Proteomic Profiling of Differentially Expressed Proteins from Bax inhibitor-1 Knockout and Wild Type Mice

Li, Bo; Reed, John C.; Kim, Hyung‐Ryong; Chae, Han-Jung

doi:10.1007/s10059-012-0001-x

Cited by 6 publications

(7 citation statements)

References 56 publications

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“…From the unique set of genes detected by CANOVA (Table 3 ), a few were reported to be relevant to kidney cancer/disease: FAH, MCM3 and UGT1A9. A defect in FAH results in the accumulation of FAA that can lead to oxidative stress and severe liver and kidney disease [ 32 , 33 ]. The MCM3 gene was found to be overexpressed in various human cancers, including kidney cancer [ 34 ].…”

Section: Resultsmentioning

confidence: 99%

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Efficient test for nonlinear dependence of two continuous variables

Wang

Cao

et al. 2015

BMC Bioinformatics

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BackgroundTesting dependence/correlation of two variables is one of the fundamental tasks in statistics. In this work, we proposed a new way of testing nonlinear dependence between two continuous variables (X and Y).ResultsWe addressed this research question by using CANOVA (continuous analysis of variance, software available at https://sourceforge.net/projects/canova/). In the CANOVA framework, we first defined a neighborhood for each data point related to its X value, and then calculated the variance of the Y value within the neighborhood. Finally, we performed permutations to evaluate the significance of the observed values within the neighborhood variance. To evaluate the strength of CANOVA compared to six other methods, we performed extensive simulations to explore the relationship between methods and compared the false positive rates and statistical power using both simulated and real datasets (kidney cancer RNA-seq dataset).ConclusionsWe concluded that CANOVA is an efficient method for testing nonlinear correlation with several advantages in real data applications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0697-7) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…1 and Table 3 ), which other methods could not easily find. These three genes were also reported to be involved in the kidney cancer development process in the literature [ 32 – 36 ].…”

Section: Discussionmentioning

confidence: 99%

Efficient test for nonlinear dependence of two continuous variables

Wang

Cao

et al. 2015

BMC Bioinformatics

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“…A defect in FAH results in the accumulation of FAA that can lead The bold means the first place result of all methods compared "~" means about or approximately to oxidative stress and severe liver and kidney disease [32,33]. The MCM3 gene was found to be overexpressed in various human cancers, including kidney cancer [34].…”

Section: Results From the Kidney Cancer Studymentioning

confidence: 99%

“…1 and Table 3), which other methods could not easily find. These three genes were also reported to be involved in the kidney cancer development process in the literature [32][33][34][35][36].…”

Section: Discussionmentioning

confidence: 99%

Efficient Test for Nonlinear Dependence of Two Continuous Variables

Ritter¹,

Li²,

Wang³

et al. 2018

Translational Bioinformatics

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“…Although seemingly ubiquitous, the endogenous expression of BI‐1 may differ among tissues or cell types and at different stages of development, leading to various cell‐type and time‐specific roles. While nonexhaustive, protein profiling by two‐dimensional electrophoresis and mass spectrometry from liver, brain, heart, lung, and kidney tissue samples identified altered differential protein expressions of GRP75, peroxiredoxin 6, fumarylacetoacetate hydrolase, selenium‐binding protein 2, phosphatidylethanolamine‐binding protein 1, and ferritin light chain 1 in tissues from BI‐1 − / − compared to BI‐1 + / + mice, leaving clues about BI‐1 function in those organs . Despite this interest, few researchers have addressed the implication of BI‐1 in disease.…”

Section: Implication Of Bi‐1 In Diseasementioning

confidence: 99%

BAX inhibitor‐1: between stress and survival

et al. 2020

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Cellular gatekeepers are essential to maintain order within a cell and anticipate signals of stress to promote survival. BCL2 associated X, apoptosis regulator (BAX) inhibitor‐1 (BI‐1), also named transmembrane BAX inhibitor motif containing‐6, is a highly conserved endoplasmic reticulum (ER) transmembrane protein. Originally identified as an inhibitor of BAX‐induced apoptosis, its pro‐survival properties have been expanded to include functions targeted against ER stress, calcium imbalance, reactive oxygen species accumulation, and metabolic dysregulation. Nevertheless, the structural biology and biochemical mechanism of action of BI‐1 are still under debate. BI‐1 has been implicated in several diseases, including chronic liver disease, diabetes, ischemia/reperfusion injury, neurodegeneration, and cancer. While most studies have demonstrated a beneficial role for BI‐1 in the ubiquitous maintenance of cellular homeostasis, its expression in cancer cells seems most often to contribute to tumorigenesis and metastasis. Here, we summarize what is known about BI‐1 and encourage future studies on BI‐1's contribution to cellular life and death decisions to advocate its potential as a target for drug development and other therapeutic strategies.

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Proteomic Profiling of Differentially Expressed Proteins from Bax inhibitor-1 Knockout and Wild Type Mice

Cited by 6 publications

References 56 publications

Efficient test for nonlinear dependence of two continuous variables

Efficient test for nonlinear dependence of two continuous variables

Efficient Test for Nonlinear Dependence of Two Continuous Variables

BAX inhibitor‐1: between stress and survival

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