当前位置： SCI文献检索 > GENOMICS期刊下所有文献 > Evolutionary rate heterogeneity between multi- and single-interface hubs across human housekeeping and tissue-specific protein interaction network: Insights from proteins' and its partners' properties.

Evolutionary rate heterogeneity between multi- and single-interface hubs across human housekeeping and tissue-specific protein interaction network: Insights from proteins' and its partners' properties.

Abstract：

:Integrating gene expression into protein-protein interaction network (PPIN) leads to the construction of tissue-specific (TS) and housekeeping (HK) sub-networks, with distinctive TS- and HK-hubs. All such hub proteins are divided into multi-interface (MI) hubs and single-interface (SI) hubs, where MI hubs evolve slower than SI hubs. Here we explored the evolutionary rate difference between MI and SI proteins within TS- and HK-PPIN and observed that this difference is present only in TS, but not in HK-class. Next, we explored whether proteins' own properties or its partners' properties are more influential in such evolutionary discrepancy. Statistical analyses revealed that this evolutionary rate correlates negatively with protein's own properties like expression level, miRNA count, conformational diversity and functional properties and with its partners' properties like protein disorder and tissue expression similarity. Moreover, partial correlation and regression analysis revealed that both proteins' and its partners' properties have independent effects on protein evolutionary rate.

journal_name

Genomics

journal_title

Genomics

authors

Biswas K,Acharya D,Podder S,Ghosh TC

doi

10.1016/j.ygeno.2017.11.006

subject

Has Abstract

pub_date

2018-09-01 00:00:00

pages

283-290

issue

5

eissn

0888-7543

issn

1089-8646

pii

S0888-7543(17)30148-9

journal_volume

110

pub_type

杂志文章

相关文献

GENOMICS文献大全
  • Genome-wide expression profiling of the transcriptomes of four Paulownia tomentosa accessions in response to drought.

    abstract：:Paulownia tomentosa is an important foundation forest tree species in semiarid areas. The lack of genetic information hinders research into the mechanisms involved in its response to abiotic stresses. Here, short-read sequencing technology (Illumina) was used to de novo assemble the transcriptome on P. tomentosa. A to...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2014.08.008

    authors： Dong Y,Fan G,Deng M,Xu E,Zhao Z

    更新日期：2014-10-01 00:00:00

  • Comparative genomic analysis of two brucellaphages of distant origins.

    abstract：:Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb) and compared it with that of Pr, a broad host-range brucellaphage recently isolated in Mexico. The genomes consist of 41,148 bp (Tb) and 38,253 bp (Pr), they differ mainly in the region encoding structural proteins, in which the genome o...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2012.01.001

    authors： Flores V,López-Merino A,Mendoza-Hernandez G,Guarneros G

    更新日期：2012-04-01 00:00:00

  • Transcriptional profiling of mefloquine-induced disruption of calcium homeostasis in neurons in vitro.

    abstract：:Mefloquine is associated with adverse neurological effects that are mediated via unknown mechanisms. Recent in vitro studies have shown that mefloquine disrupts neuronal calcium homeostasis via liberation of the endoplasmic reticulum (ER) store and induction of calcium influx across the plasma membrane. In the present...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2005.07.004

    authors： Dow GS,Caridha D,Goldberg M,Wolf L,Koenig ML,Yourick DL,Wang Z

    更新日期：2005-11-01 00:00:00

  • Random forests for genomic data analysis.

    abstract：:Random forests (RF) is a popular tree-based ensemble machine learning tool that is highly data adaptive, applies to "large p, small n" problems, and is able to account for correlation as well as interactions among features. This makes RF particularly appealing for high-dimensional genomic data analysis. In this articl...

    journal_title：Genomics

    pub_type： 杂志文章,评审

    doi：10.1016/j.ygeno.2012.04.003

    authors： Chen X,Ishwaran H

    更新日期：2012-06-01 00:00:00

  • Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor spt3 (SUPT3H).

    abstract：:Spt3 is a Saccharomyces cerevisiae transcription factor that is required in vivo for the transcription of a number of RNA polymerase II-transcribed genes. We report the cloning of the gene encoding the human homologue of Spt3, SUPT3H, and its initial functional analysis. The human and yeast Spt3 homologues share an ov...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1006/geno.1998.5500

    authors： Yu J,Madison JM,Mundlos S,Winston F,Olsen BR

    更新日期：1998-10-01 00:00:00

  • Human SLUG gene organization, expression, and chromosome map location on 8q.

