Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Chen, Bor‐Sen; Wu, Chia‐Chou

doi:10.3390/cells2040635

Cited by 36 publications

(32 citation statements)

References 93 publications

(321 reference statements)

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“…The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses were performed by a DAVID online analysis tool (http://david.abcc.ncifcrf.gov/) [34, 35]. Fisher's two-side exact test and Chi-square test were used to classify the GO categories and KEGG pathway categories, and the false discovery rate (FDR) was also calculated to correct the P values.…”

Section: Methodsmentioning

confidence: 99%

Altered microRNA profiles in plasma exosomes from mesial temporal lobe epilepsy with hippocampal sclerosis

et al. 2016

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Mesial temporal lobe epilepsy with hippocampal sclerosis (mTLE-HS) is the most common type of focal epilepsy. The present study aimed to explore the expression and functions of exosomal microRNAs in mTLE-HS. A total of 50 microRNAs were found to be differentially expressed in mTLE-HS compared with healthy controls. Among them, 2 were increased and 48 were decreased. The 6 significant differentially expressed candidate microRNAs (miR-3613-5p, miR-4668-5p, miR-8071, miR-197-5p, miR-4322, and miR-6781-5p ) in exosome were validated. The bioinformatics analysis showed that the potential target genes of these microRNAs were involved in biological processes, molecular functions, and cellular components. Similarly, these microRNAs also affected axon guidance, pathways in cancer, regulation of the actin cytoskeleton, focal adhesion, the calcium signaling pathway, the MAPK signaling pathway, and the PI3K-Akt signaling pathway. Among 6 candidate microRNAs, miR-8071 had the best diagnostic value for mTLE-HS with 83.33% sensitivity and 96.67% specificity, and was associated with seizure severity. This study indicated that exosomal microRNAs, may be regulators for the seizure development in mTLE-HS, and can be used as potential therapeutic targets and biomarker for diagnosis in mTLE-HS.

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Section: Methodsmentioning

confidence: 99%

Altered microRNA profiles in plasma exosomes from mesial temporal lobe epilepsy with hippocampal sclerosis

et al. 2016

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“…The basic information for the constructed networks is shown in Table 1 . It should be noted that all genes and their expression profiles were used to obtain the resultant networks, in contrast to a previous procedure [ 9 , 10 ] in which differentially expressed genes (DEGs) are selected. PPINs in the present study thus represent networks of all proteins, while the previously published PPINs are networks of proteins with significantly differential levels of expression only.…”

Section: Resultsmentioning

confidence: 99%

Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach

Chen

2016

IJMS

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While inflammation has generally been regarded as a negative factor in stroke recovery, this viewpoint has recently been challenged by demonstrating that inflammation is a necessary and sufficient factor for regeneration in the zebrafish brain injury model. This close relationship with inflammation suggests that a re-examination of the immune system’s role in strokes is necessary. We used a systems biology approach to investigate the role of immune-related functions via their interactions with other molecular functions in early cardioembolic stroke. Based on protein interaction models and on microarray data from the blood of stroke subjects and healthy controls, networks were constructed to delineate molecular interactions at four early stages (pre-stroke, 3 h, 5 h and 24 h after stroke onset) of cardioembolic stroke. A comparative analysis of functional networks identified interactions of immune-related functions with other molecular functions, including growth factors, neuro/hormone and housekeeping functions. These provide a potential pathomechanism for early stroke pathophysiology. In addition, several potential targets of miRNA and methylation regulations were derived based on basal level changes observed in the core networks and literature. The results provide a more comprehensive understanding of stroke progression mechanisms from an immune perspective and shed light on acute stroke treatments.

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“…Common approaches using protein–protein interactions (PPIs) or gene ontologies drive the search for modules or terms that could function as gene signatures [14]. Based on systems biology, several mathematical techniques have been developed to analyze the systematic properties of complex biological networks [15]. Network-based classification by greedy search found subnetworks providing a novel hypothesis for pathways involved in tumor progression [16].…”

Section: Introductionmentioning

confidence: 99%

Systems Biology Approaches to Investigate Genetic and Epigenetic Molecular Progression Mechanisms for Identifying Gene Expression Signatures in Papillary Thyroid Cancer

Yeh

Lin

et al. 2019

IJMS

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Thyroid cancer is the most common endocrine cancer. Particularly, papillary thyroid cancer (PTC) accounts for the highest proportion of thyroid cancer. Up to now, there are few researches discussing the pathogenesis and progression mechanisms of PTC from the viewpoint of systems biology approaches. In this study, first we constructed the candidate genetic and epigenetic network (GEN) consisting of candidate protein–protein interaction network (PPIN) and candidate gene regulatory network (GRN) by big database mining. Secondly, system identification and system order detection methods were applied to prune candidate GEN via next-generation sequencing (NGS) and DNA methylation profiles to obtain the real GEN. After that, we extracted core GENs from real GENs by the principal network projection (PNP) method. To investigate the pathogenic and progression mechanisms in each stage of PTC, core GEN was denoted in respect of KEGG pathways. Finally, by comparing two successive core signaling pathways of PTC, we not only shed light on the causes of PTC progression, but also identified essential biomarkers with specific gene expression signature. Moreover, based on the identified gene expression signature, we suggested potential candidate drugs to prevent the progression of PTC with querying Connectivity Map (CMap).

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Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Cited by 36 publications

References 93 publications

Altered microRNA profiles in plasma exosomes from mesial temporal lobe epilepsy with hippocampal sclerosis

Altered microRNA profiles in plasma exosomes from mesial temporal lobe epilepsy with hippocampal sclerosis

Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach

Systems Biology Approaches to Investigate Genetic and Epigenetic Molecular Progression Mechanisms for Identifying Gene Expression Signatures in Papillary Thyroid Cancer

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