Integrated analysis of ovarian cancer patients from prospective transcription factor activity reveals subtypes of prognostic significance

Su, Dongqing; Xiong, Yuqiang; Wei, Haodong; Wang, Shiyuan; Ke, Jiawei; Liang, Ping; Zhang, Haoxin; Yu, Yao; Zuo, Yongchun; Yang, Lei

doi:10.1016/j.heliyon.2023.e16147

Cited by 3 publications

(1 citation statement)

References 79 publications

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“…In the same year, Agrawal et al [ 11 ] used amino acid composition, dipeptide composition, terminus composition, and binary profile to develop an extra-tree-based model named AntiCP-2.0. With the rise in deep learning and protein representation learning, many new anticancer peptide recognition methods [ 11 , 12 , 13 , 14 , 15 , 16 ] (e.g., iACP-DRLF and TriNet) continue to emerge, and the performances of the methods are becoming increasingly better.…”

Section: Introductionmentioning

confidence: 99%

Using the Random Forest for Identifying Key Physicochemical Properties of Amino Acids to Discriminate Anticancer and Non-Anticancer Peptides

Deng

et al. 2023

IJMS

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Anticancer peptides (ACPs) represent a promising new therapeutic approach in cancer treatment. They can target cancer cells without affecting healthy tissues or altering normal physiological functions. Machine learning algorithms have increasingly been utilized for predicting peptide sequences with potential ACP effects. This study analyzed four benchmark datasets based on a well-established random forest (RF) algorithm. The peptide sequences were converted into 566 physicochemical features extracted from the amino acid index (AAindex) library, which were then subjected to feature selection using four methods: light gradient-boosting machine (LGBM), analysis of variance (ANOVA), chi-squared test (Chi2), and mutual information (MI). Presenting and merging the identified features using Venn diagrams, 19 key amino acid physicochemical properties were identified that can be used to predict the likelihood of a peptide sequence functioning as an ACP. The results were quantified by performance evaluation metrics to determine the accuracy of predictions. This study aims to enhance the efficiency of designing peptide sequences for cancer treatment.

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Section: Introductionmentioning

confidence: 99%

Using the Random Forest for Identifying Key Physicochemical Properties of Amino Acids to Discriminate Anticancer and Non-Anticancer Peptides

Deng

et al. 2023

IJMS

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Excavation of gene markers associated with pancreatic ductal adenocarcinoma based on interrelationships of gene expression

Zhang,

Sun,

Gao

et al. 2024

IET Systems Biology

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Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of all pancreatic cancer cases, posing grave challenges to its diagnosis and treatment. Timely diagnosis is pivotal for improving patient survival, necessitating the discovery of precise biomarkers. An innovative approach was introduced to identify gene markers for precision PDAC detection. The core idea of our method is to discover gene pairs that display consistent opposite relative expression and differential co‐expression patterns between PDAC and normal samples. Reversal gene pair analysis and differential partial correlation analysis were performed to determine reversal differential partial correlation (RDC) gene pairs. Using incremental feature selection, the authors refined the selected gene set and constructed a machine‐learning model for PDAC recognition. As a result, the approach identified 10 RDC gene pairs. And the model could achieve a remarkable accuracy of 96.1% during cross‐validation, surpassing gene expression‐based models. The experiment on independent validation data confirmed the model's performance. Enrichment analysis revealed the involvement of these genes in essential biological processes and shed light on their potential roles in PDAC pathogenesis. Overall, the findings highlight the potential of these 10 RDC gene pairs as effective diagnostic markers for early PDAC detection, bringing hope for improving patient prognosis and survival.

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An Overview of Advances in Rare Cancer Diagnosis and Treatment

Christyani,

Carswell,

Qin

et al. 2024

IJMS

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Cancer stands as the leading global cause of mortality, with rare cancer comprising 230 distinct subtypes characterized by infrequent incidence. Despite the inherent challenges in addressing the diagnosis and treatment of rare cancers due to their low occurrence rates, several biomedical breakthroughs have led to significant advancement in both areas. This review provides a comprehensive overview of state-of-the-art diagnostic techniques that encompass new-generation sequencing and multi-omics, coupled with the integration of artificial intelligence and machine learning, that have revolutionized rare cancer diagnosis. In addition, this review highlights the latest innovations in rare cancer therapeutic options, comprising immunotherapy, targeted therapy, transplantation, and drug combination therapy, that have undergone clinical trials and significantly contribute to the tumor remission and overall survival of rare cancer patients. In this review, we summarize recent breakthroughs and insights in the understanding of rare cancer pathophysiology, diagnosis, and therapeutic modalities, as well as the challenges faced in the development of rare cancer diagnosis data interpretation and drug development.

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Integrated analysis of ovarian cancer patients from prospective transcription factor activity reveals subtypes of prognostic significance

Cited by 3 publications

References 79 publications

Using the Random Forest for Identifying Key Physicochemical Properties of Amino Acids to Discriminate Anticancer and Non-Anticancer Peptides

Using the Random Forest for Identifying Key Physicochemical Properties of Amino Acids to Discriminate Anticancer and Non-Anticancer Peptides

Excavation of gene markers associated with pancreatic ductal adenocarcinoma based on interrelationships of gene expression

An Overview of Advances in Rare Cancer Diagnosis and Treatment

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