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Volumn 89, Issue 4, 2015, Pages 489-499

Network motifs that recur across species, including gene regulatory and protein–protein interaction networks

Author keywords

Cancer; Network motif; Subgraph; Toxicology

Indexed keywords

ANIMAL; GENE REGULATORY NETWORK; HUMAN; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SPECIES DIFFERENCE; TOXICITY TESTING;

EID: 84939882730     PISSN: 03405761     EISSN: 14320738     Source Type: Journal    
DOI: 10.1007/s00204-014-1274-y     Document Type: Review
Times cited : (4)

References (63)
  • 1
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • Albert R, Barabasi AL (2002) Statistical mechanics of complex networks. Rev Mod Phys 74:47–97
    • (2002) Rev Mod Phys , vol.74 , pp. 47-97
    • Albert, R.1    Barabasi, A.L.2
  • 3
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: theory and experimental approaches
    • COI: 1:CAS:528:DC%2BD2sXlsVSktro%3D
    • Alon U (2007b) Network motifs: theory and experimental approaches. Nat Genet 8:450–461
    • (2007) Nat Genet , vol.8 , pp. 450-461
    • Alon, U.1
  • 4
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • PID: 10521342
    • Barabasi AL, Albert R (1999) Emergence of scaling in random networks. Science 286:509–512
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 5
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell’s functional organization
    • COI: 1:CAS:528:DC%2BD2cXovV2mtg%3D%3D
    • Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Genet 5:101–113
    • (2004) Nat Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 7
    • 2942552376 scopus 로고    scopus 로고
    • Dorbin R, Beg QK, Barabasi AL, Oltvai ZN (2004) Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinform 5
    • Dorbin R, Beg QK, Barabasi AL, Oltvai ZN (2004) Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinform 5
  • 8
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • COI: 1:CAS:528:DC%2BD2cXlvFWjtrc%3D, PID: 15197165
    • Duarte NC, Herrgård MJ, Palsson BØ (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14:1298–1309
    • (2004) Genome Res , vol.14 , pp. 1298-1309
    • Duarte, N.C.1    Herrgård, M.J.2    Palsson, B.Ø.3
  • 9
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • COI: 1:CAS:528:DC%2BD2sXitVaqu7w%3D, PID: 17267599
    • Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci 104(6):1777–1782
    • (2007) Proc Natl Acad Sci , vol.104 , Issue.6 , pp. 1777-1782
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3    Thiele, I.4    Mo, M.L.5    Vo, T.D.6    Srivas, R.7    Palsson, B.Ø.8
  • 10
    • 33746051644 scopus 로고    scopus 로고
    • Exploring local structural organization of metabolic networks using subgraph patterns
    • PID: 16504210
    • Eom Y, Lee S, Jeong H (2006) Exploring local structural organization of metabolic networks using subgraph patterns. J Theor Biol 241:823–829
    • (2006) J Theor Biol , vol.241 , pp. 823-829
    • Eom, Y.1    Lee, S.2    Jeong, H.3
  • 11
    • 33645462347 scopus 로고    scopus 로고
    • Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
    • PID: 16738551
    • Feist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2(2006):0004
    • (2006) Mol Syst Biol , vol.2 , Issue.2006 , pp. 0004
    • Feist, A.M.1    Scholten, J.C.M.2    Palsson, B.Ø3    Brockman, F.J.4    Ideker, T.5
  • 13
    • 38349178598 scopus 로고    scopus 로고
    • Reconstruction, modeling and analysis of Halobacterium salinarum R-1 metabolism
    • COI: 1:CAS:528:DC%2BD1cXovFKmsA%3D%3D, PID: 18213408
    • Gonzalez O, Gronau S, Falb M, Pfeiffer F, Mendoza E, Zimmerb R, Oesterhelta D (2008) Reconstruction, modeling and analysis of Halobacterium salinarum R-1 metabolism. Mol BioSyst 4:148–159
    • (2008) Mol BioSyst , vol.4 , pp. 148-159
    • Gonzalez, O.1    Gronau, S.2    Falb, M.3    Pfeiffer, F.4    Mendoza, E.5    Zimmerb, R.6    Oesterhelta, D.7
  • 14
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • COI: 1:CAS:528:DC%2BD38Xjt1Knsrs%3D, PID: 11967534
