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  1. Article ; Online: Gene Co-Expression Network Analysis Reveals Key Regulatory Genes in Metisa plana Hormone Pathways

    Vinothienii Vengatharajuloo / Hoe-Han Goh / Maizom Hassan / Nisha Govender / Suhaila Sulaiman / Nor Afiqah-Aleng / Sarahani Harun / Zeti-Azura Mohamed-Hussein

    Insects, Vol 14, Iss 503, p

    2023  Volume 503

    Abstract: Metisa plana Walker (Lepidoptera: Psychidae) is a major oil palm pest species distributed across Southeast Asia. M. plana outbreaks are regarded as serious ongoing threats to the oil palm industry due to their ability to significantly reduce fruit yield ... ...

    Abstract Metisa plana Walker (Lepidoptera: Psychidae) is a major oil palm pest species distributed across Southeast Asia. M. plana outbreaks are regarded as serious ongoing threats to the oil palm industry due to their ability to significantly reduce fruit yield and subsequent productivity. Currently, conventional pesticide overuses may harm non-target organisms and severely pollute the environment. This study aims to identify key regulatory genes involved in hormone pathways during the third instar larvae stage of M. plana gene co-expression network analysis. A weighted gene co-expression network analysis (WGCNA) was conducted on the M. plana transcriptomes to construct a gene co-expression network. The transcriptome datasets were obtained from different development stages of M. plana , i.e., egg, third instar larvae, pupa, and adult. The network was clustered using the DPClusO algorithm and validated using Fisher’s exact test and receiver operating characteristic (ROC) analysis. The clustering analysis was performed on the network and 20 potential regulatory genes (such as MTA1-like , Nub , Grn , and Usp ) were identified from ten top-most significant clusters. Pathway enrichment analysis was performed to identify hormone signalling pathways and these pathways were identified, i.e., hormone-mediated signalling, steroid hormone-mediated signalling, and intracellular steroid hormone receptor signalling as well as six regulatory genes Hnf4 , Hr4 , MED14 , Usp , Tai , and Trr . These key regulatory genes have a potential as important targets in future upstream applications and validation studies in the development of biorational pesticides against M. plana and the RNA interference (RNAi) gene silencing method.
    Keywords Metisa plana ; WGCNA ; functional enrichment analysis ; protein–protein interaction ; network clustering ; pathway analysis ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors

    Rabiatul-Adawiah Zainal-Abidin / Nor Afiqah-Aleng / Muhammad-Redha Abdullah-Zawawi / Sarahani Harun / Zeti-Azura Mohamed-Hussein

    Life, Vol 12, Iss 650, p

    A Bioinformatics Workflow

    2022  Volume 650

    Abstract: Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have ... ...

    Abstract Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI network has been widely applied in biomedical research to understand the pathobiology of human diseases. It has also been used to understand the plant physiology that relates to crop improvement. However, the application of the PPI network in aquaculture is limited as compared to humans and plants. This review aims to demonstrate the workflow and step-by-step instructions for constructing a PPI network using bioinformatics tools and PPI databases that can help to predict potential interaction between proteins. We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network. Thus, serving as a guide for future steps in exploring potential mechanisms on the organismal physiology of interest that ultimately benefit aquaculture research.
    Keywords bioinformatics ; oestrogen receptor ; network analysis ; protein–protein interaction ; network ; zebrafish ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism

    Sarahani Harun / Nor Afiqah-Aleng / Fatin Izzati Abdul Hadi / Su Datt Lam / Zeti-Azura Mohamed-Hussein

    Life, Vol 12, Iss 326, p

    2022  Volume 326

    Abstract: Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana , the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and ... ...

    Abstract Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana , the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting of 1267 nodes and 14,308 edges. In addition, 1151 co-expressed genes were annotated, integrated, and visualised using relevant bioinformatic tools. Based on three criteria, 21 potential GSL genes encoding TPs were selected. The AST68 and ABCG40 potential GSL TPs were chosen for further investigation because their subcellular localisation is similar to that of known GSL TPs (SULTR1;1 and SULTR1;2) and ABCG36, respectively. However, AST68 was selected for a molecular-docking analysis using AutoDOCK Vina and AutoDOCK 4.2 with the generated 3D model, showing that both domains were well superimposed on the homologs. Both molecular-docking tools calculated good binding-energy values between the sulphate ion and Ser419 and Val172, with the formation of hydrogen bonds and van der Waals interactions, respectively, suggesting that AST68 was one of the sulphate transporters involved in GSL biosynthesis. This finding illustrates the ability to use computational analysis on gene co-expression data to screen and characterise plant TPs on a large scale to comprehensively elucidate GSL metabolism in A. thaliana . Most importantly, newly identified potential GSL transporters can serve as molecular tools in improving the nutritional value of crops.
    Keywords glucosinolate ; co-expression network ; molecular docking ; transporter proteins ; Science ; Q
    Subject code 580
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Protein–Protein Interaction Network Analysis Reveals Several Diseases Highly Associated with Polycystic Ovarian Syndrome