    abstract：:SLUG is a member of the snail family of zinc finger proteins. It is involved in epithelial to mesenchyme cell transition during neurulation and plays a role in limb bud development. We have isolated and described the human SLUG gene by sequencing a region spanning 4034 bp. The human SLUG gene contains three exons. The...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1006/geno.1998.5367

    authors： Cohen ME,Yin M,Paznekas WA,Schertzer M,Wood S,Jabs EW

    更新日期：1998-08-01 00:00:00

  • The L19 ribosomal protein gene (RPL19): gene organization, chromosomal mapping, and novel promoter region.

    abstract：:The intron-containing genes encoding rat and human ribosomal protein L19 (RPL19) have been cloned. The DNA sequences of the entire rat RPL19 gene and the 5' end of the human RPL19 gene have been determined. Sequence comparison of corresponding regions of the two genes reveals a striking interspecies homology in the 5'...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/0888-7543(95)80036-l

    authors： Davies B,Fried M

    更新日期：1995-01-20 00:00:00

  • Human retinal guanylate cyclase (GUC2D) maps to chromosome 17p13.1.

    abstract：:3',5'-Cyclic guanosine monophosphate is the intracellular second messenger regulating phototransduction in mammals. The level of cGMP in photoreceptor cells is controlled by the cGMP-hydrolyzing enzyme cGMP phosphodiesterase and the cGMP-producing enzyme guanylate cyclase. Identification of a photoreceptor-specific gu...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1006/geno.1994.1415

    authors： Oliveira L,Miniou P,Viegas-Pequignot E,Rozet JM,Dollfus H,Pittler SJ

    更新日期：1994-07-15 00:00:00

  • Functional analysis of bacterial artificial chromosomes in mammalian cells: mouse Cdc6 is associated with the mitotic spindle apparatus.

    abstract：:Bacterial artificial chromosomes (BACs) provide a well-characterized resource for studying the functional organization of genes and other large chromosomal domains. To facilitate functional studies in cell cultures, we have developed a simple approach for generating stable cell lines with variable copy numbers of any ...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/s0888-7543(03)00205-2

    authors： Illenye S,Heintz NH

    更新日期：2004-01-01 00:00:00

  • A mutation in apolipoprotein A-I in the Iowa type of familial amyloidotic polyneuropathy.

    abstract：:Immunoblotting of isoelectric focusing gels of plasma and direct genomic DNA sequencing have been used to characterize a mutation in apolipoprotein A-I associated with the familial amyloidotic polyneuropathy originally described by Van Allen in an Iowa kindred. An arginine for glycine substitution in apolipoprotein A-...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/0888-7543(90)90288-6

    authors： Nichols WC,Gregg RE,Brewer HB Jr,Benson MD

    更新日期：1990-10-01 00:00:00

  • Linkage mapping of human chromosome 10 microsatellite polymorphisms.

    abstract：:Ten microsatellite DNA polymorphisms located on human chromosome 10 were regionally mapped using subchromosomal somatic cell hybrids and linkage analysis. The resulting order of the markers from pter-qter was [D10S89, D10S111], D10S107, D10S109, [D10S91, D10S110, D10S108, D10S88, D10S168], and D10S169. Order of the ma...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/0888-7543(92)90455-2

    authors： Decker RA,Moore J,Ponder B,Weber JL

    更新日期：1992-03-01 00:00:00

  • Linkage of plasminogen (PLG) and apolipoprotein(a) (LPA) in baboons.

    abstract：:Four allelic forms of serum plasminogen (PLG) were detected in baboons (Papio hamadryas Linneaus 1758) by isoelectric focusing and were determined to be inherited as autosomal codominant traits. Linkage analysis of data from 179 progeny and their parents revealed that PLG is tightly linked (lod score = 30.20) to the g...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/0888-7543(91)90016-8

    authors： VandeBerg JL,Weitkamp L,Kammerer CM,Weill P,Aivaliotis MJ,Rainwater DL

    更新日期：1991-12-01 00:00:00

  • Expression analysis of microRNAs and their target mRNAs of testes with high and low sperm motility in domestic pigeons (Columba livia).

    abstract：:Sperm motility is one of the most important indicators to evaluate poultry fertility. In order to explore key molecular regulation roles related to sperm motility, we employed testicular RNA sequencing of pigeon. A total of 705 known and 385 novel microRNAs were identified. Compared with the low sperm motility group, ...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2020.12.024

    authors： Yin Z,Xu X,Tan Y,Cao H,Zhou W,Dong X,Mao H

    更新日期：2021-01-01 00:00:00

  • Maternal and paternal chromosomes 7 show differential methylation of many genes in lymphoblast DNA.

