Abstract:
:Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of cis-regulatory elements such as microRNA (miRNA) target sites in the 3'-untranslated region (3'-UTRs) of genes. Although previous computational APA studies focused on a subset of genes strongly affected by APA (APA genes), we identify miRNAs of which widespread APA events collectively increase or decrease the number of target sites [probabilistic inference of microRNA target site modification through APA (PRIMATA-APA)]. Using PRIMATA-APA on the cancer genome atlas (TCGA) breast cancer data, we found that the global APA events change the number of the target sites of particular microRNAs [target sites modified miRNA (tamoMiRNA)] enriched for cancer development and treatments. We also found that when knockdown (KD) of NUDT21 in HeLa cells induces a different set of widespread 3'-UTR shortening than TCGA breast cancer data, it changes the target sites of the common tamoMiRNAs. Since the NUDT21 KD experiment previously demonstrated the tumorigenic role of APA events in a miRNA dependent fashion, this result suggests that the APA-initiated tumorigenesis is attributable to the miRNA target site changes, not the APA events themselves. Further, we found that the miRNA target site changes identify tumor cell proliferation and immune cell infiltration to the tumor microenvironment better than the miRNA expression levels or the APA events themselves. Altogether, our computational analyses provide a proof-of-concept demonstration that the miRNA target site information indicates the effect of global APA events with a potential as predictive biomarker.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Kim S,Bai Y,Fan Z,Diergaarde B,Tseng GC,Park HJdoi
10.1093/bib/bbaa191subject
Has Abstractpub_date
2020-08-26 00:00:00eissn
1467-5463issn
1477-4054pii
5897059pub_type
杂志文章abstract::CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) d...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa375
更新日期:2020-12-16 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa304
更新日期:2020-11-25 00:00:00
abstract::The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa109
更新日期:2020-06-10 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/5.3.237
更新日期:2004-09-01 00:00:00
abstract::Broader functional annotation of known as well as putative genetic variations is a valuable mean for prioritizing targets in disease studies and large-scale genotyping projects. In this article, we present a practical guide to SNPnexus, a web-based tool that provides an aggregate set of functional annotations for geno...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbs006
更新日期:2013-01-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bby104
更新日期:2018-11-07 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbq063
更新日期:2010-11-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbp046
更新日期:2010-03-01 00:00:00
abstract::We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we prov...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbn023
更新日期:2008-09-01 00:00:00
abstract::In clinical cancer treatment, genomic alterations would often affect the response of patients to anticancer drugs. Studies have shown that molecular features of tumors could be biomarkers predictive of sensitivity or resistance to anticancer agents, but the identification of actionable mutations are often constrained ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz109
更新日期:2020-12-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa033
更新日期:2021-01-18 00:00:00
abstract::Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference tre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbr034
更新日期:2011-09-01 00:00:00
abstract::Moonlighting proteins provide more options for cells to execute multiple functions without increasing the genome and transcriptome complexity. Although there have long been calls for computational methods for the prediction of moonlighting proteins, no method has been designed for determining moonlighting long noncodi...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz154
更新日期:2021-01-18 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbr030
更新日期:2011-09-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs049
更新日期:2014-01-01 00:00:00
abstract::The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbu016
更新日期:2015-05-01 00:00:00
abstract::Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predic...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz047
更新日期:2020-05-21 00:00:00
abstract::Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systemat...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbr076
更新日期:2012-09-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa332
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx010
更新日期:2018-09-28 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx055
更新日期:2018-11-27 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 历史文章,杂志文章,评审
doi:10.1093/bib/bby063
更新日期:2019-11-27 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw072
更新日期:2017-11-01 00:00:00
abstract::Cooperative regulation among multiple microRNAs (miRNAs) is a complex type of posttranscriptional regulation in human; however, the global view of the system-level regulatory principles across cancers is still unclear. Here, we investigated miRNA-miRNA cooperative regulatory landscape across 18 cancer types and summar...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bby038
更新日期:2019-09-27 00:00:00
abstract::Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a number of technical and statistical problems. Possible remedies on the level of computational analysis lie in appropriate pr...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbl002
更新日期:2006-06-01 00:00:00
abstract::Prognostic tests using expression profiles of several dozen genes help provide treatment choices for prostate cancer (PCa). However, these tests require improvement to meet the clinical need for resolving overtreatment, which continues to be a pervasive problem in PCa management. Genomic selection (GS) methodology, wh...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa197
更新日期:2020-09-08 00:00:00
abstract::Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa162
更新日期:2020-08-11 00:00:00