J Integr Bioinform - The topology of the growing human interactome data.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ gene(2352) biolog(1181) express(1162) }
{ howev(809) still(633) remain(590) }
{ network(2748) neural(1063) input(814) }
{ import(1318) role(1303) understand(862) }
{ first(2504) two(1366) second(1323) }
{ can(981) present(881) function(850) }
{ data(1737) use(1416) pattern(1282) }
{ data(3963) clinic(1234) research(1004) }
{ blood(1257) pressur(1144) flow(957) }
{ measur(2081) correl(1212) valu(896) }
{ algorithm(1844) comput(1787) effici(935) }
{ risk(3053) factor(974) diseas(938) }
{ model(3480) simul(1196) paramet(876) }
{ data(3008) multipl(1320) sourc(1022) }
{ cancer(2502) breast(956) screen(824) }
{ model(3404) distribut(989) bayesian(671) }
{ system(1976) rule(880) can(841) }
{ treatment(1704) effect(941) patient(846) }
{ method(1557) propos(1049) approach(1037) }
{ visual(1396) interact(850) tool(830) }
{ activ(1138) subject(705) human(624) }
{ process(1125) use(805) approach(778) }
{ method(2212) result(1239) propos(1039) }
{ imag(1057) registr(996) error(939) }
{ method(1219) similar(1157) match(930) }
{ take(945) account(800) differ(722) }
{ motion(1329) object(1292) video(1091) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ data(1714) softwar(1251) tool(1186) }
{ general(901) number(790) one(736) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ use(2086) technolog(871) perceiv(783) }
{ structur(1116) can(940) graph(676) }
{ method(1969) cluster(1462) data(1082) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ bind(1733) structur(1185) ligand(1036) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ studi(1410) differ(1259) use(1210) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ activ(1452) weight(1219) physic(1104) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

We have long moved past the one-gene–one-function concept originally proposed by Beadle and Tatum back in 1941; but the full understanding of genotype–phenotype relations still largely relies on the analysis of static, snapshot-like, interaction data sets. Here, we look at what global patterns can be uncovered if we simply trace back the human interactome network over the last decade of protein- protein interaction (PPI) screening. We take a purely topological approach and find that as the human interactome is getting denser, it is not only gaining in structure (in terms of now being better fit by structured network models than before), but also there are patterns in the way in which it is growing: (a) newly added proteins tend to get linked to existing proteins in the interactome that are not know to interact; and (b) new proteins tend to link to already well connected proteins. Moreover, the alignment between human and yeast interactomes spanning over 40% of yeast’s proteins — that are involved in regulation of transcription, RNA splicing and other cellcycle-related processes—suggests the existence of a part of the interactome which remains topologically and functionally unaffected through evolution. Furthermore, we find a small sub-network, specific to the “core” of the human interactome and involved in regulation of transcription and cancer development, whose wiring has not changed within the human interactome over the last 10 years of interacome data acquisition. Finally, we introduce a generalisation of the clustering coefficient of a network as a new measure called the cycle coefficient, and use it to show that PPI networks of human and model organisms are wired in a tight way which forbids the occurrence large cycles.

Resumo Limpo

long move past onegenendashonefunct concept origin propos beadl tatum back full understand genotypendashphenotyp relat still larg reli analysi static snapshotlik interact data set look global pattern can uncov simpli trace back human interactom network last decad protein protein interact ppi screen take pure topolog approach find human interactom get denser gain structur term now better fit structur network model also pattern way grow newli ad protein tend get link exist protein interactom know interact b new protein tend link alreadi well connect protein moreov align human yeast interactom span yeastrsquo protein mdash involv regul transcript rna splice cellcyclerel processesmdashsuggest exist part interactom remain topolog function unaffect evolut furthermor find small subnetwork specif ldquocorerdquo human interactom involv regul transcript cancer develop whose wire chang within human interactom last year interacom data acquisit final introduc generalis cluster coeffici network new measur call cycl coeffici use show ppi network human model organ wire tight way forbid occurr larg cycl

