Abstract:
BACKGROUND:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibility we created Web-TCGA, a web based, freely accessible online tool, which can also be run in a private instance, for integrated analysis of molecular cancer data sets provided by TCGA. In contrast to already available tools, Web-TCGA utilizes different methods for analysis and visualization of TCGA data, allowing users to generate global molecular profiles across different cancer entities simultaneously. In addition to global molecular profiles, Web-TCGA offers highly detailed gene and tumor entity centric analysis by providing interactive tables and views. CONCLUSIONS:As a supplement to other already available tools, such as cBioPortal (Sci Signal 6:pl1, 2013, Cancer Discov 2:401-4, 2012), Web-TCGA is offering an analysis service, which does not require any installation or configuration, for molecular data sets available at the TCGA. Individual processing requests (queries) are generated by the user for mutation, methylation, expression and copy number variation (CNV) analyses. The user can focus analyses on results from single genes and cancer entities or perform a global analysis (multiple cancer entities and genes simultaneously).
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Deng M,Brägelmann J,Schultze JL,Perner Sdoi
10.1186/s12859-016-0917-9subject
Has Abstractpub_date
2016-02-06 00:00:00pages
72issn
1471-2105pii
10.1186/s12859-016-0917-9journal_volume
17pub_type
杂志文章abstract:BACKGROUND AND GOAL:The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing with logistic regression in many innovation-friendly scientific fields. RESULTS:In this conte...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2264-5
更新日期:2018-07-17 00:00:00
abstract:BACKGROUND:Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-287
更新日期:2008-06-18 00:00:00
abstract:BACKGROUND:Analyses of molecular high-throughput data often lack in robustness, i.e. results are very sensitive to the addition or removal of a single observation. Therefore, the identification of extreme observations is an important step of quality control before doing further data analysis. Standard outlier detection...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1645-5
更新日期:2017-05-02 00:00:00
abstract:BACKGROUND:Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-164
更新日期:2005-06-29 00:00:00
abstract:BACKGROUND:High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of pr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03827-5
更新日期:2020-11-04 00:00:00
abstract:BACKGROUND:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S11-S16
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Selecting a parsimonious set of informative genes to build highly generalized performance classifier is the most important task for the analysis of tumor microarray expression data. Many existing gene pair evaluation methods cannot highlight diverse patterns of gene pairs only used one strategy of vertical c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0893-0
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1875-6
更新日期:2017-12-01 00:00:00
abstract:BACKGROUND:In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-15
更新日期:2012-01-26 00:00:00
abstract:BACKGROUND:In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniq...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-S5-S5
更新日期:2006-12-18 00:00:00
abstract:BACKGROUND:Genome scale data on protein interactions are generally represented as large networks, or graphs, where hundreds or thousands of proteins are linked to one another. Since proteins tend to function in groups, or complexes, an important goal has been to reliably identify protein complexes from these graphs. Th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-99
更新日期:2009-03-30 00:00:00
abstract:BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-45
更新日期:2013-02-08 00:00:00
abstract:BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S8-S6
更新日期:2009-08-27 00:00:00
abstract:BACKGROUND:Modules of interacting components arranged in specific network topologies have evolved to perform a diverse array of cellular functions. For a network with a constant topological structure, its function within a cell may still be tuned by changing the number of instances of a particular component (e.g., gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2866-6
更新日期:2019-05-14 00:00:00
abstract:BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-316
更新日期:2014-09-25 00:00:00
abstract:BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S1-S3
更新日期:2009-01-30 00:00:00
abstract:BACKGROUND:Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often repre...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1740-7
更新日期:2017-07-11 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03646-8
更新日期:2020-07-21 00:00:00
abstract:BACKGROUND:A massive amount of proteomic data is generated on a daily basis, nonetheless annotating all sequences is costly and often unfeasible. As a countermeasure, machine learning methods have been used to automatically annotate new protein functions. More specifically, many studies have investigated hierarchical m...
journal_title:BMC bioinformatics
pub_type: 杂志文章,评审
doi:10.1186/s12859-019-3060-6
更新日期:2019-09-23 00:00:00
abstract::In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S19-S1
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures is still relatively slow using existing methods. There is a need for new techniques which can rapidly...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S1-S46
更新日期:2010-01-18 00:00:00
abstract:BACKGROUND:Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-94
更新日期:2004-07-13 00:00:00
abstract:BACKGROUND:New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-100
更新日期:2010-02-22 00:00:00
abstract:BACKGROUND:Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientifi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-159
更新日期:2014-05-23 00:00:00
abstract:BACKGROUND:Biological data often originate from samples containing mixtures of subpopulations, corresponding e.g. to distinct cellular phenotypes. However, identification of distinct subpopulations may be difficult if biological measurements yield distributions that are not easily separable. RESULTS:We present Multire...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-240
更新日期:2014-07-11 00:00:00
abstract:BACKGROUND:HIV/AIDS is a serious threat to public health. The emergence of drug resistance mutations diminishes the effectiveness of drug therapy for HIV/AIDS. Developing a computational prediction of drug resistance phenotype will enable efficient and timely selection of the best treatment regimens. RESULTS:A unified...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1114-6
更新日期:2016-08-31 00:00:00
abstract:BACKGROUND:Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to populatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-255
更新日期:2013-08-21 00:00:00
abstract:BACKGROUND:Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-182
更新日期:2014-06-12 00:00:00
abstract:BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-227
更新日期:2014-06-30 00:00:00
abstract::Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S17-I1
更新日期:2014-01-01 00:00:00