Revealing shared differential co-expression profiles in rice infected by virus from reoviridae and sequiviridae group

Sahu, Jagajjit; Panda, Debashis; Baruah, Geetanjali; Patar, Lochana; Sen, Priyabrata; Borah, Bibha Chetia; Modi, Mahendra Kumar

doi:10.1016/j.gene.2019.02.063

Cited by 6 publications

(5 citation statements)

References 31 publications

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“…With the development of sequencing technology, the systematic study of massive amounts of genomic, transcriptomic, and metabolomic data using co-expression networks has gained immense attention for data processing ( Xie et al., 2022 ). The WGCNA is an effective method for co-expression network analysis, capable of specifically screening out co-expression modules with high biological significance to the target trait, and has proven to be an efficient data mining method in a variety of plants ( Sahu et al., 2019 ; Lu et al, 2019 ). In traditional methods, differential trait comparison is often focused on finding differential genes, thus neglecting the inter-genes correlation.…”

Section: Discussionmentioning

confidence: 99%

Integration of comparative transcriptomics and WGCNA characterizes the regulation of anthocyanin biosynthesis in mung bean (Vigna radiata L.)

Li,

Gao,

et al. 2023

Front. Plant Sci.

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Mung bean is a dual-use crop widely cultivated in Southeast Asia as a food and medicine resource. The development of new functional mung bean varieties demands identifying new genes regulating anthocyanidin synthesis and investigating their molecular mechanism. In this study, we used high-throughput sequencing technology to generate transcriptome sequence of leaves, petioles, and hypocotyls for investigating the anthocyanins accumulation in common mung bean variety as well as anthocyanidin rich mung bean variety, and to elucidate their molecular mechanisms. 29 kinds of anthocyanin compounds were identified. Most of the anthocyanin components contents were significantly higher in ZL23 compare with AL12. Transcriptome analysis suggested that a total of 93 structural genes encoding the anthocyanin biosynthetic pathway and 273 regulatory genes encoding the ternary complex of MYB-bHLH-WD40 were identified, of which 26 and 78 were differentially expressed in the two varieties. Weighted gene co-expression network analysis revealed that VrMYB3 and VrMYB90 might have enhanced mung bean anthocyanin content by inducing the expression of structural genes such as PAL, 4CL, F3’5’H, LDOX, and F3’H, which was consistent with qRT-PCR results. These findings are envisaged to provide a reference for studying the molecular mechanism of anthocyanin accumulation in mung beans.

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Section: Discussionmentioning

confidence: 99%

Integration of comparative transcriptomics and WGCNA characterizes the regulation of anthocyanin biosynthesis in mung bean (Vigna radiata L.)

Li,

Gao,

et al. 2023

Front. Plant Sci.

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“…Gene–gene networks are a very popular area of research that has been obtained by various methods. There is co-expression network that is immensely informative concerning the system-wide understanding of regulatory circuits [ 26 , 27 ]. Gene–gene co-expression networks are generally built upon the expression datasets generated from experiments such as microarray, next-generation sequencing, etc.…”

Section: Discussionmentioning

confidence: 99%

Mining Proteome Research Reports: A Bird’s Eye View

Sahu

2021

Proteomes

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The complexity of data has burgeoned to such an extent that scientists of every realm are encountering the incessant challenge of data management. Modern-day analytical approaches with the help of free source tools and programming languages have facilitated access to the context of the various domains as well as specific works reported. Here, with this article, an attempt has been made to provide a systematic analysis of all the available reports at PubMed on Proteome using text mining. The work is comprised of scientometrics as well as information extraction to provide the publication trends as well as frequent keywords, bioconcepts and most importantly gene–gene co-occurrence network. Out of 33,028 PMIDs collected initially, the segregation of 24,350 articles under 28 Medical Subject Headings (MeSH) was analyzed and plotted. Keyword link network and density visualizations were provided for the top 1000 frequent Mesh keywords. PubTator was used, and 322,026 bioconcepts were able to extracted under 10 classes (such as Gene, Disease, CellLine, etc.). Co-occurrence networks were constructed for PMID-bioconcept as well as bioconcept–bioconcept associations. Further, for creation of subnetwork with respect to gene–gene co-occurrence, a total of 11,100 unique genes participated with mTOR and AKT showing the highest (64) number of connections. The gene p53 was the most popular one in the network in accordance with both the degree and weighted degree centrality, which were 425 and 1414, respectively. The present piece of study is an amalgam of bibliometrics and scientific data mining methods looking deeper into the whole scale analysis of available literature on proteome.

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“…The weighted gene co-expression network analysis (WGCNA) method, as a network approach, can group genes into specified modules based on the high correlations between co-expression genes across the samples, resulting in a cluster of genes that share a similar function. Several studies on the transcriptome data utilizing the WGCNA method to investigate complex traits in plants’ reactions to stress, such as salt stress [ 20 ], chilling stress [ 21 ], γ radiation stress [ 22 ] and biotic stress [ 23 , 24 ] have been reported.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Sugar Beet to Salt Stress of Different Durations

Cui

Dai

et al. 2022

IJMS

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Salinity is one of the most serious threats to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt; however, the genome-wide dynamic response to salt stress remains largely unknown in sugar beet. In the present study, physiological and transcriptome analyses of sugar beet leaves and roots were compared under salt stress at five time points. The results showed that different salt stresses influenced phenotypic characteristics, leaf relative water content and root activity in sugar beet. The contents of chlorophyll, malondialdehyde (MDA), the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) were also affected by different salt stresses. Compared with control plants, there were 7391 and 8729 differentially expressed genes (DEGs) in leaves and roots under salt stress, respectively. A total of 41 hub genes related to salt stress were identified by weighted gene co-expression network analysis (WGCNA) from DEGs, and a transcriptional regulatory network based on these genes was constructed. The expression pattern of hub genes under salt stress was confirmed by qRT-PCR. In addition, the metabolite of sugar beet was compared under salt stress for 24 h. A total of 157 and 157 differentially accumulated metabolites (DAMs) were identified in leaves and roots, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that DEGs and DAMs act on the starch and sucrose metabolism, alpha-linolenic acid metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction pathway. In this study, RNA-seq, WGCNA analysis and untargeted metabolomics were combined to investigate the transcriptional and metabolic changes of sugar beet during salt stress. The results provided new insights into the molecular mechanism of sugar beet response to salt stress, and also provided candidate genes for sugar beet improvement.

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Revealing shared differential co-expression profiles in rice infected by virus from reoviridae and sequiviridae group

Cited by 6 publications

References 31 publications

Integration of comparative transcriptomics and WGCNA characterizes the regulation of anthocyanin biosynthesis in mung bean (Vigna radiata L.)

Integration of comparative transcriptomics and WGCNA characterizes the regulation of anthocyanin biosynthesis in mung bean (Vigna radiata L.)

Mining Proteome Research Reports: A Bird’s Eye View

Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Sugar Beet to Salt Stress of Different Durations

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