Identifying condition specific key genes from basal-like breast cancer gene expression data

Maind, Ankush; Raut, Shital

doi:10.1016/j.compbiolchem.2018.12.022

Cited by 9 publications

(4 citation statements)

References 22 publications

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“…The methylation levels of the ZNF215 gene and the PTGS2 gene were negatively correlated with their expression levels. Furthermore, the ZNF215 gene can be used as a diagnostic and prognostic biomarker for basal-like breast cancer and acute myeloid leukemia ( 42 , 43 ). Among them, the view that S. saccharolyticus can further promote the proliferation and cloning of gastric cells by regulating the gene expression level of ZNF215 has been verified by cell experiments in this paper, which increased the reliability of our data analysis results.…”

Section: Discussionmentioning

confidence: 99%

Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma

et al. 2023

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The burgeoning field of oncobiome research declared that members of the intratumoral microbiome besides Helicobacter pylori existed in tumor tissues and participated in the occurrence and development of gastric cancer, and the methylation of host DNA may be a potential target of microbes and their metabolites. Current research focuses mostly on species composition, but the functional genes of the members of the microbiota are also key to their interaction with the host.

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Section: Discussionmentioning

confidence: 99%

Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma

et al. 2023

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“…an independent prognostic biomarker in prostate cancer (Angulo et al, 2016) and Maind and Raut (2019) reported its expression as a diagnostic and prognostic biomarker of basal-like breast cancer.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, its expression was associated with poor outcomes in hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (Li et al, 2019). The hypermethylation of ZNF215 has been found an independent prognostic biomarker in prostate cancer (Angulo et al, 2016) and Maind and Raut (2019) reported its expression as a diagnostic and prognostic biomarker of basal‐like breast cancer. Additionally, loss of ZNF215 imprinting has been also associated with poor 5‐year survival (Yang et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Oral cancers preceded by proliferative verrucous leukoplakia exhibit distinctive molecular features

et al. 2023

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ObjectiveProliferative verrucous leukoplakia (PVL) has high rates of malignant transformation into oral squamous cell carcinoma (OSCC), but the clinical and evolutionary pattern of OSCC from PVL (PVL‐OSCC) is more favorable than that of OSCC not preceded by PVL (OSCC). Here, we aimed to explore the pathophysiologic differences between PVL‐OSCC and OSCC through transcriptomic and DNA methylation analyses.Materials and methodsIn this case‐control study, oral biopsies from 8 PVL‐OSCC and 10 OSCC patients were obtained for global sequencing using RNAseq and a genome‐wide DNA methylation analysis via the Infinium EPIC Platform (graphical abstract).ResultsOne hundred and thirty‐three differentially expressed genes (DEGs) were detected, 94 of them upregulated in OSCC. Most of these genes were previously described in cancer and associated with prognosis. The integrative analysis revealed 26 DEGs, corresponding to 37 CpGs, whose promoters were regulated by DNA methylation. Twenty‐nine of the CpGs were found as hypermethylated in PVL‐OSCC. Only 5 of the genes that were aberrantly methylated and differentially expressed were upregulated in PVL‐OSCC patients, whereas 21 were underexpressed.ConclusionsPVL‐OSCC patients presented lower expression of cancer‐related genes. Hypermethylation of the promoter region of many genes was also noticed, indicating that DNA methylation could be a regulatory mechanism.

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“…More specifically in gene expression data, discriminative patterns play an essential role to discover outcome-specific regulatory modules for knowledge acquisition, biomarking phenotypes of interest [ 7 ], or serve as the basis for drug targeting (e.g. cancer) after rigorous validation [ 8 ]. Discriminative pattern mining also plays a role in unraveling complex interactions in biological processes such as the condition-specific interplay among transcription factors in organisms [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

DISA tool: Discriminative and informative subspace assessment with categorical and numerical outcomes

Alexandre

Costa²,

Henriques³

2022

PLoS ONE

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Pattern discovery and subspace clustering play a central role in the biological domain, supporting for instance putative regulatory module discovery from omics data for both descriptive and predictive ends. In the presence of target variables (e.g. phenotypes), regulatory patterns should further satisfy delineate discriminative power properties, well-established in the presence of categorical outcomes, yet largely disregarded for numerical outcomes, such as risk profiles and quantitative phenotypes. DISA (Discriminative and Informative Subspace Assessment), a Python software package, is proposed to evaluate patterns in the presence of numerical outcomes using well-established measures together with a novel principle able to statistically assess the correlation gain of the subspace against the overall space. Results confirm the possibility to soundly extend discriminative criteria towards numerical outcomes without the drawbacks well-associated with discretization procedures. Results from four case studies confirm the validity and relevance of the proposed methods, further unveiling critical directions for research on biotechnology and biomedicine. Availability: DISA is freely available at https://github.com/JupitersMight/DISA under the MIT license.

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Identifying condition specific key genes from basal-like breast cancer gene expression data

Cited by 9 publications

References 22 publications

Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma

Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma

Oral cancers preceded by proliferative verrucous leukoplakia exhibit distinctive molecular features

DISA tool: Discriminative and informative subspace assessment with categorical and numerical outcomes

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