Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

Abstract:

:Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/TPEA/.

journal_name

Brief Bioinform

authors

Yang Q,Wang S,Dai E,Zhou S,Liu D,Liu H,Meng Q,Jiang B,Jiang W

doi

10.1093/bib/bbx091

subject

Has Abstract

pub_date

2019-01-18 00:00:00

pages

168-177

issue

1

eissn

1467-5463

issn

1477-4054

pii

4083289

journal_volume

20

pub_type

杂志文章
  • LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor.

    abstract::Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, ...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbz141

    authors: Yang JF,Wang F,Chen YZ,Hao GF,Yang GF

    更新日期:2020-12-01 00:00:00

  • Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction.

    abstract::Programs for RNA mutational analysis that are structure-based and rely on secondary structure prediction have been developed and expanded in the past several years. They can be used for a variety of purposes, such as in suggesting point mutations that will alter RNA virus replication or translation initiation, investi...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章,评审

    doi:10.1093/bib/bbq059

    authors: Barash D,Churkin A

    更新日期:2011-03-01 00:00:00

  • Bioinformatics education--perspectives and challenges out of Africa.

    abstract::The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of ...

    journal_title:Briefings in bioinformatics

    pub_type: 历史文章,杂志文章

    doi:10.1093/bib/bbu022

    authors: Tastan Bishop Ö,Adebiyi EF,Alzohairy AM,Everett D,Ghedira K,Ghouila A,Kumuthini J,Mulder NJ,Panji S,Patterton HG,H3ABioNet Consortium.,H3Africa Consortium.

    更新日期:2015-03-01 00:00:00

  • Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations.

    abstract:BACKGROUND:The most frequently mutated gene pairs in pancreatic adenocarcinoma (PAAD) are KRAS and TP53, and our goal is to illustrate the multiomics and molecular dynamics landscapes of KRAS/TP53 mutation and also to obtain prospective novel drugs for KRAS- and TP53-mutated PAAD patients. Moreover, we also made an att...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbaa149

    authors: Kaushik AC,Wang YJ,Wang X,Wei DQ

    更新日期:2020-07-31 00:00:00

  • Improving structure-based virtual screening performance via learning from scoring function components.

    abstract::Scoring functions (SFs) based on complex machine learning (ML) algorithms have gradually emerged as a promising alternative to overcome the weaknesses of classical SFs. However, extensive efforts have been devoted to the development of SFs based on new protein-ligand interaction representations and advanced alternativ...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbaa094

    authors: Xiong GL,Ye WL,Shen C,Lu AP,Hou TJ,Cao DS

    更新日期:2020-06-04 00:00:00

  • Are dropout imputation methods for scRNA-seq effective for scHi-C data?

    abstract::The prevalence of dropout events is a serious problem for single-cell Hi-C (scHiC) data due to insufficient sequencing depth and data coverage, which brings difficulties in downstream studies such as clustering and structural analysis. Complicating things further is the fact that dropouts are confounded with structura...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbaa289

    authors: Han C,Xie Q,Lin S

    更新日期:2020-11-17 00:00:00

  • Methods and resources to access mutation-dependent effects on cancer drug treatment.

    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

    authors: Yao H,Liang Q,Qian X,Wang J,Sham PC,Li MJ

    更新日期:2020-12-01 00:00:00

  • Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes.

    abstract::Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and m...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbw081

    authors: Xia S,Feng J,Lei L,Hu J,Xia L,Wang J,Xiang Y,Liu L,Zhong S,Han L,He C

    更新日期:2017-11-01 00:00:00

  • Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification.

    abstract::For many complex diseases, an earlier and more reliable diagnosis is considered a key prerequisite for developing more effective therapies to prevent or delay disease progression. Classical statistical learning approaches for specimen classification using omics data, however, often cannot provide diagnostic models wit...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbv044

    authors: Glaab E

    更新日期:2016-05-01 00:00:00

  • Common introns within orthologous genes: software and application to plants.

    abstract::The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related gen...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbp051

    authors: Wilkerson MD,Ru Y,Brendel VP

    更新日期:2009-11-01 00:00:00

  • HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly.

    abstract::Heterophylly, i.e. morphological changes in leaves along the axis of an individual plant, is regarded as a strategy used by plants to cope with environmental change. However, little is known of the extent to which heterophylly is controlled by genes and how each underlying gene exerts its effect on heterophyllous vari...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbx011

    authors: Sun L,Wang J,Zhu X,Jiang L,Gosik K,Sang M,Sun F,Cheng T,Zhang Q,Wu R

    更新日期:2018-07-20 00:00:00

  • Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls.

    abstract::The use of multiple testing procedures in the context of gene-set testing is an important but relatively underexposed topic. If a multiple testing method is used, this is usually a standard familywise error rate (FWER) or false discovery rate (FDR) controlling procedure in which the logical relationships that exist be...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbv091

    authors: Meijer RJ,Goeman JJ

    更新日期:2016-09-01 00:00:00

  • Computational recognition for long non-coding RNA (lncRNA): Software and databases.

