Abstract:
BACKGROUND:One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. RESULTS:We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers. CONCLUSIONS:We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Wu G,Feng X,Stein Ldoi
10.1186/gb-2010-11-5-r53subject
Has Abstractpub_date
2010-01-01 00:00:00pages
R53issue
5eissn
1474-7596issn
1474-760Xpii
gb-2010-11-5-r53journal_volume
11pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-7-r143
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-12-r257
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of monocytes to osteocla...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-9-r99
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:The H subunit of the purple bacterial photosynthetic reaction center (PRC-H) is important for the assembly of the photosynthetic reaction center and appears to regulate electron transfer during the reduction of the secondary quinone. It contains a distinct cytoplasmic beta-barrel domain whose fold has no clo...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-11-research0061
更新日期:2002-10-14 00:00:00
abstract::High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-2-207
更新日期:2008-01-01 00:00:00
abstract::Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish bo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-017-1236-9
更新日期:2017-05-23 00:00:00
abstract::The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2003-4-12-240
更新日期:2003-01-01 00:00:00
abstract::The N 6-methyladenosine (m6A) modification of mRNA has a crucial function in regulating pluripotency in murine stem cells: it facilitates resolution of naïve pluripotency towards differentiation. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-015-0609-1
更新日期:2015-02-22 00:00:00
abstract:BACKGROUND:Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellul...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-5-r42
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1894-x
更新日期:2020-01-07 00:00:00
abstract:BACKGROUND:The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-10-r152
更新日期:2008-10-14 00:00:00
abstract::In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...
journal_title:Genome biology
pub_type: 评论,信件
doi:10.1186/s13059-017-1172-8
更新日期:2017-02-27 00:00:00
abstract::The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2013-14-2-202
更新日期:2013-02-28 00:00:00
abstract::The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1612-0
更新日期:2019-01-03 00:00:00
abstract::Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2003-4-4-210
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1101-2
更新日期:2016-11-25 00:00:00
abstract:BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-9-r99
更新日期:2009-01-01 00:00:00
abstract::We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-9-r96
更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-9-r50
更新日期:2012-09-26 00:00:00
abstract:BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1771-7
更新日期:2019-08-06 00:00:00
abstract::Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-2-r18
更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-1-r8
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune m...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-3-r50
更新日期:2014-03-05 00:00:00
abstract::The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-015-0793-z
更新日期:2015-10-26 00:00:00
abstract:BACKGROUND:Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r222
更新日期:2007-01-01 00:00:00
abstract::Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be emplo...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02161-6
更新日期:2020-10-06 00:00:00
abstract::In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-s1-s6
更新日期:2008-01-01 00:00:00
abstract::Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-10-r82
更新日期:2004-01-01 00:00:00
abstract::Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-016-0965-5
更新日期:2016-05-09 00:00:00
abstract:BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0655-8
更新日期:2015-04-30 00:00:00