Hierarchical modularity and the evolution of genetic interactomes across species.

scientific article

Hierarchical modularity and the evolution of genetic interactomes across species. is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1016/J.MOLCEL.2012.05.028
P3181OpenCitations bibliographic resource ID773612
P932PMC publication ID3380636
P698PubMed publication ID22681890
P5875ResearchGate publication ID225289350

P50authorTrey IdekerQ16335202
Michael-Christopher KeoghQ28324309
Nevan KroganQ28450952
Sean R CollinsQ37393509
Gerard CagneyQ37393538
Pedro BeltraoQ41044831
J Peter SvenssonQ41049883
Colm J. RyanQ55143837
Padraig CunninghamQ57418766
Joseph I KliegmanQ58810238
P2093author name stringHyun-Soo Kim
Michael Shales
Kevan M Shokat
Christine Guthrie
Zongtian Tong
Chao Tang
Winfried Edelmann
Hong Qu
Assen Roguev
Derek Greene
Elena Tosti
Peter J Espenshade
Lingli Jiang
Jiewei Xu
Dwight Kuo
Harlizawati Jahari
Kristin Patrick
P2860cites workThe evolutionary origin of orphan genesQ22122002
Epistasis--the essential role of gene interactions in the structure and evolution of genetic systemsQ22122008
Finding the missing heritability of complex diseasesQ22122198
A DNA damage response screen identifies RHINO, a 9-1-1 and TopBP1 interacting protein required for ATR signalingQ24306275
Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acidsQ24306330
pICln inhibits snRNP biogenesis by binding core spliceosomal proteinsQ24517638
Bub3 interaction with Mad2, Mad3 and Cdc20 is mediated by WD40 repeats and does not require intact kinetochoresQ24534626
Functional organization of the S. cerevisiae phosphorylation networkQ24634340
High-quality binary protein interaction map of the yeast interactome networkQ24651397
A membrane coat complex essential for endosome-to-Golgi retrograde transport in yeastQ24670484
A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatinQ24801790
Where does fission yeast sit on the tree of life?Q24804391
Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore functionQ27303046
Functional profiling of the Saccharomyces cerevisiae genomeQ27860544
ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complexQ27929959
The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene programQ27931213
A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondriaQ27931884
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcriptionQ27932406
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicingQ27932638
The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complexQ27932742
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.Q27933672
Global mapping of the yeast genetic interaction networkQ27934987
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complexQ27935315
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profileQ27935813
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal traffickingQ27937526
Degradation of misfolded endoplasmic reticulum glycoproteins in Saccharomyces cerevisiae is determined by a specific oligosaccharide structureQ27938571
Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeQ27938796
Functional discovery via a compendium of expression profilesQ27938962
Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexesQ27939264
The genetic landscape of a cellQ28131628
The BioGRID Interaction Database: 2011 updateQ28298160
Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathwaysQ28478052
The mystery of missing heritability: Genetic interactions create phantom heritabilityQ28732355
A gene-coexpression network for global discovery of conserved genetic modulesQ29614451
Genome-wide association studies for common diseases and complex traitsQ29615822
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction mapQ29618911
The DASH complex and Klp5/Klp6 kinesin coordinate bipolar chromosome attachment in fission yeastQ30476087
HOPS interacts with Apl5 at the vacuole membrane and is required for consumption of AP-3 transport vesiclesQ30491341