    abstract：:Genomic imprinting, the differential expression of paternal and maternal alleles, involves many chromosomal regions and plays a role in development and growth. Differential methylation of maternal and paternal alleles is a hallmark of imprinted genes, and thus methylation assays are widely used to support the identifi...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1006/geno.2001.6502

    authors： Hannula K,Lipsanen-Nyman M,Scherer SW,Holmberg C,Höglund P,Kere J

    更新日期：2001-04-01 00:00:00

  • Core proteome mediated therapeutic target mining and multi-epitope vaccine design for Helicobacter pylori.

    abstract：:Helicobacter pylori is a Gram-negative spiral-shaped bacterium that infects half of the human population worldwide and causes chronic inflammation. In the present study, we used the art of computational biology for therapeutic drug targets identification and a multi-epitope vaccine against multi-strains of H. pylori. ...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2020.06.026

    authors： Rahman N,Ajmal A,Ali F,Rastrelli L

    更新日期：2020-09-01 00:00:00

  • Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma.

    abstract：:Elucidating the molecular basis of hepatocellular carcinoma (HCC) is crucial to developing targeted diagnostics and therapies for this deadly disease. The landscape of somatic genomic rearrangements (GRs), which can lead to oncogenic gene fusions, remains poorly characterized in HCC. We have predicted 4314 GRs includi...

    journal_title：Genomics

    pub_type： 临床试验,杂志文章

    doi：10.1016/j.ygeno.2014.01.003

    authors： Fernandez-Banet J,Lee NP,Chan KT,Gao H,Liu X,Sung WK,Tan W,Fan ST,Poon RT,Li S,Ching K,Rejto PA,Mao M,Kan Z

    更新日期：2014-02-01 00:00:00

  • ReTRN: a retriever of real transcriptional regulatory network and expression data for evaluating structure learning algorithm.

    abstract：:One of the important goals in systems biology is to infer transcription network based on gene expression data. Validation of the reconstructed network often requires benchmark datasets, e.g. gene expression data, which are usually unattainable. Synthetic datasets are therefore often needed to test the structure learni...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2009.08.009

    authors： Li Y,Zhu Y,Bai X,Cai H,Ji W,Guo D

    更新日期：2009-11-01 00:00:00

  • Epigenetic status of the H19 locus in human oocytes following in vitro maturation.

    abstract：:Imprinting is an epigenetic modification that is reprogrammed in the germ line and leads to the monoallelic expression of some genes. Imprinting involves DNA methylation. Maternal imprint is reset during oocyte growth and maturation. In vitro maturation (IVM) of oocytes may, therefore, interfere with imprint acquisiti...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2005.10.008

    authors： Borghol N,Lornage J,Blachère T,Sophie Garret A,Lefèvre A

    更新日期：2006-03-01 00:00:00

  • Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom.

    abstract：:We conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2013.02.008

    authors： Sablok G,Wu X,Kuo J,Nayak KC,Baev V,Varotto C,Zhou F

    更新日期：2013-05-01 00:00:00

  • Identification and characterization of a cDNA and the structural gene encoding the mouse epithelial membrane protein-1.

    abstract：:The PMP22/EMP/MP20 gene family includes four closely related proteins, peripheral myelin protein-22 (PMP22), epithelial membrane protein-1 (EMP-1), epithelial membrane protein-2 (EMP-2), and epithelial membrane protein-3 (EMP-3), which share amino acid identities ranging from 33 to 43%. In addition, the lens-specific ...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1006/geno.1996.0482

    authors： Lobsiger CS,Magyar JP,Taylor V,Wulf P,Welcher AA,Program AE,Suter U

    更新日期：1996-09-15 00:00:00

  • Molecular mapping and cloning of the breakpoints of a chromosome 11p14.1-p13 deletion associated with the AGR syndrome.

    abstract：:Chromosome 11p13 is frequently rearranged in individuals with the WAGR syndrome (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) or parts of this syndrome. To map the cytogenetic aberrations molecularly, we screened DNA from cell lines with known WAGR-related chromosome abnormalities for rearra...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/0888-7543(88)90141-3

    authors： Gessler M,Bruns GA

    更新日期：1988-08-01 00:00:00

  • The HNF-3 gene family of transcription factors in mice: gene structure, cDNA sequence, and mRNA distribution.

    abstract：:The rat HNF-3 (hepatocyte nuclear factor 3) gene family encodes three transcription factors known to be important in the regulation of gene expression in liver and lung. We have cloned and characterized the mouse genes and cDNAs for HNF-3 alpha, beta, and gamma and analyzed their expression patterns in various adult t...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1006/geno.1994.1191

    authors： Kaestner KH,Hiemisch H,Luckow B,Schütz G

    更新日期：1994-04-01 00:00:00

  • A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes.

