Abstract:
:Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cellular function. Prediction of interaction partners from different protein families exploits the property that interacting proteins can follow similar patterns and relative rates of evolution. Current methods for detecting coevolution based on the similarity of phylogenetic trees or evolutionary distance matrices have, however, been limited by requiring coevolution over the entire evolutionary history considered and are inaccurate in the presence of paralogous copies. We present a novel method for determining coevolving protein partners by finding the largest common submatrix in a given pair of distance matrices, with the size of the largest common submatrix measuring the strength of coevolution. This approach permits us to consider matrices of different size and scale, to find lineage-specific coevolution, and to predict multiple interaction partners. We used MatrixMatchMaker to predict protein-protein interactions in the human genome. We show that proteins that are known to interact physically are more strongly coevolving than proteins that simply belong to the same biochemical pathway. The human coevolution network is highly connected, suggesting many more protein-protein interactions than are currently known from high-throughput and other experimental evidence. These most strongly coevolving proteins suggest interactions that have been maintained over long periods of evolutionary time, and that are thus likely to be of fundamental importance to cellular function.
journal_name
Genome Resjournal_title
Genome researchauthors
Tillier ER,Charlebois RLdoi
10.1101/gr.092452.109subject
Has Abstractpub_date
2009-10-01 00:00:00pages
1861-71issue
10eissn
1088-9051issn
1549-5469pii
gr.092452.109journal_volume
19pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.146084.112
更新日期:2013-05-01 00:00:00
abstract::Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinatio...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.118992.110
更新日期:2011-07-01 00:00:00
abstract::Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4759706
更新日期:2006-06-01 00:00:00
abstract::In comparison to genotypes, knowledge about haplotypes (the combination of alleles present on a single chromosome) is much more useful for whole-genome association studies and for making inferences about human evolutionary history. Haplotypes are typically inferred from population genotype data using computational met...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.077065.108
更新日期:2008-08-01 00:00:00
abstract::To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.520702
更新日期:2002-11-01 00:00:00
abstract::Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.205955.116
更新日期:2016-10-01 00:00:00
abstract::Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.173641.114
更新日期:2015-02-01 00:00:00
abstract::Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence collected for duplicated metabolic enzymes and in global physical interaction surveys had suggested widespread function...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.076174.108
更新日期:2008-07-01 00:00:00
abstract::CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.124818.111
更新日期:2012-08-01 00:00:00
abstract::A genome-wide search for multiple loci influencing salt-loaded systolic blood pressure (NaSBP) variation among 188 F2 progeny from a cross between the Brown-Norway and spontaneously hypertensive rat strains was pursued in an effort to gain insight into the polygenic basis of blood pressure regulation. The results sugg...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5.2.164
更新日期:1995-09-01 00:00:00
abstract::Hearing impairment is clinically and genetically heterogeneous. There are >400 disorders in which hearing impairment is a characteristic of the syndrome, and family studies demonstrate that there are at least 30 autosomal loci for nonsyndromic hearing impairment. The genes that have been identified encode diaphanous (...
journal_title:Genome research
pub_type: 历史文章,杂志文章,评审
doi:
更新日期:1999-01-01 00:00:00
abstract::Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.114280.110
更新日期:2011-03-01 00:00:00
abstract::Facio-scapulo-humeral dystrophy (FSHD), a muscular hereditary disease with a prevalence of 1 in 20,000, is caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. Earlier, we demonstrated the existence in the vicinity of the D4Z4 repeat of a nuclear matrix attachment site, FR-MAR, efficient in no...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6620908
更新日期:2008-01-01 00:00:00
abstract::Chronic neuropathic pain is affected by specifics of the precipitating neural pathology, psychosocial factors, and by genetic predisposition. Little is known about the identity of predisposing genes. Using an integrative approach, we discovered that CACNG2 significantly affects susceptibility to chronic pain following...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.104976.110
更新日期:2010-09-01 00:00:00
abstract::Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome seque...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3002305
更新日期:2005-01-01 00:00:00
abstract::Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.110702
更新日期:2002-12-01 00:00:00
abstract::Primate pericentromeric regions recently have been shown to exhibit extraordinary evolutionary plasticity. In this paper we report an additional peculiar feature of these regions that we discovered while analyzing, by FISH, the evolutionary conservation of primate phylogenetic chromosome IX. If the position of the cen...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.9.12.1184
更新日期:1999-12-01 00:00:00
abstract::The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.255703.119
更新日期:2020-05-01 00:00:00
abstract::One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproduct...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.195743.115
更新日期:2016-04-01 00:00:00
abstract::Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.241653.118
更新日期:2019-04-01 00:00:00
abstract::Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212316.116
更新日期:2017-01-01 00:00:00
abstract::Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.175240.114
更新日期:2015-03-01 00:00:00
abstract::Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.171439.113
更新日期:2014-07-01 00:00:00
abstract::The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data fo...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6307307
更新日期:2007-08-01 00:00:00
abstract::Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6661308
更新日期:2008-02-01 00:00:00
abstract::Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.113381.110
更新日期:2011-05-01 00:00:00
abstract::Here we describe a high-throughput screen to isolate transcripts with spatially restricted patterns of expression in early embryos. Our approach utilizes robotic automation for rapid analysis of sequence-selected cDNAs in a whole-mount in situ hybridization assay. We determined the spatial distribution of a random col...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.84402
更新日期:2002-07-01 00:00:00
abstract::Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy num...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.174623.114
更新日期:2015-03-01 00:00:00
abstract::The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.180601
更新日期:2001-09-01 00:00:00
abstract::We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being approximately 1:1:2. We estimate that t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.172702
更新日期:2002-06-01 00:00:00