A strategy for extracting and analyzing large-scale quantitative epistatic interaction dataQ31049488
Functional maps of protein complexes from quantitative genetic interaction dataQ31153034
Genome-wide association data reveal a global map of genetic interactions among protein complexesQ33521286
Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.Q33579032
Systematic interpretation of genetic interactions using protein networksQ33622989
Conserved patterns of protein interaction in multiple speciesQ33837704
Improved functional overview of protein complexes using inferred epistatic relationships.Q33909267
PomBase: a comprehensive online resource for fission yeastQ34228886
Rewiring of genetic networks in response to DNA damage.Q34425692
The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genesQ34613438
Novel genes exhibit distinct patterns of function acquisition and network integrationQ34613793
Modelling genotype-phenotype relationships and human disease with genetic interaction networksQ34621400
High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombeQ34692755
eSGA: E. coli synthetic genetic array analysisQ34803849
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotesQ34860078
Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.Q34874112
High-throughput, quantitative analyses of genetic interactions in E. coliQ34927322
Detecting gene-gene interactions that underlie human diseasesQ34980492
Quantitative analysis of fitness and genetic interactions in yeast on a genome scaleQ35051808
The Ubiquitous Nature of Epistasis in Determining Susceptibility to Common Human DiseasesQ35582337
Transcriptional regulation of protein complexes within and across speciesQ35611673
Yeast sterol regulatory element-binding protein (SREBP) cleavage requires Cdc48 and Dsc5, a ubiquitin regulatory X domain-containing subunit of the Golgi Dsc E3 ligaseQ35643838
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPKQ35749976
Conserved pathways within bacteria and yeast as revealed by global protein network alignmentQ36160907
Modeling cellular machinery through biological network comparisonQ36443509
A global analysis of genetic interactions in Caenorhabditis elegansQ36640170
The TSC1-TSC2 complex is required for proper activation of mTOR complex 2Q36710799
The S. pombe SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8.Q36995417
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environmentQ37038553
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseasesQ37190495
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.Q37365634
Epistatic relationships reveal the functional organization of yeast transcription factorsQ38339973
Mapping of signaling networks through synthetic genetic interaction analysis by RNAiQ39580460
Optimal stepwise experimental design for pairwise functional interaction studiesQ41346415
Quantitative genetic interactions reveal biological modularityQ41830607
Quantitative genetic interaction mapping using the E-MAP approachQ42407989
Violations of robustness trade-offsQ42618981
Two kinesin-like Kin I family proteins in fission yeast regulate the establishment of metaphase and the onset of anaphase A.Q48307683
Epistasis: too often neglected in complex trait studies?Q48541812
LAMMER kinase Kic1 is involved in pre-mRNA processing.Q50516987
Vacuolar protein sorting receptor in Schizosaccharomyces pombe.Q50733234
Evolutionary plasticity of genetic interaction networksQ55554510
Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathwaysQ55554520
P433issue5
P407language of work or nameEnglishQ1860
P921main subjectcell biologyQ7141
Ubiquitin-protein ligase TUL1 YKL034WQ27547589
Dsc2p YOL073CQ27548181
Dsc3p YOR223WQ27550208
Ubx3p YDL091CQ27551361
P304page(s)691-704
P577publication date2012-06-08
P1433published inMolecular CellQ3319468
P1476titleHierarchical modularity and the evolution of genetic interactomes across species.
P478volume46

