Negative regulation of tumor suppressor p53 by microRNA miR-504
Tumor suppressor p53 plays a central role in tumor prevention. p53 protein levels and
activity are under a tight and complex regulation in cells to maintain the proper function of …
activity are under a tight and complex regulation in cells to maintain the proper function of …
Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers
Motivation Chromosomal patterning of gene expression in cancer can arise from
aneuploidy, genome disorganization or abnormal DNA methylation. To map such patterns …
aneuploidy, genome disorganization or abnormal DNA methylation. To map such patterns …
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers
Somatic rearrangements contribute to the mutagenized landscape of cancer genomes.
Here, we systematically interrogated rearrangements in 560 breast cancers by using a …
Here, we systematically interrogated rearrangements in 560 breast cancers by using a …
Network modeling of the transcriptional effects of copy number aberrations in glioblastoma
R Jörnsten, T Abenius, T Kling, L Schmidt… - Molecular systems …, 2011 - embopress.org
DNA copy number aberrations (CNAs) are a hallmark of cancer genomes. However, little is
known about how such changes affect global gene expression. We develop a modeling …
known about how such changes affect global gene expression. We develop a modeling …
Functional dissection of inherited non-coding variation influencing multiple myeloma risk
R Ajore, A Niroula, M Pertesi, C Cafaro… - Nature …, 2022 - nature.com
Thousands of non-coding variants have been associated with increased risk of human
diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an …
diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an …
[HTML][HTML] Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers
Background Complex clusters of rearrangements are a challenge in interpretation of cancer
genomes. Some clusters of rearrangements demarcate clear amplifications of driver …
genomes. Some clusters of rearrangements demarcate clear amplifications of driver …
Gene set enrichment analysis using linear models and diagnostics
AP Oron, Z Jiang, R Gentleman - Bioinformatics, 2008 - academic.oup.com
Motivation: Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model
(regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential …
(regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential …
VEGA: variational segmentation for copy number detection
S Morganella, L Cerulo, G Viglietto… - Bioinformatics, 2010 - academic.oup.com
Motivation: Genomic copy number (CN) information is useful to study genetic traits of many
diseases. Using array comparative genomic hybridization (aCGH), researchers are able to …
diseases. Using array comparative genomic hybridization (aCGH), researchers are able to …
Bayesian DNA copy number analysis
Background Some diseases, like tumors, can be related to chromosomal aberrations,
leading to changes of DNA copy number. The copy number of an aberrant genome can be …
leading to changes of DNA copy number. The copy number of an aberrant genome can be …
SegCorr a statistical procedure for the detection of genomic regions of correlated expression
EI Delatola, E Lebarbier, T Mary-Huard, F Radvanyi… - BMC …, 2017 - Springer
Background Detecting local correlations in expression between neighboring genes along
the genome has proved to be an effective strategy to identify possible causes of …
the genome has proved to be an effective strategy to identify possible causes of …