    Balqis Ramly / Nor Afiqah-Aleng / Zeti-Azura Mohamed-Hussein

    International Journal of Molecular Sciences, Vol 20, Iss 12, p

    2019  Volume 2959

    Abstract: Based on clinical observations, women with polycystic ovarian syndrome (PCOS) are prone to developing several other diseases, such as metabolic and cardiovascular diseases. However, the molecular association between PCOS and these diseases remains poorly ...

    Abstract Based on clinical observations, women with polycystic ovarian syndrome (PCOS) are prone to developing several other diseases, such as metabolic and cardiovascular diseases. However, the molecular association between PCOS and these diseases remains poorly understood. Recent studies showed that the information from protein−protein interaction (PPI) network analysis are useful in understanding the disease association in detail. This study utilized this approach to deepen the knowledge on the association between PCOS and other diseases. A PPI network for PCOS was constructed using PCOS-related proteins (PCOSrp) obtained from PCOSBase. MCODE was used to identify highly connected regions in the PCOS network, known as subnetworks. These subnetworks represent protein families, where their molecular information is used to explain the association between PCOS and other diseases. Fisher’s exact test and comorbidity data were used to identify PCOS−disease subnetworks. Pathway enrichment analysis was performed on the PCOS−disease subnetworks to identify significant pathways that are highly involved in the PCOS−disease associations. Migraine, schizophrenia, depressive disorder, obesity, and hypertension, along with twelve other diseases, were identified to be highly associated with PCOS. The identification of significant pathways, such as ribosome biogenesis, antigen processing and presentation, and mitophagy, suggest their involvement in the association between PCOS and migraine, schizophrenia, and hypertension.
    Keywords polycystic ovarian syndrome ; PCOS ; PPI ; MCODE ; pathway ; network ; subnetwork ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2019-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Bridging the gap between sustainability and profitability

    Muhammad Fatratullah Muhsin / Yushinta Fujaya / Andi Aliah Hidayani / Hanafiah Fazhan / Wan Adibah Wan Mahari / Su Shiung Lam / Alexander Chong Shu-Chien / Youji Wang / Nor Afiqah-Aleng / Nita Rukminasari / Khor Waiho

    PeerJ, Vol 11, p e

    unveiling the untapped potential of sea cucumber viscera

    2023  Volume 16252

    Abstract: Sea cucumbers have high economic value, and in most forms of trade, their body wall is typically the only part that is harvested and sold. The organs of the sea cucumber, collectively known as the viscera, are frequently discarded, contributing to land ... ...

    Abstract Sea cucumbers have high economic value, and in most forms of trade, their body wall is typically the only part that is harvested and sold. The organs of the sea cucumber, collectively known as the viscera, are frequently discarded, contributing to land and water pollution. However, discarded sea cucumber viscera contain various nutrients that can be used in many applications. Therefore, this review highlights the biological and economic aspects of sea cucumbers, followed by a critical discussion of the nutritional value of their internal organs and possible applications, including as functional feed additives in the aquaculture industry, sources of natural testosterone for application in sex reversal and production of monosex population, of neuroprotective agents against central nervous system disorders and of cosmetic ingredients, especially for skin whitening and anti-ageing products. The review further highlights the valorisation potential of viscera to maximize their economic potential, thus providing an enormous prospect for reusing sea cucumber waste, thereby reducing the negative impact of the sea cucumber fishery sector on the environment.
    Keywords Sea cucumber ; Viscera ; Waste ; Bioactive compound ; Valorisation ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 333
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach

    Sarahani Harun / Nor Afiqah-Aleng / Mohammad Bozlul Karim / Md Altaf Ul Amin / Shigehiko Kanaya / Zeti-Azura Mohamed-Hussein

    PeerJ, Vol 9, p e

    2021  Volume 11876

    Abstract: Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data ...

