Genetic association between CDKN2B/CDKN2B-AS1 gene polymorphisms with primary glaucoma in a North Indian cohort: an original study and an updated meta-analysis

Thakur, Nanamika; Kupani, Manu; Mannan, Rifat; Pruthi, Archna; Mehrotra, Sanjana

doi:10.1186/s12920-020-00855-1

Cited by 27 publications

(18 citation statements)

References 42 publications

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“…As the first use case, we studied the target genes and pathway networks of CDKN2B-AS1, a gene that has been previously described in humans and associated with various functions [87,88]. CDKN2B-AS1 is involved in a large number of pathways, as shown in Figure 3A, including ‘Human immunodeficiency virus 1 infection’ and ‘coronavirus disease-COVID-19’.…”

Section: Resultsmentioning

confidence: 99%

NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways

Chen

Zhang

et al. 2022

Preprint

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Noncoding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the existing signaling pathway databases do not include information on miRNA and lncRNA. Here, we redesigned a novel pathway database named NcPath by integrating and visualizing a total of 178,308 human experimentally-validated miRNA-target interactions (MTIs), 36,537 experimentally-verified lncRNA target interactions (LTIs), and 4,879 experimentally-validated human ceRNA networks across 222 KEGG pathways (including 27 sub-categories). To expand the application potential of the redesigned NcPath database, we identified 553,523 reliable lncRNA-PCG interaction pairs by integrating co-expression relations, ceRNA relations, co-TF-binding interactions, co-Histone-modification interactions, cis-regulation relations and lncPro Tool predictions between lncRNAs and protein-coding genes. In addition, to determine the pathways in which miRNA/lncRNA targets are involved, we performed a KEGG enrichment analysis using an hypergeometric test. The NcPath database also provides information on MTIs/LTIs/ceRNA networks, PubMed IDs, gene annotations and the experimental verification method used. In summary, the NcPath database will serve as an important and continually updated platform that provides annotation and visualization of the pathways on which noncoding RNAs (miRNA and lncRNA) are involved, and provide support to multimodal noncoding RNAs enrichment analysis. The NcPath database is freely accessible at http://ncpath.pianlab.cn/.

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Section: Resultsmentioning

confidence: 99%

NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways

Chen

Zhang

et al. 2022

Preprint

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“…Meanwhile, other three pan HDAC inhibitors are being studied in MPM patients (NCT00365053, Nct00128102 and NCT00535951). 44 In addition, there are also many biomarker-related experiments that have been proved to be related to the occurrence and development of MPM. A study using bioinformatics tools demonstrated that EZH2 and HMMR were found over-expressed in MPM tissues and the patients with elevated EZH2 and HMMR expressions had poor overall survival.…”

Section: Biomarkers For Mpmmentioning

confidence: 99%

Advances in Immunotherapy of Malignant Pleural Mesothelioma

Liao¹,

Yu²,

Mei³

et al. 2021

OTT

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Malignant pleural mesothelioma (MPM) represents the uncommon cancer originating from pleural mesothelial cells, which is associated with dismal prognostic outcome. According to CheckMate-743 results, nivolumab plus ipilimumab has been approved to treat the unresectable MPM in treatment-naive patients as a first-line therapy by the FDA in October 2020. Immunotherapy is expected to be the best choice for MPM treatment. In the following article, the past treatment plan and the progress of immunotherapy for MPM will be reviewed.

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“…LR is a statistical ML model which models a set of input features (X: input) into target variables (Y: output) by means of a sigmoid function which is an 'S' shaped curve and restricts Y in the range of 0 and 1 (De Cock et al, 2021). Sigmoid function σ : R −→ (0,1) is defined as:…”

Section: Logistic Regressionmentioning

confidence: 99%

Sentiment classification for employees reviews using regression vector- stochastic gradient descent classifier (RV-SGDC)

Gaye

Zhang

Wulamu

2021

PeerJ Computer Science

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The satisfaction of employees is very important for any organization to make sufficient progress in production and to achieve its goals. Organizations try to keep their employees satisfied by making their policies according to employees’ demands which help to create a good environment for the collective. For this reason, it is beneficial for organizations to perform staff satisfaction surveys to be analyzed, allowing them to gauge the levels of satisfaction among employees. Sentiment analysis is an approach that can assist in this regard as it categorizes sentiments of reviews into positive and negative results. In this study, we perform experiments for the world’s big six companies and classify their employees’ reviews based on their sentiments. For this, we proposed an approach using lexicon-based and machine learning based techniques. Firstly, we extracted the sentiments of employees from text reviews and labeled the dataset as positive and negative using TextBlob. Then we proposed a hybrid/voting model named Regression Vector-Stochastic Gradient Descent Classifier (RV-SGDC) for sentiment classification. RV-SGDC is a combination of logistic regression, support vector machines, and stochastic gradient descent. We combined these models under a majority voting criteria. We also used other machine learning models in the performance comparison of RV-SGDC. Further, three feature extraction techniques: term frequency-inverse document frequency (TF-IDF), bag of words, and global vectors are used to train learning models. We evaluated the performance of all models in terms of accuracy, precision, recall, and F1 score. The results revealed that RV-SGDC outperforms with a 0.97 accuracy score using the TF-IDF feature due to its hybrid architecture.

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Genetic association between CDKN2B/CDKN2B-AS1 gene polymorphisms with primary glaucoma in a North Indian cohort: an original study and an updated meta-analysis

Cited by 27 publications

References 42 publications

NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways

NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways

Advances in Immunotherapy of Malignant Pleural Mesothelioma

Sentiment classification for employees reviews using regression vector- stochastic gradient descent classifier (RV-SGDC)

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