    abstract::Since the completion of the Human Genome Project, it has been widely established that most DNA is not transcribed into proteins. These non-protein-coding regions are believed to be moderators within transcriptional and post-transcriptional processes, which play key roles in the onset of diseases. Long non-coding RNAs ...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章,评审

    doi:10.1093/bib/bbv114

    authors: Yotsukura S,duVerle D,Hancock T,Natsume-Kitatani Y,Mamitsuka H

    更新日期:2017-01-01 00:00:00

  • Advanced bioinformatics methods for practical applications in proteomics.

    abstract::Mass spectrometry (MS)-based proteomics has undergone rapid advancements in recent years, creating challenging problems for bioinformatics. We focus on four aspects where bioinformatics plays a crucial role (and proteomics is needed for clinical application): peptide-spectra matching (PSM) based on the new data-indepe...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbx128

    authors: Goh WWB,Wong L

    更新日期:2019-01-18 00:00:00

  • Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor.

    abstract::The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge owing to the vast amounts of data and the large variety of preprocessing and filtering steps used before the actual analysis is ca...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbt011

    authors: Rodrigo-Domingo M,Waagepetersen R,Bødker JS,Falgreen S,Kjeldsen MK,Johnsen HE,Dybkær K,Bøgsted M

    更新日期:2014-07-01 00:00:00

  • Strategies for calibrating models of biology.

    abstract::Computational and mathematical modelling has become a valuable tool for investigating biological systems. Modelling enables prediction of how biological components interact to deliver system-level properties and extrapolation of biological system performance to contexts and experimental conditions where this is unknow...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bby092

    authors: Read MN,Alden K,Timmis J,Andrews PS

    更新日期:2018-09-18 00:00:00

  • TOD-CUP: a gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary.

    abstract::Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbaa031

    authors: Shen Y,Chu Q,Yin X,He Y,Bai P,Wang Y,Fang W,Timko MP,Fan L,Jiang W

    更新日期:2020-04-08 00:00:00

  • Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability.

    abstract::Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial can...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbx109

    authors: Deng Y,Luo S,Deng C,Luo T,Yin W,Zhang H,Zhang Y,Zhang X,Lan Y,Ping Y,Xiao Y,Li X

    更新日期:2019-01-18 00:00:00

  • Data-driven rational biosynthesis design: from molecules to cell factories.

    abstract::A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially b...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbz065

    authors: Chen F,Yuan L,Ding S,Tian Y,Hu QN

    更新日期:2020-07-15 00:00:00

  • Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties.

    abstract::Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has be...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章,评审

    doi:10.1093/bib/bbt071

    authors: Castelhano Santos N,Pereira MO,Lourenço A

    更新日期:2015-01-01 00:00:00

  • Comparative analysis of methods for genome-wide nucleosome cartography.

    abstract::Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome ...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbu037

    authors: Quintales L,Vázquez E,Antequera F

    更新日期:2015-07-01 00:00:00

  • Gene-based mediation analysis in epigenetic studies.

    abstract::Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studi...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbaa113

    authors: Fang R,Yang H,Gao Y,Cao H,Goode EL,Cui Y

    更新日期:2020-07-01 00:00:00

  • RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.

    abstract::RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a v...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbz054

    authors: Gupta A,Bansal M

    更新日期:2020-07-15 00:00:00

  • A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.

    abstract::The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions. It is therefore essential to differentiate and annotate functions for individual isoforms. Computational approaches provide an efficient complemen...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbv109

    authors: Li HD,Omenn GS,Guan Y

    更新日期:2016-11-01 00:00:00

  • Closing the gap between formats for storing layout information in systems biology.

    abstract::The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network la...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbz067

    authors: Hoksza D,Gawron P,Ostaszewski M,Hasenauer J,Schneider R

    更新日期:2020-07-15 00:00:00

  • Comparative genome assembly.

    abstract::One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/5.3.237

    authors: Pop M,Phillippy A,Delcher AL,Salzberg SL

    更新日期:2004-09-01 00:00:00

  • Circular RNA identification based on multiple seed matching.

    abstract::Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maxi...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbx014

    authors: Gao Y,Zhang J,Zhao F

    更新日期:2018-09-28 00:00:00

  • Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning.

    abstract::The number of bioinformatics tools and resources that support molecular and cell biology approaches is continuously expanding. Moreover, systems and network biology analyses are accompanied more and more by integrated bioinformatics methods. Traditional information-centered university teaching methods often fail, as (...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbt024

    authors: Korcsmaros T,Dunai ZA,Vellai T,Csermely P

    更新日期:2013-09-01 00:00:00

  • Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine.

    abstract::Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut micr...

    journal_title:Briefings in bioinformatics

    pub_type: 杂志文章

    doi:10.1093/bib/bbaa292

    authors: Hassan R,Allali I,Agamah FE,Elsheikh SSM,Thomford NE,Dandara C,Chimusa ER

    更新日期:2020-12-01 00:00:00

  • Comparison and integration of computational methods for deleterious synonymous mutation prediction.

    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

    authors: Cheng N,Li M,Zhao L,Zhang B,Yang Y,Zheng CH,Xia J

    更新日期:2020-05-21 00:00:00