    Abstract Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset. Methods We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters. Results The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clustering approach in identifying potential GSL ...
    Keywords Secondary metabolites ; Nitrogen-containing compounds ; Aliphatic glucosinolates ; Indolic glucosinolates ; Graph clustering ; Gene network analysis ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Non-Lethal Heat Shock of the Asian Green Mussel, Perna viridis, Promotes Hsp70 Synthesis, Induces Thermotolerance and Protects Against Vibrio Infection.

    Nor Afiqah Aleng / Yeong Yik Sung / Thomas H MacRae / Mohd Effendy Abd Wahid

    PLoS ONE, Vol 10, Iss 8, p e

    2015  Volume 0135603

    Abstract: Mild heat stress promotes thermotolerance and protection against several different stresses in aquatic animals, consequences correlated with the accumulation of heat shock protein 70 (Hsp70). The purpose of this study was to determine if non-lethal heat ... ...

    Abstract Mild heat stress promotes thermotolerance and protection against several different stresses in aquatic animals, consequences correlated with the accumulation of heat shock protein 70 (Hsp70). The purpose of this study was to determine if non-lethal heat shock (NLHS) of the Asian green mussel, Perna viridis, an aquatic species of commercial value, promoted the production of Hsp70 and enhanced its resistance to stresses. Initially, the LT50 and LHT for P. viridis were determined to be 42°C and 44°C, respectively, with no heat shock induced death of mussels at 40°C or less. Immunoprobing of western blots revealed augmentation of constitutive (PvHsp70-1) and inducible (PvHsp70-2) Hsp70 in tissue from adductor muscle, foot, gill and mantel of P. viridis exposed to 38°C for 30 min followed by 6 h recovery, NLHS conditions for this organism. Characterization by liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that PvHsp70-1 and PvHsp70-2 respectively corresponded most closely to Hsp70 from P. viridis and Mytilus galloprovincialis. Priming of adult mussels with NLHS promoted thermotolerance and increased resistance to V. alginolyticus. The induction of Hsp70 in parallel with enhanced thermotolerance and improved protection against V. alginolyticus, suggests Hsp70 functions in P. viridis as a molecular chaperone and as a stimulator of the immune system.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: TCGA-My

    Mohd Amin Azuwar / Nor Azlan Nor Muhammad / Nor Afiqah-Aleng / Nurul-Syakima Ab Mutalib / Najwa Farhah Md. Yusof / Ryia Illani Mohd Yunos / Muhiddin Ishak / Sazuita Saidin / Isa Mohamed Rose / Ismail Sagap / Luqman Mazlan / Zairul Azwan Mohd Azman / Musalmah Mazlan / Sharaniza Ab Rahim / Wan Zurinah Wan Ngah / Sheila Nathan / Nurul Azmir Amir Hashim / Zeti-Azura Mohamed-Hussein / Rahman Jamal

    Life, Vol 12, Iss 772, p

    A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer

    2022  Volume 772

    Abstract: Colorectal cancer (CRC) ranks second among the most commonly occurring cancers in Malaysia, and unfortunately, its pathobiology remains unknown. CRC pathobiology can be understood in detail with the implementation of omics technology that is able to ... ...

    Abstract Colorectal cancer (CRC) ranks second among the most commonly occurring cancers in Malaysia, and unfortunately, its pathobiology remains unknown. CRC pathobiology can be understood in detail with the implementation of omics technology that is able to generate vast amounts of molecular data. The generation of omics data has introduced a new challenge for data organization. Therefore, a knowledge-based repository, namely TCGA-My, was developed to systematically store and organize CRC omics data for Malaysian patients. TCGA-My stores the genome and metabolome of Malaysian CRC patients. The genome and metabolome datasets were organized using a Python module, pandas. The variants and metabolites were first annotated with their biological information using gene ontologies (GOs) vocabulary. The TCGA-My relational database was then built using HeidiSQL PorTable 9.4.0.512, and Laravel was used to design the web interface. Currently, TCGA-My stores 1,517,841 variants, 23,695 genes, and 167,451 metabolites from the samples of 50 CRC patients. Data entries can be accessed via search and browse menus. TCGA-My aims to offer effective and systematic omics data management, allowing it to become the main resource for Malaysian CRC research, particularly in the context of biomarker identification for precision medicine.
    Keywords colorectal cancer ; CRC database ; CRC repository ; TCGA-My ; genome ; metabolome ; Science ; Q
    Subject code 020
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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