InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment

Koido, Masaru; Tani, Yuri; Tsukahara, Satomi; Okamoto, Yuka; Tomida, Akihiro

doi:10.18632/oncotarget.25624

Cited by 8 publications

(3 citation statements)

References 44 publications

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“…In addition to evaluating the functional profile of all the associated genes within the modules selected, we performed inferences into the importance of the genes with high centrality within a GCN - hubs, which may be described as core regulators (Amrine et al, 2015) . Through the criteria defined for selecting hubs, we could identify the hub for each cluster of the cold stress gene modules, being considered key elements into the cold resistance definition (Carlson et al, 2006; Koido et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Genes with high centrality within a GCN may be described as core regulators (Amrine et al, 2015), which are known as hubs. Through the criteria defined for selecting hubs, we could identify hub genes for each cluster of the cold stress gene modules, which are considered key elements in the definition of cold resistance (Carlson et al, 2006;Koido et al, 2018).…”

Section: Identification Of Key Elements Within Cold Response-associated Modulesmentioning

confidence: 99%

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A deeper cascade of mechanisms involved in cold resistance inHevea brasiliensis

Silva

Bajay

Aono

et al. 2021

Preprint

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Hevea brasiliensis, a tropical tree species from the Amazon rainforest, is the main source of natural rubber worldwide. Due to the high pressure of fungal diseases in hot, humid regions, rubber plantations have been moved to “escape areas”, which are dryer and have lower temperatures during the winter. Here, we combined gene expression data of a primary (GT1) and a secondary (RRIM600) young rubber tree clones, which present different cold tolerance strategies, to analyze rubber tree gene expression regulation during 24 h of cold exposure (10°C). Together with traditional differential expression approaches, a RNA sequencing (RNA-seq) gene coexpression network (GCN) comprising 27,220 genes was established in which the genes were grouped into 832 clusters. In the GCN, most of the rubber tree molecular responses to cold stress were grouped in 26 clusters, which were divided into three GCN modules: a downregulated group comprising 12 clusters and two upregulated groups comprising eleven and three clusters. Considering the three modules identified, the general Hevea response to short-term cold exposure involved downregulation of gibberellin (GA) signaling, complex regulation of jasmonic acid (JA) stress responses and programmed cell death (PCD) and upregulation of ethylene responsive genes. The hub genes of the cold-responsive modules were subsequently identified and analyzed. As a result of the GCN strategy applied in this study, we could not only access individual DEGs related to the Hevea cold response, but also provide insights into a deeper cascade of associated mechanisms involved in the response to cold stress in young rubber trees. Our results may represent the genetic stress responses of the species, developed during its evolution, since the varieties chosen for this work are genotypes that were selected during the early years of rubber tree domestication. The understanding of H. brasiliensis cold response mechanisms can greatly improve the breeding strategies for this crop, which has a narrow genetic base, is impacted by climate change and is the only source for large-scale rubber production.

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Section: Discussionmentioning

confidence: 99%

Section: Identification Of Key Elements Within Cold Response-associated Modulesmentioning

confidence: 99%

A deeper cascade of mechanisms involved in cold resistance inHevea brasiliensis

Silva

Bajay

Aono

et al. 2021

Preprint

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“…In the gene co-expression network, highly connected genes are called central genes, and central genes play an important role in response to stress (Koido et al, 2018). We selected genes with an MM > 0.85 and GS > 0.6 in module turquoise (Figure S3), introduced them into Cytoscape, and screened them using the MMC algorithm, and selected the gene with the highest connectivity as the hub gene.…”

Section: Analysis Of the Co-expression Network Of The Hub Gene In The...mentioning

confidence: 99%

Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1

Jiang

Zhou²,

Ma³

et al. 2023

Front. Plant Sci.

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IntroductionThe soybean cyst nematode (SCN) is a major disease in soybean production thatseriously affects soybean yield. At present, there are no studies on weighted geneco-expression network analysis (WGCNA) related to SCN resistance.MethodsHere, transcriptome data from 36 soybean roots under SCN HG Type 0 (race 3) stresswere used in WGCNA to identify significant modules.Results and DiscussionA total of 10,000 differentially expressed genes and 21 modules were identified, of which the module most related to SCN was turquoise. In addition, the hub gene GmHg1 with high connectivity was selected, and its function was verified. GmHg1 encodes serine/threonine protein kinase (PK), and the expression of GmHg1 in SCN-resistant cultivars (‘Dongnong L-204’) and SCN-susceptible cultivars (‘Heinong 37’) increased significantly after HG Type 0 stress. Soybean plants transformed with GmHg1-OX had significantly increased SCN resistance. In contrast, the GmHg1-RNAi transgenic soybean plants significantly reduced SCN resistance. In transgenic materials, the expression patterns of 11 genes with the same expression trend as the GmHg1 gene in the ‘turquoise module’ were analyzed. Analysis showed that 11genes were co-expressed with GmHg1, which may be involved in the process of soybean resistance to SCN. Our work provides a new direction for studying the Molecular mechanism of soybean resistance to SCN.

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Challenges and Opportunities of Genomic Approaches in Therapeutics Development

Gray

Campbell

2020

Methods in Molecular Biology

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InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment

Cited by 8 publications

References 44 publications

A deeper cascade of mechanisms involved in cold resistance inHevea brasiliensis

A deeper cascade of mechanisms involved in cold resistance inHevea brasiliensis

Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1

Challenges and Opportunities of Genomic Approaches in Therapeutics Development

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