Resumos Similares

Comput Math Methods Med - Mathematical model of dynamic protein interactions regulating p53 protein stability for tumor suppression. ( 0,700044680946627 )
J. Comput. Biol. - Node fingerprinting: an efficient heuristic for aligning biological networks. ( 0,694025212589261 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,691010188201012 )
Brief. Bioinformatics - Application of second-generation sequencing to cancer genomics. ( 0,686699342985655 )
J Integr Bioinform - BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. ( 0,682875190610207 )
J. Comput. Biol. - In silico prediction of escherichia coli proteins targeting the host cell nucleus, with special reference to their role in colon cancer etiology. ( 0,674334159304059 )
Comput Biol Chem - Structural characteristics of genomic islands associated with GMP synthases as integration hotspot among sequenced microbial genomes. ( 0,669737800958149 )
Comput Biol Chem - Gene expression regulation of the PF00480 or PF14340 domain proteins suggests their involvement in sulfur metabolism. ( 0,669141063152809 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,668748774096681 )
Comput Biol Chem - In silico characterization and evolutionary analyses of CCAAT binding proteins in the lycophyte plant Selaginella moellendorffii genome: a growing comparative genomics resource. ( 0,667436662835794 )
J Integr Bioinform - Community structure of non-coding RNA interaction network. ( 0,666639739392938 )
Comput Biol Chem - In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. ( 0,664937667906739 )
Comput Biol Chem - Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes. ( 0,663460175632877 )
Brief. Bioinformatics - Applications of alignment-free methods in epigenomics. ( 0,654141694338286 )
Wiley Interdiscip Rev Syst Biol Med - Functional genomics of the brain: uncovering networks in the CNS using a systems approach. ( 0,653721435646293 )
J Integr Bioinform - LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe. ( 0,653574535575231 )
Sci Data - A draft genome for the African crocodilian trypanosome Trypanosoma grayi. ( 0,650663841459621 )
Comput Biol Chem - Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress. ( 0,649030146407317 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,648632515413797 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,647132282466261 )
Comput Biol Chem - Computational identification and characterization of primate-specific microRNAs in human genome. ( 0,645427679021634 )
Brief. Bioinformatics - Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. ( 0,643528341724464 )
Artif Intell Med - Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. ( 0,643381386694866 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,6401561570954 )
Comput. Biol. Med. - Impact of TGF-b on breast cancer from a quantitative proteomic analysis. ( 0,638296413465719 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,633709402840982 )
Brief. Bioinformatics - Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. ( 0,631685555802135 )
Brief. Bioinformatics - The genomic and functional characteristics of disease genes. ( 0,631669752048587 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,630605678222946 )
J. Comput. Biol. - A probabilistic model of neutral and selective dynamics of protein network evolution. ( 0,628449120585624 )
Comput Biol Chem - Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. ( 0,627368444234859 )
J. Comput. Biol. - Comparison of phylogenetic trees and search for a central trend in the forest of life. ( 0,622396297646793 )
Comput Biol Chem - Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments. ( 0,620937719805549 )
Brief. Bioinformatics - Sequencing technologies and tools for short tandem repeat variation detection. ( 0,620573334189884 )
Brief. Bioinformatics - Toward the dynamic interactome: it's about time. ( 0,619636027701551 )
Brief. Bioinformatics - Positional orthology: putting genomic evolutionary relationships into context. ( 0,617830241295126 )
J. Comput. Biol. - Catching the genomic wave in oligonucleotide single-nucleotide polymorphism arrays by modeling sequence binding. ( 0,616413790966376 )
Wiley Interdiscip Rev Syst Biol Med - Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. ( 0,615571146009869 )
Comput Biol Chem - Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. ( 0,612122586699822 )
Brief. Bioinformatics - Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. ( 0,61048389910093 )
BMC Med Inform Decis Mak - Improved method for protein complex detection using bottleneck proteins. ( 0,609514673768674 )
Brief. Bioinformatics - Evolution of gene regulation--on the road towards computational inferences. ( 0,607320851604283 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,606724862063857 )
Comput Biol Chem - Identification of potential drug targets by subtractive genome analysis of Bacillus anthracis A0248: An in silico approach. ( 0,606576159510459 )
Comput Biol Chem - Functional characterization of plant small RNAs based on next-generation sequencing data. ( 0,605005120507715 )
Brief. Bioinformatics - Pattern recognition and probabilistic measures in alignment-free sequence analysis. ( 0,604685265808908 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,604382688580591 )
Wiley Interdiscip Rev Syst Biol Med - Postgenomic technologies targeting the Wnt signaling network. ( 0,603995401554565 )
Comput Biol Chem - Genome-wide identification and predictive modeling of lincRNAs polyadenylation in cancer genome. ( 0,603041724604742 )