    • Guelzim N, Bottani S, Bourgine P, Képès F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31:60–63
    • (2002) Nat Genet , vol.31 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3    Képès, F.4
  • 15
    • 65249176527 scopus 로고    scopus 로고
    • Stress-dependent coordination of transcriptome and translatome in yeast
    • PID: 19419242
    • Halbeisen RE, Gerber AP (2009) Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol 7(5):e1000105
    • (2009) PLoS Biol , vol.7 , Issue.5 , pp. 1000105
    • Halbeisen, R.E.1    Gerber, A.P.2
  • 19
    • 33745780500 scopus 로고    scopus 로고
    • Ingram PJ, Stumpf MPH, Stark J (2006) Network motifs: structure does not determine function. BMC Gen 7(108)
    • Ingram PJ, Stumpf MPH, Stark J (2006) Network motifs: structure does not determine function. BMC Gen 7(108)
  • 20
    • 0035170506 scopus 로고    scopus 로고
    • DBTBS: a database of Bacillus subtilis promoters and transcription factors
    • COI: 1:CAS:528:DC%2BD3MXjtlWmt7c%3D, PID: 11125112
    • Ishii T, Yoshida K, Terai G, Fujita Y, Nakai K (2001) DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucl Acids Res 29(1):278–280
    • (2001) Nucl Acids Res , vol.29 , Issue.1 , pp. 278-280
    • Ishii, T.1    Yoshida, K.2    Terai, G.3    Fujita, Y.4    Nakai, K.5
  • 21
    • 82255181552 scopus 로고    scopus 로고
    • Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast
    • COI: 1:CAS:528:DC%2BC3MXhsFCisLfI, PID: 21840901
    • Joshi A, van de Peer Y, Michoel T (2011) Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. Nucl Acids Res 39(21):9108–9117
    • (2011) Nucl Acids Res , vol.39 , Issue.21 , pp. 9108-9117
    • Joshi, A.1    van de Peer, Y.2    Michoel, T.3
  • 22
    • 0033453040 scopus 로고    scopus 로고
    • Simple Markov-chain algorithms for generating bipartite graphs and tournaments
    • Kannen R, Tetali P, Vempala S (1997) Simple Markov-chain algorithms for generating bipartite graphs and tournaments. Random Struct Algorithms 14:293
    • (1997) Random Struct Algorithms , vol.14 , pp. 293
    • Kannen, R.1    Tetali, P.2    Vempala, S.3
  • 23
    • 70449631149 scopus 로고    scopus 로고
    • Kashani ZRM, Ahrabian H, Elahi E, Nowzari-Dalini A, Ansari ES, Asadi S, Mohammadi S, Schreiber F, Masoudi-Nejad A (2009) Kavosh: a new algorithm for finding network motifs. BMC Bioinform 10
    • Kashani ZRM, Ahrabian H, Elahi E, Nowzari-Dalini A, Ansari ES, Asadi S, Mohammadi S, Schreiber F, Masoudi-Nejad A (2009) Kavosh: a new algorithm for finding network motifs. BMC Bioinform 10
  • 24
    • 4444268694 scopus 로고    scopus 로고
    • Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs
    • Kashtan N, Itzkovitz S, Milo R, Alon U (2004) Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 20(11):1745–1758
    • (2004) Bioinformatics , vol.20 , Issue.11 , pp. 1745-1758
    • Kashtan, N.1    Itzkovitz, S.2    Milo, R.3    Alon, U.4
  • 26
    • 84255194431 scopus 로고    scopus 로고
    • Biological network motif detection and evaluation
    • Kim W, Li M, Wang J, Pan Y (2011) Biological network motif detection and evaluation. BMC Syst Biol 5(Suppl 3):S5
    • (2011) BMC Syst Biol , vol.5 , pp. 5
    • Kim, W.1    Li, M.2    Wang, J.3    Pan, Y.4
  • 27
    • 52449085728 scopus 로고    scopus 로고
    • On the origin of distribution patterns of motifs in biological networks
    • Konagurthu AS, Lesk AM (2008a) On the origin of distribution patterns of motifs in biological networks. BMC Syst Biol 2(73)
    • (2008) BMC Syst Biol , vol.2 , Issue.73
    • Konagurthu, A.S.1    Lesk, A.M.2
  • 28
    • 52249117613 scopus 로고    scopus 로고
    • Single and multiple input modules in regulatory networks
    • COI: 1:CAS:528:DC%2BD1cXhtFOisb3M
    • Konagurthu AS, Lesk AM (2008b) Single and multiple input modules in regulatory networks. Proteins Struct Funct Bioinform 73(2):320–324
    • (2008) Proteins Struct Funct Bioinform , vol.73 , Issue.2 , pp. 320-324
    • Konagurthu, A.S.1    Lesk, A.M.2
  • 29
    • 79851515763 scopus 로고    scopus 로고
    • Metabolic reconstruction of the archaeon methanogen Methanosarcina acetivorans
