Set-Wise Differential Interaction between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways

Abstract

The integrative analysis of copy number alteration (CNA) and gene expression (GE) is an essential part of cancer research considering the impact of CNAs on cancer progression and prognosis. In this research, an integrative analysis was performed with generalized differentially coexpressed gene sets (gdCoxS), which is a modification of dCoxS. In gdCoxS, set-wise interaction is measured using the correlation of sample-wise distances with Renyi’s relative entropy, which requires an estimation of sample density based on omics profiles. To capture correlations between the variables, multivariate density estimation with covariance was applied. In the simulation study, the power of gdCoxS outperformed dCoxS that did not use the correlations in the density estimation explicitly. In the analysis of the lower-grade glioma of the cancer genome atlas program (TCGA-LGG) data, the gdCoxS identified 577 pathway CNAs and GEs pairs that showed significant changes of interaction between the survival and non-survival group, while other benchmark methods detected lower numbers of such pathways. The biological implications of the significant pathways were well consistent with previous reports of the TCGA-LGG. Taken together, the gdCoxS is a useful method for an integrative analysis of CNAs and GEs.

Entropy analysis and grey cluster analysis of multiple indexes of 5 kinds of genuine medicinal materials

“…According to the combustion heat, thermogravimetric parameters, fat content, calcium content, trace element content and ash content, the multi-index comprehensive evaluation systems of five kinds of genuine medicinal materials including Diding, Purslane, straw sandal board, June snow, pine vine rattan were established by entropy method 67 – 72 .…”

Entropy analysis and grey correlation coefficient cluster analysis of multiple indexes of 5 kinds of condiments

“…According to the combustion heat, thermo gravimetric analysis parameters, fat, calcium, ash, crude fiber, trace element content data for five condiments, construction of multi-index comprehensive evaluation system for condiments including cinnamon, tangerine peel, clove, licorice, amomum in Guangx, China by entropy method (Aide et al, 2021;Álvarez et al, 2020;Arch-Tirado et al, 2020;Bostian et al, 2020;Chen et al, 2020a;Cho, 2020). a large correlation coefficient in indicator X4, mainly reflecting the ash content of condiments (Zhou, 2017b).…”

Multiple indicators metrological analysis for 5 kinds of tea produced in Yunnan, China

“…Construction of a multi-index analysis and comprehensive evaluation system by entropy analysis According to combustion heat, differential thermogravimetric, fat content, crude fiber content, ash content, and trace element content data for 5 kinds of tea, multi-index comprehensive evaluation systems for 5 kinds of tea, including camphorscented palace tea, fossil glutinous rice tea, old tree white tea, Brown Mountain ancient tree tea, and pure Banzhang tea, were established by the entropy method (Aide et al, 2021;Álvarez et al, 2020;Arch-Tirado et al, 2020;Bostian et al, 2020;Chen et al, 2020;Cho, 2020). (Deng et al, 2020;Galas et al, 2021;Gupta & Chokshi, 2020;Hu et al, 2020) According to the characteristics of entropy, this paper judges the randomness and degree of disorder of an event by calculating the entropy value and judges the degree of dispersion of an index by using the entropy value.…”