Brief. Bioinformatics - Methodological aspects of whole-genome bisulfite sequencing analysis. ( 0,60069164370942 )
Brief. Bioinformatics - Comparative analysis of methods for genome-wide nucleosome cartography. ( 0,600657680044496 )
Brief. Bioinformatics - Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. ( 0,600279641744127 )
J Integr Bioinform - Construction of coffee transcriptome networks based on gene annotation semantics. ( 0,598739731220081 )
J Integr Bioinform - Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data. ( 0,598557222899622 )
Comput Math Methods Med - Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. ( 0,592501210154514 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,591420922179507 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,591398620470105 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology of lung development and regeneration: current knowledge and recommendations for future research. ( 0,591356021786062 )
J. Comput. Biol. - Learning cellular sorting pathways using protein interactions and sequence motifs. ( 0,590849217599923 )
Brief. Bioinformatics - A review of statistical methods for prediction of proteolytic cleavage. ( 0,589766050089236 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,588761963728589 )
Wiley Interdiscip Rev Syst Biol Med - How changes in fibril-level organization correlate with the macrolevel behavior of articular cartilage. ( 0,588323241141101 )
J Chem Inf Model - Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study. ( 0,586936065321125 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,58656370097874 )
Brief. Bioinformatics - Computational challenges of sequence classification in microbiomic data. ( 0,586047224499781 )
Comput. Biol. Med. - Evolution of the mir-181 microRNA family. ( 0,585140434010104 )
Comput Biol Chem - All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC. ( 0,58461593727462 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,584385505895755 )
Wiley Interdiscip Rev Syst Biol Med - Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. ( 0,584194858012066 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,584081047149291 )
Wiley Interdiscip Rev Syst Biol Med - Role of fibroblast growth factor signaling in vascular formation and maintenance: orchestrating signaling networks as an integrated system. ( 0,582439755972321 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,582229145628047 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,582211374094157 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,581734456749689 )
Wiley Interdiscip Rev Syst Biol Med - Mediators and dynamics of DNA methylation. ( 0,581734406700683 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,580629694149643 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,580137654507469 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,578530283665142 )
Med Biol Eng Comput - Cell sheet integrity and nanomechanical breakdown during programmed cell death. ( 0,578189703470223 )
Comput. Biol. Med. - Genome-wide identification and structure-function studies of proteases and protease inhibitors in Cicer arietinum (chickpea). ( 0,577480585653133 )
Wiley Interdiscip Rev Syst Biol Med - Genome network medicine: innovation to overcome huge challenges in cancer therapy. ( 0,576857492019555 )
J. Comput. Biol. - eALPS: estimating abundance levels in pooled sequencing using available genotyping data. ( 0,575993515721685 )
Comput Biol Chem - Circular code motifs in transfer and 16S ribosomal RNAs: a possible translation code in genes. ( 0,574887814117729 )
J. Comput. Biol. - Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization. ( 0,574396752599242 )
Comput Biol Chem - Identification of novel splice variants and exons of human endothelial cell-specific chemotaxic regulator (ECSCR) by bioinformatics analysis. ( 0,574330971471151 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,574100023657673 )
Brief. Bioinformatics - High-performance analysis of biological systems dynamics with the DiVinE model checker. ( 0,573875052472392 )
Wiley Interdiscip Rev Syst Biol Med - Genome-wide approaches in the study of microRNA biology. ( 0,573681590248149 )
Brief. Bioinformatics - Towards a comprehensive picture of the genetic landscape of complex traits. ( 0,573567987360706 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,573088125237093 )
Comput Biol Chem - ISDTool: a computational model for predicting immunosuppressive domain of HERVs. ( 0,57204266746691 )
Comput Biol Chem - Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: a molecular dynamics study. ( 0,571683321938512 )
Wiley Interdiscip Rev Syst Biol Med - Toward a systems-level understanding of the Hedgehog signaling pathway: defining the complex, robust, and fragile. ( 0,571493640306747 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,570911309789981 )
Comput Biol Chem - Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection. ( 0,570044264760797 )
Wiley Interdiscip Rev Syst Biol Med - Integrating omics into the cardiac differentiation of human pluripotent stem cells. ( 0,56916243573736 )
Wiley Interdiscip Rev Syst Biol Med - Hierarchical approaches for systems modeling in cardiac development. ( 0,569068436450323 )
Brief. Bioinformatics - Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. ( 0,568728222076536 )
Brief. Bioinformatics - Next generation sequencing in functional genomics. ( 0,568685401515774 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,568673963634141 )