Skip to main content
Top

2015 | OriginalPaper | Chapter

87. Function Annotation of Proteins in Eriocheir sinensis Based on the Protein-Protein Interaction Network

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

Eriocheir sinensis is a highly-commercial aquaculture species as an important aquatic product source. The protein-protein interaction network (PIN) of E. sinensis has been constructed based on the RNA transcriptional sequencing. Many unknown proteins exist in the PIN, which seriously restricts the further mechanism researches on regulation, immunity and development of E. sinensis. In this work, we predicted the functions of the unknown proteins in E. sinensis based on the modularity feature of the PIN. The functions of 677 (93 %) proteins were annotated. The analysis of ribosome module indicates that the annotation of proteins and modules provides important references to be studied in the further in vivo experiment as well as the biological capability of the E. sinensis PIN.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literature
1.
go back to reference Zhang Y, Sun Y, Liu Y, Geng X, Wang X, Wang Y, Sun J, Yang W (2011) Molt-inhibiting hormone from Chinese mitten crab (Eriocheir sinensis): cloning, tissue expression and effects of recombinant peptide on ecdysteroid secretion of YOs. Gen Comp Endocrinol 173:467–474CrossRef Zhang Y, Sun Y, Liu Y, Geng X, Wang X, Wang Y, Sun J, Yang W (2011) Molt-inhibiting hormone from Chinese mitten crab (Eriocheir sinensis): cloning, tissue expression and effects of recombinant peptide on ecdysteroid secretion of YOs. Gen Comp Endocrinol 173:467–474CrossRef
2.
go back to reference Yu AQ, Jin XK, Guo XN, Li S, Wu MH, Li WW, Wang Q (2013) Two novel Toll genes (EsToll1 and EsToll2) from Eriocheir sinensis are differentially induced by lipopolysaccharide, peptidoglycan and zymosan. Fish Shellfish Immunol 35:1282–1292CrossRef Yu AQ, Jin XK, Guo XN, Li S, Wu MH, Li WW, Wang Q (2013) Two novel Toll genes (EsToll1 and EsToll2) from Eriocheir sinensis are differentially induced by lipopolysaccharide, peptidoglycan and zymosan. Fish Shellfish Immunol 35:1282–1292CrossRef
3.
go back to reference Yanhua Wang YZ, Sun Y, Liu Y, Geng X, Sun J (2013) Cloning and molecular structure analysis of crustacean hyperglycemic hormone (Ers-CHH) in Eriocheir sinensis. J Fish China 37:987–993CrossRef Yanhua Wang YZ, Sun Y, Liu Y, Geng X, Sun J (2013) Cloning and molecular structure analysis of crustacean hyperglycemic hormone (Ers-CHH) in Eriocheir sinensis. J Fish China 37:987–993CrossRef
4.
go back to reference Li X, Cui Z, Liu Y, Song C, Shi G (2013) Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis. PLoS One 8:e68233CrossRef Li X, Cui Z, Liu Y, Song C, Shi G (2013) Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis. PLoS One 8:e68233CrossRef
5.
go back to reference Hao T, Zeng Z, Wang B, Zhang Y, Liu Y, Geng X, Sun J (2014) The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis. BMC Syst Biol 8 Hao T, Zeng Z, Wang B, Zhang Y, Liu Y, Geng X, Sun J (2014) The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis. BMC Syst Biol 8
6.
go back to reference Mosca R, Pons T, Ceol A, Valencia A, Aloy P (2013) Towards a detailed atlas of protein-protein interactions. Curr Opin Struct Biol 23(6):929–940 Mosca R, Pons T, Ceol A, Valencia A, Aloy P (2013) Towards a detailed atlas of protein-protein interactions. Curr Opin Struct Biol 23(6):929–940
7.
go back to reference Chen B, Fan W, Liu J, Wu FX (2014) Identifying protein complexes and functional modules from static PPI networks to dynamic PPI networks. Brief Bioinform 15(2):177–194 Chen B, Fan W, Liu J, Wu FX (2014) Identifying protein complexes and functional modules from static PPI networks to dynamic PPI networks. Brief Bioinform 15(2):177–194
8.
go back to reference Navlakha S, Gitter A, Bar-Joseph Z (2012) A network-based approach for predicting missing pathway interactions. PLoS Comput Biol 8:e1002640CrossRef Navlakha S, Gitter A, Bar-Joseph Z (2012) A network-based approach for predicting missing pathway interactions. PLoS Comput Biol 8:e1002640CrossRef
9.
go back to reference Zeng E, Ding C, Narasimhan G, Holbrook SR (2008) Estimating support for protein-protein interaction data with applications to function prediction. Comput Syst Bioinformatics Conf 7:73–84 Zeng E, Ding C, Narasimhan G, Holbrook SR (2008) Estimating support for protein-protein interaction data with applications to function prediction. Comput Syst Bioinformatics Conf 7:73–84
10.
go back to reference Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S (2011) A protein complex network of Drosophila melanogaster. Cell 147:690–703CrossRef Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S (2011) A protein complex network of Drosophila melanogaster. Cell 147:690–703CrossRef
11.
go back to reference Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castano-Diez D, Chen WH, Devos D, Guell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Bottcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC (2009) Proteome organization in a genome-reduced bacterium. Science 326:1235–1240CrossRef Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castano-Diez D, Chen WH, Devos D, Guell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Bottcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC (2009) Proteome organization in a genome-reduced bacterium. Science 326:1235–1240CrossRef
12.
go back to reference Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7:e96CrossRef Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7:e96CrossRef
13.
go back to reference Schwikowski B, Uetz P, Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18:1257–1261CrossRef Schwikowski B, Uetz P, Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18:1257–1261CrossRef
14.
go back to reference Kim KK, Kim HB (2009) Protein interaction network related to Helicobacter pylori infection response. World J Gastroenterol 15:4518–4528CrossRef Kim KK, Kim HB (2009) Protein interaction network related to Helicobacter pylori infection response. World J Gastroenterol 15:4518–4528CrossRef
15.
go back to reference Marchadier E, Carballido-Lopez R, Brinster S, Fabret C, Mervelet P, Bessieres P, Noirot-Gros MF, Fromion V, Noirot P (2011) An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: exploration by an integrative approach. Proteomics 11:2981–2991CrossRef Marchadier E, Carballido-Lopez R, Brinster S, Fabret C, Mervelet P, Bessieres P, Noirot-Gros MF, Fromion V, Noirot P (2011) An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: exploration by an integrative approach. Proteomics 11:2981–2991CrossRef
16.
go back to reference Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623–627CrossRef Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623–627CrossRef
17.
go back to reference Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP et al (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322:104–110CrossRef Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP et al (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322:104–110CrossRef
18.
go back to reference Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY et al (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173–1178CrossRef Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY et al (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173–1178CrossRef
19.
go back to reference Garrido C, Brunet M, Didelot C, Zermati Y, Schmitt E, Kroemer G (2006) Heat shock proteins 27 and 70: anti-apoptotic proteins with tumorigenic properties. Cell Cycle 5:2592–2601CrossRef Garrido C, Brunet M, Didelot C, Zermati Y, Schmitt E, Kroemer G (2006) Heat shock proteins 27 and 70: anti-apoptotic proteins with tumorigenic properties. Cell Cycle 5:2592–2601CrossRef
Metadata
Title
Function Annotation of Proteins in Eriocheir sinensis Based on the Protein-Protein Interaction Network
Authors
Tong Hao
Ailing Yu
Bin Wang
Anan Liu
Jinsheng Sun
Copyright Year
2015
DOI
https://doi.org/10.1007/978-3-319-08991-1_87