Functional clusters analysis and research based on differential coexpression networks

Background: Osteosarcoma (OS) is one of the most common primary malignant bone tumors in teenagers. Emerging studies demonstrated TWEAK and Fn14 were involved in regulating cancer cell differentiation, proliferation, apoptosis, migration and invasion. Objective: The present study identified differently expressed mRNAs and lncRNAs after anti-TWEAK treatment in OS cells using GSE41828. Methods: We identified 922 up-regulated mRNAs, 863 downregulated mRNAs, 29 up-regulated lncRNAs, and 58 down-regulated lncRNAs after anti-TWEAK treatment in OS cells. By constructing PPI networks, we identified several key proteins involved in anti-TWEAK treatment in OS cells, including MYC, IL6, CD44, ITGAM, STAT1, CCL5, FN1, PTEN, SPP1, TOP2A, and NCAM1. By constructing lncRNAs coexpression networks, we identified several key lncRNAs, including LINC00623, LINC00944, PSMB8-AS1, LOC101929787. Result: Bioinformatics analysis revealed DEGs after anti-TWEAK treatment in OS were involved in regulating type I interferon signaling pathway, immune response related pathways, telomere organization, chromatin silencing at rDNA, and DNA replication. Bioinformatics analysis revealed differently expressed lncRNAs after antiTWEAK treatment in OS were related to telomere organization, protein heterotetramerization, DNA replication, response to hypoxia, TNF signaling pathway, PI3K-Akt signaling pathway, Focal adhesion, Apoptosis, NF-kappa B signaling pathway, MAPK signaling pathway, FoxO signaling pathway. Conclusion: : This study provided useful information for understanding the mechanisms of TWEAK underlying OS progression and identifying novel therapeutic markers for OS.

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Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Genes ◽

10.3390/genes12050665 ◽

2021 ◽

Vol 12 (5) ◽

pp. 665

Author(s):

Hui Yu ◽

Yan Guo ◽

Jingchun Chen ◽

Xiangning Chen ◽

Peilin Jia ◽

...

Keyword(s):

Gene Expression ◽

Focal Adhesion ◽

Biological Pathways ◽

Postmortem Brain ◽

Rna Seq ◽

Hub Genes ◽

Differential Coexpression ◽

Pathway Crosstalk ◽

Microarray Datasets ◽

Transcriptomic Studies

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

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Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

BMC Ecology and Evolution ◽

10.1186/s12862-021-01787-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Pooja Singh ◽

Ehsan Pashay Ahi ◽

Christian Sturmbauer

Keyword(s):

In Silico ◽

Regulatory Networks ◽

Evolutionary Significance ◽

Cichlid Species ◽

Cichlid Fishes ◽

Gene Coexpression ◽

Modular Evolution ◽

Jaw Apparatus ◽

Coexpression Networks ◽

Pharyngeal Jaw

Abstract Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

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The state of the art in soybean transcriptomics resources and gene coexpression networks

in silico Plants ◽

10.1093/insilicoplants/diab005 ◽

2021 ◽

Author(s):

Fabricio Almeida-Silva ◽

Kanhu C Moharana ◽

Thiago M Venancio

Keyword(s):

State Of The Art ◽

The State ◽

Gene Coexpression Network ◽

Rna Seq ◽

Transcriptomic Data ◽

The Past ◽

Gene Coexpression ◽

Genomics Research ◽

Public Repositories ◽

Coexpression Networks

Abstract In the past decade, over 3000 samples of soybean transcriptomic data have accumulated in public repositories. Here, we review the state of the art in soybean transcriptomics, highlighting the major microarray and RNA-seq studies that investigated soybean transcriptional programs in different tissues and conditions. Further, we propose approaches for integrating such big data using gene coexpression network and outline important web resources that may facilitate soybean data acquisition and analysis, contributing to the acceleration of soybean breeding and functional genomics research.

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Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

Scientific Data ◽

10.1038/s41597-021-00828-8 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Hui Li ◽

Xingyu Yang ◽

Yue Zhang ◽

Zhiyan Gao ◽

Yuting Liang ◽

...

Keyword(s):

Gene Expression ◽

Plant Species ◽

Aquatic Plant ◽

Molecular Breeding ◽

Nelumbo Nucifera ◽

Sequence Analyses ◽

Genome Database ◽

Future Studies ◽

Sacred Lotus ◽

Coexpression Networks

AbstractSacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

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