Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer

Banaganapalli, Babajan; Mallah, B.; Alghamdi, Kawthar Saad; Albaqami, Walaa F.; Alshaer, Dalal Sameer; Alrayes, Nuha; Elango, Ramu; Shaik, Noor Ahmad

doi:10.1371/journal.pone.0274629

Cited by 13 publications

(6 citation statements)

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“…We considered the network’s hubs, motifs, and modules equally when identifying candidate genes and regulatory pathways rather than focusing solely on over-represented hub genes. 17 - 20 , 46 , 47 We identified 10 PD key genes with higher centrality scores in the interactive regulatory networks. SRC, ESR1 , and SUMO1 were found only in blood, and CREBBP, BDNF, CDK1 , and CAT were only found in SN tissue.…”

Section: Discussionmentioning

confidence: 99%

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Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues

Elango

Banaganapalli

Mujalli

et al. 2023

Bioinform Biol Insights

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The Parkinson disease (PD) is the second most common neurodegenerative disorder affecting the central nervous system and motor functions. The biological complexity of PD is yet to reveal potential targets for intervention or to slow the disease severity. Therefore, this study aimed to compare the fidelity of blood to substantia nigra (SN) tissue gene expression from PD patients to provide a systematic approach to predict role of the key genes of PD pathobiology. Differentially expressed genes (DEGs) from multiple microarray data sets of PD blood and SN tissue from GEO database are identified. Using the theoretical network approach and variety of bioinformatic tools, we prioritized the key genes from DEGs. A total of 540 and 1024 DEGs were identified in blood and SN tissue samples, respectively. Functional pathways closely related to PD such as ERK1 and ERK2 cascades, mitogen-activated protein kinase (MAPK) signaling, Wnt, nuclear factor-κB (NF-κB), and PI3K-Akt signaling were observed by enrichment analysis. Expression patterns of 13 DEGs were similar in both blood and SN tissues. Comprehensive network topological analysis and gene regulatory networks identified additional 10 DEGs functionally connected with molecular mechanisms of PD through the mammalian target of rapamycin (mTOR), autophagy, and AMP-activated protein kinase (AMPK) signaling pathways. Potential drug molecules were identified by chemical-protein network and drug prediction analysis. These potential candidates can be further validated in vitro/in vivo to be used as biomarkers and/or novel drug targets for the PD pathology and/or to arrest or delay the neurodegeneration over the years, respectively.

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Section: Discussionmentioning

confidence: 99%

“…Similarly, we have used the Bioconductor Package (Lumi pipeline) exclusively built for the Illumina microarray platform (BeadChip). [17][18][19][20]…”

Section: Microarray Data Sets' Collection and Pre-processingmentioning

confidence: 99%

Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues

Elango

Banaganapalli

Mujalli

et al. 2023

Bioinform Biol Insights

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“…Cases of cancer are OPEN ACCESS EDITED BY rapidly becoming a risk factor for various malignancies, most notably lung, liver, colorectal, and breast cancers. Because of the disease's high notoriety, therapy has been a never-ending fight with few results (Mullard, 2020;Banaganapalli et al, 2022). One of the deadliest and most ubiquitous forms of cancer in people is lung cancer.…”

Section: Introductionmentioning

confidence: 99%

Molecular Level Atomistic and Structural Insights on Biological Macromolecules, Inhibition, and Dynamics Studies

2024

Frontiers Research Topics

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Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

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“…Cases of cancer are rapidly becoming a risk factor for various malignancies, most notably lung, liver, colorectal, and breast cancers. Because of the disease’s high notoriety, therapy has been a never-ending fight with few results ( Mullard, 2020 ; Banaganapalli et al, 2022 ). One of the deadliest and most ubiquitous forms of cancer in people is lung cancer.…”

Section: Introductionmentioning

confidence: 99%

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Kirubhanand

Leonora²,

Anitha³

et al. 2023

Front. Mol. Biosci.

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Introduction: Non-Small Cell Lung Cancer is the most prevalent type of cancer in lung cancer. Chemotherapy, radiation therapy, and other conventional cancer treatments have a low success rate. Thus, creating new medications is essential to halt the spread of lung cancer.Methods: In this study bioactive nature of lochnericine against Non-Small Cell Lung Cancer (NSCLC) was analyzed using various computational approaches such as quantum chemical calculations, molecular docking, and molecular dynamic simulation. Furthermore, the MTT assay shows the anti-proliferation activity of lochnericine.Results and Discussion: Using Frontier Molecular Orbital (FMO), the calculated band gap energy value associated with bioactive compounds and the molecule’s potential bioactivity is confirmed. The H38 hydrogen atom and O1 oxygen atom in the molecule are effectively electrophilic, and potential nucleophilic attack sites were confirmed through analysis of the Molecular electrostatic potential surface. Furthermore, the electrons within the molecule were delocalized, which confers bioactivity on the title molecule and was authorized through Mulliken atomic charge distribution analysis. A molecular docking study revealed that lochnericine inhibits non-small cell lung cancer-associated targeted protein. The lead molecule and targeted protein complex were stable during molecular dynamics simulation studies till the simulation period. Further, lochnericine demonstrated remarkable anti-proliferative and apoptotic features against A549 lung cancer cells. The current investigation powerfully suggests that lochnericine is a potential candidate for lung cancer.

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Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer

Cited by 13 publications

References 63 publications

Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues

Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues

Molecular Level Atomistic and Structural Insights on Biological Macromolecules, Inhibition, and Dynamics Studies

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

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