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UnknownIdentifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data.
The driver genetic aberrations collectively regulate core cellular processes underlying cancer development. However, identifying the modules of driver genetic alterations and characterizing their functional mechanisms are still major challenges for cancer studies. Here, we developed an integrative m...
S-EPMC4344511 | biostudies-literature
UnknownComprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements.
Over the past decade, thousands of long noncoding RNAs (lncRNAs) have been identified, many of which play crucial roles in normal physiology and human disease. LncRNAs can interact with chromatin and then recruit protein complexes to remodel chromatin states, thus regulating gene expression. However...
S-EPMC6816106 | biostudies-literature
UnknownIdentifying Cancer Driver lncRNAs Bridged by Functional Effectors through Integrating Multi-omics Data in Human Cancers.
The accumulation of somatic driver mutations in the human genome enables cells to gradually acquire a growth advantage and contributes to tumor development. Great efforts on protein-coding cancer drivers have yielded fruitful discoveries and clinical applications. However, investigations on cancer d...
S-EPMC6626872 | biostudies-literature
UnknownCapturing functional long non-coding RNAs through integrating large-scale causal relations from gene perturbation experiments.
Characterizing functions of long noncoding RNAs (lncRNAs) remains a major challenge, mostly due to the lack of lncRNA-involved regulatory relationships. A wide array of genome-wide expression profiles generated by gene perturbation have been widely used to capture causal links between perturbed gene...
S-EPMC6156711 | biostudies-literature
UnknownIdentifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines.
Epigenetic modifications play critical roles in modulating gene expression, yet their roles in regulatory networks in human cell lines remain poorly characterized. We integrated multiomics data to construct directed regulatory networks with nodes and edges labeled with chromatin states in human cell...
S-EPMC6962092 | biostudies-literature
UnknownCombined homologous recombination repair deficiency and immune activation analysis for predicting intensified responses of anthracycline, cyclophosphamide and taxane chemotherapy in triple-negative breast cancer.

Background

Triple-negative breast cancer (TNBC) is a clinically aggressive disease with abundant variants that cause homologous recombination repair deficiency (HRD). Whether TNBC patients with HRD are sensitive to anthracycline, cyclophosphamide and taxane (ACT), and whether the combination...
S-EPMC8408988 | biostudies-literature
UnknownGenome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis.

Background

DNA methylation is thought to be extensively involved in the pathogenesis of many diseases, including major psychosis. However, most studies focus on DNA methylation alteration at promoters of protein-coding genes, despite the poor correlation between DNA methylation and gene expr...
S-EPMC4604612 | biostudies-literature
ProteomicsOviposition control genes and expression of functional interference in D.citri
The research on oviposition related genes is the focus of insect molecular biology. Some studies have gradually understood the mechanism of oviposition related genes, including oviposition-gland-related genes, oogenesis-related genes, oviposition-location-related genes, and genes related to ovulatio...
ORGANISM(S): Diaphorina Citri 
2020-11-04 | PXD022359 |
ProteomicsMass-spectroscopic quantification of CHAC1-regulated protein cysteine S-glutathionylation
S-glutathionylation is an important post-translational modification of a cysteine residue of target protein. We applied a quantitative redox proteomics approach to identify the specific cysteine residues as targets of S-glutathionylation. Using this approach, we profiled CHAC1-associated changes in ...
ORGANISM(S): Mus Musculus 
2024-03-12 | PXD050569 |
ProteomicsThe global succinylation of SARS-CoV-2-infect host cells reveals potential drug targets
Here we show a quantitative mass spectrometry-based succinylproteomics analysis of SARS-CoV-2 infection in Caco-2 cells, revealing dramatic reshape of succinylation on host and viral proteins.
ORGANISM(S): Homo Sapiens 
2021-12-06 | PXD030197 |
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