Reverse relations

cites work (P2860)
Q46002486A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events.
Q38838357A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy.
Q37636592A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation
Q89831441A Quantitative Genetic Interaction Map of HIV Infection
Q64120456A genetic approach to study polyubiquitination in Saccharomyces cerevisiae
Q41971229A genetic screen for functional partners of condensin in fission yeast.
Q34466080A map of directional genetic interactions in a metazoan cell
Q34441358A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast
Q34581520A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility
Q38955424A tool named Iris for versatile high-throughput phenotyping in microorganisms.
Q34036638All or nothing: protein complexes flip essentiality between distantly related eukaryotes.
Q26786228An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System
Q38563463Bacterial protein networks: properties and functions
Q33742644Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection
Q38622324Cell-based screens and phenomics with fission yeast.
Q33557346Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.
Q35555201Chemical genomics approach to identify genes associated with sensitivity to rapamycin in the fission yeast Schizosaccharomyces pombe.
Q34850230Comparison of profile similarity measures for genetic interaction networks
Q35006955Conserved abundance and topological features in chromatin-remodeling protein interaction networks
Q36998501Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast
Q37184407Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways
Q28550285Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation
Q38076910Design principles of regulatory networks: searching for the molecular algorithms of the cell
Q35086186Development of ultra-high-density screening tools for microbial "omics".
Q40366064Differential genetic interactions of yeast stress response MAPK pathways
Q30663150Dissection of DNA damage responses using multiconditional genetic interaction maps
Q62673364Drug combinations: a strategy to extend the life of antibiotics in the 21st century
Q36658548Epigenetic epistatic interactions constrain the evolution of gene expression
Q37157035Evolution of a G protein-coupled receptor response by mutations in regulatory network interactions
Q43079790Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity
Q34306599Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells
Q41882250From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
Q26830798From systems to structure: bridging networks and mechanism
Q36215342Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae.
Q35583065Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants
Q60302058Genetic analysis reveals functions of atypical polyubiquitin chains
Q90475922Genetic correlation network prediction of forest soil microbial functional organization
Q42272826Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations
Q35235099Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast
Q27023184Genetic interaction networks: better understand to better predict
Q35132881Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression.
Q37399103Genotype to phenotype via network analysis
Q38077445Genotype to phenotype: lessons from model organisms for human genetics
Q55384044Harnessing synthetic lethality to predict the response to cancer treatment.
Q38667267High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.
Q33623110High-resolution network biology: connecting sequence with function
Q35105750High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions.
Q34391566How the nucleus copes with proteotoxic stress
Q37671487Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function
Q34468295Identification of candidate substrates for the Golgi Tul1 E3 ligase using quantitative diGly proteomics in yeast.
Q92898651Identification of proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1 in the fission yeast Schizosaccharomyces pombe
Q30797535Imputing missing values for genetic interaction data
Q64019134Integrating genetic and protein-protein interaction networks maps a functional wiring diagram of a cell
Q95940288Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions
Q26824897Integrative approaches for finding modular structure in biological networks
Q36958121Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast
Q30834280Kinesin-8 effects on mitotic microtubule dynamics contribute to spindle function in fission yeast.
Q36713548Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines
Q36185332Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity
Q42369678Lingering single-strand breaks trigger Rad51-independent homology-directed repair of collapsed replication forks in the polynucleotide kinase/phosphatase mutant of fission yeast
Q64232908Modular epistasis and the compensatory evolution of gene deletion mutants
Q50211661Native gel analysis of macromolecular protein complexes in cultured mammalian cells
Q36238554Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes.
Q92131450PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks
Q34923804Parallel profiling of fission yeast deletion mutants for proliferation and for lifespan during long-term quiescence.
Q42425984Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures
Q58098406Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions
Q45826942Predicting functional gene interactions with the hierarchical interaction score
Q35130411Protein complexes in bacteria.
Q35689663Quantitative Fitness Analysis Identifies exo1∆ and Other Suppressors or Enhancers of Telomere Defects in Schizosaccharomyces pombe.
Q35204646Quantitative analysis of triple-mutant genetic interactions
Q36811345Quantitative genetic-interaction mapping in mammalian cells
Q35400929Rapid epigenetic adaptation to uncontrolled heterochromatin spreading
Q41758914Rewiring of genetic networks in response to modification of genetic background
Q35247564SANTA: quantifying the functional content of molecular networks
Q43625940Schizosaccharomyces pombe centromere protein Mis19 links Mis16 and Mis18 to recruit CENP-A through interacting with NMD factors and the SWI/SNF complex
Q41825385Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons
Q45141810Shelterin components mediate genome reorganization in response to replication stress.
Q38783458Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures
Q56170738Species-specific activity of antibacterial drug combinations
Q41826440Splicing functions and global dependency on fission yeast slu7 reveal diversity in spliceosome assembly
Q35922301Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways
Q37175122Subunit architecture of the Golgi Dsc E3 ligase required for sterol regulatory element-binding protein (SREBP) cleavage in fission yeast
Q89187412Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls
Q57190621Synthetic Lethality and Cancer - Penetrance as the Major Barrier
Q38709651Synthetic lethality and cancer.
Q64082743Systematic analysis reveals the prevalence and principles of bypassable gene essentiality
Q36701055Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae
Q35086142Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth.
Q37032537Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation.
Q30276470Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation
Q30009309The Cdc15 and Imp2 SH3 domains cooperatively scaffold a network of proteins that redundantly ensure efficient cell division in fission yeast
Q37193578The Effect of G-ORS Along With Rice Soup in the Treatment of Acute Diarrhea in Children: A Single-Blind Randomized Controlled Trial
Q52376069The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation.
Q55077869The contribution of non-essential Schizosaccharomyces pombe genes to fitness in response to altered nutrient supply and target of rapamycin activity.
Q90187249The fission yeast FHIT homolog affects checkpoint control of proliferation and is regulated by mitochondrial electron transport
Q37318693The fission yeast cell wall stress sensor-like proteins Mtl2 and Wsc1 act by turning on the GTPase Rho1p but act independently of the cell wall integrity pathway
Q38818040The histone variant H2A.Z promotes splicing of weak introns.
Q104100296The phosphatase inhibitor Sds23 promotes symmetric spindle positioning in fission yeast
Q36258476Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
Q91011163Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments
Q48042369Using genetic buffering relationships identified in fission yeast to reveal susceptibilities in cells lacking hamartin or tuberin function.
Q28818537Widespread Genetic Incompatibilities between First-Step Mutations during Parallel Adaptation of Saccharomyces cerevisiae to a Common Environment

Search more.