception and design, 23Financial support, Administrative support, Provision of study material, Data analysis and interpretation, Manuscript24 writing, Final approval of manuscript.; BCW: Experiment conception and design, Financial support, 25 Administrative support, Provision of study material, Data analysis and interpretation, Manuscript writing, Final 26 approval of manuscript. 28Abstract 29

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“…As quality based analyses methods, these approaches provided new knowledge regarding the interaction between genes and prevents false positive significant expression (quantity based method) which is the common problem in expression analysis [29]. It should be noted that expression level alone cannot be announced as the sole criterion of gene significance whereas some genes with lower expression levels (such as transcription factors and microRNAs) play a prominent role in systems biology [4,24,25,34].…”

Section: Discussionmentioning

confidence: 99%

Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders

et al. 2015

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Pandemic influenza remains as a substantial threat to humans with a widespread panic worldwide. In contrast, seasonal (non-pandemic) has a mild non-lethal infection each year. The underlying mechanisms governing the detrimental effects of pandemic influenza are yet to be known. Transcriptomic-based network discovery and gene ontology (GO) analysis of host response to pandemic influenza, compared to seasonal influenza, can shed light on the differential mechanisms which pandemic influenza is employed during evolution. Here, using microarray data of infected ferrets with pandemic and seasonal influenza (as a model), we evaluated the possible link between altered genes after pandemic infection with activation of neuronal disorders. To this end, we utilized novel computational biology techniques including differential transcriptome analysis, network construction, GO enrichment, and GO network to investigate the underlying mechanisms of pandemic influenza infection and host interaction. In comparison to seasonal influenza, pandemic influenza differentially altered the expression of 31 genes with direct involvement in activity of central nervous system (CNS). Network topology highlighted the high interactions of IRF1, NKX2-1 and NR5A1 as well as MIR27A, MIR19A, and MIR17. TGFB2, NCOA3 and SP1 were the central transcription factors in the networks. Pandemic influenza remarkably downregulated GPM6A and GTPase. GO network demonstrated the key roles of GPM6A and GTPase in regulation of important functions such as synapse assembly and neuron projection. For the first time, we showed that besides interference with cytokine/chemokine storm and neuraminidase enzyme, H1N1 pandemic influenza is able to directly affect neuronal gene networks. The possibility of application of some key regulators such as GPM6A protein, MIR128, and MIR367 as candidate therapeutic agents is discussed. The presented approach established a new way to unravel unknown pathways in virus-associated CNS dysfunction by utilizing global transcriptomic data, network and GO analysis.

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Underlying functional genomics of fat deposition in adipose tissue

Cited by 62 publications

References 48 publications

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

SalmonellaEnhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells

Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders

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