    • Kumar VS, Ferry JG, Marana CD (2011) Metabolic reconstruction of the archaeon methanogen Methanosarcina acetivorans. BMC Syst Biol 5:28
    • (2011) BMC Syst Biol , vol.5 , pp. 28
    • Kumar, V.S.1    Ferry, J.G.2    Marana, C.D.3
  • 31
    • 43549114744 scopus 로고    scopus 로고
    • Alternative methods to safety studies in experimental animals: role in the risk assessment of chemicals under the new European Chemicals Legislation (REACH)
    • COI: 1:CAS:528:DC%2BD1cXjvFKgt7c%3D, PID: 18322675
    • Lilienblum W, Dekant W, Foth H, Gebel T, Hengstler JG, Kahl R, Kramer PJ, Schweinfurth H, Wollin KM (2008) Alternative methods to safety studies in experimental animals: role in the risk assessment of chemicals under the new European Chemicals Legislation (REACH). Arch Toxicol 82:211–223
    • (2008) Arch Toxicol , vol.82 , pp. 211-223
    • Lilienblum, W.1    Dekant, W.2    Foth, H.3    Gebel, T.4    Hengstler, J.G.5    Kahl, R.6    Kramer, P.J.7    Schweinfurth, H.8    Wollin, K.M.9
  • 32
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • COI: 1:CAS:528:DC%2BD2cXnsFaiu74%3D, PID: 15372033
    • Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308–312
    • (2004) Nature , vol.431 , Issue.7006 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 33
    • 13544269611 scopus 로고    scopus 로고
    • An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
    • COI: 1:CAS:528:DC%2BD2MXkt1ansg%3D%3D, PID: 15604458
    • Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, Zeng AP (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucl Acids Res 32(22):6643–6649
    • (2004) Nucl Acids Res , vol.32 , Issue.22 , pp. 6643-6649
    • Ma, H.W.1    Kumar, B.2    Ditges, U.3    Gunzer, F.4    Buer, J.5    Zeng, A.P.6
  • 35
    • 0036765785 scopus 로고    scopus 로고
    • Nuclear pregnane X receptor and constitutive androstane receptor regulate overlapping but distinct sets of genes involved in xenobiotic detoxification
    • COI: 1:CAS:528:DC%2BD38XmsVKmurk%3D, PID: 12181440
    • Maglich JM, Stoltz CM, Goodwin B, Hawkins-Brown D, Moore JT, Kliewer SA (2002) Nuclear pregnane X receptor and constitutive androstane receptor regulate overlapping but distinct sets of genes involved in xenobiotic detoxification. Mol Pharmacol 62:638–646
    • (2002) Mol Pharmacol , vol.62 , pp. 638-646
    • Maglich, J.M.1    Stoltz, C.M.2    Goodwin, B.3    Hawkins-Brown, D.4    Moore, J.T.5    Kliewer, S.A.6
  • 38
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • COI: 1:CAS:528:DC%2BD38XjsFymsr8%3D, PID: 11988575
    • Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296:910–913
    • (2002) Science , vol.296 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2
  • 39
    • 28844434073 scopus 로고    scopus 로고
    • An evolutionary and functional assessment of regulatory network motifs
    • Mazurie A, Bottani S, Vergassola M (2005) An evolutionary and functional assessment of regulatory network motifs. Genome Biol 6(4)
    • (2005) Genome Biol , vol.6 , Issue.4
    • Mazurie, A.1    Bottani, S.2    Vergassola, M.3
  • 40
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: simple building blocks of complex networks
    • COI: 1:CAS:528:DC%2BD38XotFSntb4%3D, PID: 12399590
    • Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298(5594):824–827
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 44
    • 0242559054 scopus 로고    scopus 로고
    • Pathway studio—the analysis and navigation of molecular networks
    • COI: 1:CAS:528:DC%2BD3sXovVelu7k%3D, PID: 14594725
    • Nikitin A, Sergei E, Nikolai D, Ilya M (2003) Pathway studio—the analysis and navigation of molecular networks. Bioinformatics 19(16):2155–2157
    • (2003) Bioinformatics , vol.19 , Issue.16 , pp. 2155-2157
    • Nikitin, A.1    Sergei, E.2    Nikolai, D.3    Ilya, M.4
  • 47
    • 84871284029 scopus 로고    scopus 로고
    • Network reconstruction and systems analysis of cardiac myocyte hypertrophy signaling
    • COI: 1:CAS:528:DC%2BC38Xhslyks73P, PID: 23091058