    abstract：:Sequence tag count-based gene expression analysis is potent for the identification of candidate genes relevant to the cancerous phenotype. With the public availability of count-based data, the computational approaches for differentially expressed genes, which are mainly based on Binomial or beta-Binomial distribution,...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2009.05.003

    authors： Lü B,Yu J,Xu J,Chen J,Lai M

    更新日期：2009-09-01 00:00:00

  • Retroposon compensatory mechanism hypothesis not supported: Zfa knockout mice are fertile.

    abstract：:It is hypothesized that autosomal retroposons compensate for the loss of their inactivated essential X-chromosome progenitors during spermatogenesis. Here we test this Retroposon Compensatory Mechanism (RCM) hypothesis using the Zfy gene family. The mouse autosomal retroposon Zfa is expressed in testes at the same dev...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/s0888-7543(03)00155-1

    authors： Banks KG,Johnson KA,Lerner CP,Mahaffey CL,Bronson RT,Simpson EM

    更新日期：2003-09-01 00:00:00

  • Transcriptome profiling of different developmental stages of corpus luteum during the estrous cycle in pigs.

    abstract：:To better understand the molecular basis of corpus luteum (CL) development and function RNA-Seq was utilized to identify differentially expressed genes (DEGs) in porcine CL during different physiological stages of the estrous cycle viz. early (EL), mid (ML), late (LL) and regressed (R) luteal. Stage wise comparisons o...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2020.12.008

    authors： Bharati J,Mohan NH,Kumar S,Gogoi J,Kumar S,Jose B,Punetha M,Borah S,Kumar A,Sarkar M

    更新日期：2021-01-01 00:00:00

  • Exonic SINE insertion in STK38L causes canine early retinal degeneration (erd).

    abstract：:Fine mapping followed by candidate gene analysis of erd - a canine hereditary retinal degeneration characterized by aberrant photoreceptor development - established that the disease cosegregates with a SINE insertion in exon 4 of the canine STK38L/NDR2 gene. The mutation removes exon 4 from STK38L transcripts and is p...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2010.09.003

    authors： Goldstein O,Kukekova AV,Aguirre GD,Acland GM

    更新日期：2010-12-01 00:00:00

  • Genes regulating the serotonin metabolic pathway in the brain stem and their role in the etiopathogenesis of the sudden infant death syndrome.

    abstract：:Genotypes and allelic frequencies of TPH2, 5-HTTLPR, the 5-HTT (SLC6A4) intron 2 variable-number tandem repeat (VNTR) region, and the MAOA VNTR region were determined in brain-stem samples of 20 "genuine" SIDS cases and compared with results obtained from 150 healthy controls. The SNP G1463A responsible for 80% functi...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2008.01.010

    authors： Nonnis Marzano F,Maldini M,Filonzi L,Lavezzi AM,Parmigiani S,Magnani C,Bevilacqua G,Matturri L

    更新日期：2008-06-01 00:00:00

  • Identification of a new murine runt domain-containing gene, Cbfa3, and localization of the human homolog, CBFA3, to chromosome 1p35-pter.

    abstract：:Core binding factor (CBF) is a heterodimeric transcription factor composed of two distinct subunits. The monomeric beta subunit is ubiquitously expressed, whereas expression of the three alpha subunits isolated previously seems to be restricted mainly to hematopoietic tissues. To isolate additional alpha genes, degene...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/0888-7543(95)80185-o

    authors： Wijmenga C,Speck NA,Dracopoli NC,Hofker MH,Liu P,Collins FS

    更新日期：1995-04-10 00:00:00

  • Homozygosity mapping in an Irish ALS case-control cohort describes local demographic phenomena and points towards potential recessive risk loci.

    abstract：:Runs of homozygosity are common in European populations and are indicative of consanguinity, restricted population size and recessively inherited traits. Here, we map runs of homozygosity (ROHs) in an Irish case-control cohort for amyotrophic lateral sclerosis (ALS), a devastating neurological condition with high heri...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2015.01.002

    authors： McLaughlin RL,Kenna KP,Vajda A,Heverin M,Byrne S,Donaghy CG,Cronin S,Bradley DG,Hardiman O

    更新日期：2015-04-01 00:00:00

  • Construction, database integration, and application of an Oenothera EST library.

    abstract：:Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmenta...

    journal_title：Genomics

    pub_type： 杂志文章

    doi：10.1016/j.ygeno.2006.05.010

    authors： Mrácek J,Greiner S,Cho WK,Rauwolf U,Braun M,Umate P,Altstätter J,Stoppel R,Mlcochová L,Silber MV,Volz SM,White S,Selmeier R,Rudd S,Herrmann RG,Meurer J

    更新日期：2006-09-01 00:00:00