    • Ryall KA, Holland DO, Delaney KA, Kraeutler MJ, Parker AJ, Saucerman JJ (2012) Network reconstruction and systems analysis of cardiac myocyte hypertrophy signaling. J Biol Chem 287:42259–42268
    • (2012) J Biol Chem , vol.287 , pp. 42259-42268
    • Ryall, K.A.1    Holland, D.O.2    Delaney, K.A.3    Kraeutler, M.J.4    Parker, A.J.5    Saucerman, J.J.6
  • 50
    • 34547555796 scopus 로고    scopus 로고
    • Global and local architecture of the mammalian microRNA-transcription factor regulatory network
    • COI: 1:CAS:528:DC%2BD2sXps1ansLk%3D
    • Shalgi R, Lieber D, Oren M, Pilpel Y (2007) Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol 3(7):1291–1304
    • (2007) PLoS Comput Biol , vol.3 , Issue.7 , pp. 1291-1304
    • Shalgi, R.1    Lieber, D.2    Oren, M.3    Pilpel, Y.4
  • 51
    • 84875852744 scopus 로고    scopus 로고
    • Network motifs provide signatures that characterize metabolism
    • COI: 1:CAS:528:DC%2BC3sXitVequ70%3D, PID: 23287894
    • Shellman ER, Burant CF, Schnell S (2013) Network motifs provide signatures that characterize metabolism. Mol BioSyst 9:352–360
    • (2013) Mol BioSyst , vol.9 , pp. 352-360
    • Shellman, E.R.1    Burant, C.F.2    Schnell, S.3
  • 52
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • COI: 1:CAS:528:DC%2BD38Xjt1Kns70%3D, PID: 11967538
    • Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31:64–68
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 53
    • 77957766590 scopus 로고    scopus 로고
    • SnapShot: network motifs
    • PID: 20946989
    • Shoval O, Alon U (2010) SnapShot: network motifs. Cell 143:326–326e1
    • (2010) Cell , vol.143 , pp. 326-3261
    • Shoval, O.1    Alon, U.2
  • 54
    • 49749111671 scopus 로고    scopus 로고
    • Frequency concepts and pattern detection for the analysis of motifs in networks
    • Shreiber F, Schwöbbermeyer H (2005) Frequency concepts and pattern detection for the analysis of motifs in networks. Trans Comput Syst Biol 3:89–104
    • (2005) Trans Comput Syst Biol , vol.3 , pp. 89-104
    • Shreiber, F.1    Schwöbbermeyer, H.2
  • 57
    • 44349182094 scopus 로고    scopus 로고
    • Post-transcriptional regulation of human pregnane X receptor by micro-RNA affects the expression of cytrochrome P450 3A4
    • COI: 1:CAS:528:DC%2BD1cXkt1aksLs%3D, PID: 18268015
    • Takagi S, Nakajima M, Mohri T, Yokoi T (2008) Post-transcriptional regulation of human pregnane X receptor by micro-RNA affects the expression of cytrochrome P450 3A4. J Biol Chem 283(15):9674–9680
    • (2008) J Biol Chem , vol.283 , Issue.15 , pp. 9674-9680
    • Takagi, S.1    Nakajima, M.2    Mohri, T.3    Yokoi, T.4
  • 59
    • 0016870630 scopus 로고
    • An algorithm for subgraph isomorphism
    • Ullmann JR (1976) An algorithm for subgraph isomorphism. J Assoc Comput Mach 23(1):31–42
    • (1976) J Assoc Comput Mach , vol.23 , Issue.1 , pp. 31-42
    • Ullmann, J.R.1
  • 60
    • 33646153295 scopus 로고    scopus 로고
    • FANMOD: a tool for fast network motif detection
    • COI: 1:CAS:528:DC%2BD28XjslKrsbs%3D, PID: 16455747
    • Wernicke S, Rasche R (2006) FANMOD: a tool for fast network motif detection. Bioinformatics 22(9):1152–1153
    • (2006) Bioinformatics , vol.22 , Issue.9 , pp. 1152-1153
    • Wernicke, S.1    Rasche, R.2
  • 61
    • 84863253706 scopus 로고    scopus 로고
    • Biological network motif detection: principles and practice
    • PID: 22396487
    • Wong E, Baur B, Quader S, Huang CH (2012) Biological network motif detection: principles and practice. Brief Bioinform 13(2):202–205
    • (2012) Brief Bioinform , vol.13 , Issue.2 , pp. 202-205
    • Wong, E.1    Baur, B.2    Quader, S.3    Huang, C.H.4
  • 62
    • 1942469444 scopus 로고    scopus 로고
    • Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction
    • Yeger-Logem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H (2004) Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction. PNAS 101(16):5939
    • (2004) PNAS , vol.101 , Issue.16 , pp. 5939
    • Yeger-Logem, E.1    Sattath, S.2    Kashtan, N.3    Itzkovitz, S.4    Milo, R.5    Pinter, R.Y.6    Alon, U.7    Margalit, H.8


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