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1、蛋白质注释及功能分析蛋白质注释及功能分析 利用基因本体 GO(gene ontology)或者其它的功能注释系统（工具）来分析蛋白质的功能。然后提供蛋白质功能注释的统计分布情况。（如表 1 和图 1 所示）该分析结果可以给出差异表达蛋白质总体的功能分布，从而使研究人员整体上把握疾病与分子功能之间的相关性。Table 1 Protein functional distribution in XXX CategoryBaitsignal transduction93(30.8%)cell differentiation18(6.0%)apoptosis55(18.2%)cell organizat
2、ion and biogenesis20(6.6%)cell proliferation30(9.9%)transcription75(24.8%)transport47(15.6%)development56(18.5%)metabolism222(73.5%)biosynthesis42(13.9%)cytosol31(11.6%)endoplasmic reticulum15(5.6%)cytoskeleton14(5.2%)nucleus132(49.3%)membrane68(25.4%)CategoryBaitsignal transduction93(30.8%)cell dif
3、ferentiation18(6.0%)apoptosis55(18.2%)cell organization and biogenesis20(6.6%)cell proliferation30(9.9%)transcription75(24.8%)transport47(15.6%)development56(18.5%)metabolism222(73.5%)biosynthesis42(13.9%)cytosol31(11.6%)endoplasmic reticulum15(5.6%)cytoskeleton14(5.2%)nucleus132(49.3%)membrane68(25
4、4%)CategoryBaitsignal transduction93(30.8%)cell differentiation18(6.0%)apoptosis55(18.2%)cell organization and biogenesis20(6.6%)cell proliferation30(9.9%)transcription75(24.8%)transport47(15.6%)development56(18.5%)metabolism222(73.5%)biosynthesis42(13.9%)cytosol31(11.6%)endoplasmic reticulum15(5.6
5、)cytoskeleton14(5.2%)nucleus132(49.3%)membrane68(25.4%)#of Protein1%1%1%3%7%2%1%1%2%4%3%3%1%2%11%9%20%2%2%3%1%21%reproduction cell killing immune system process metabolic process cellular process viral reproduction reproductive process biological adhesion multicellular organismal process developmen
6、tal process growth locomotion pigmentation rhythmic process 050100150200250300350400450reproductionimmune system processcellular processreproductive processmulticellular organisma.growthpigmentationpositive regulation of.regulation of biologica.localizationmulti-organism processCategories#of Protein
7、 Figure 1 Protein functional distribution in XXX 以下，引用一些已在文章上发表的关于蛋白质功能分析方面例子：An outline of the functional classification of differentially expressed proteins.A,functional distribution of all 160 identities in different categories.(Dai S et al.Mol Cell Proteomics 2007;6:207-230)Distribution of our d
8、ifferentially expressed protein species with isoforms by function(A)and those identified from mature rice pollen grains(14)(B).(Dai S et al.Mol Cell Proteomics 2007;6:207-230)GO analysis of the identified proteins and phosphoproteins.The identified rice proteins,rice phosphoproteins,Arabidopsis prot
9、eins,and Arabidopsis phosphoproteins are represented by blue,red,green,and purple bars,respectively.A,Cellular localization.B,Molecular function.C,Biological process.（Hirofumi Nakagami et.al.Plant Physiol.Vol.153,2010）附件信息：(如下图所示)在附件文件中，提供每个蛋白质不同层次的 GO 功能注释；以及各个层次 GO 功能所对应的蛋白质分布。蛋白质相互作用网络构建及分析蛋白质相互作
10、用网络构建及分析（一）蛋白质相互作用构建及可视化 蛋白质相互作用网络可视化展示，图中的网络节点可以编辑，直观地展示蛋白质间的相互作用情况，挑选重要蛋白。（A）（B）Figure 2 Visualization of PPI Network in XXX Supporting Evidence for the Protein Interactions:IPI_A IPI_B ProName_A ProName_BScore PPI_DatabaseInterologInteracting_DomainGO_CoannotationGenome_ContextNetwork_Topology IP
11、I00003865IPI00012535 HSPA8 DNAJA1 429446186.8V V V V V V IPI00292026IPI00386448 CEBPD RELA 1320.0 X X V V X X IPI00032179IPI00300407 SERPINC1 SDC2 1.7e-001 X X X X X X IPI00291578IPI00642461 PRPSAP1 PRPS2 1.0 X X X X X X IPI00010320IPI00011857 CBX1 CHAF1B 219.0 V X X V X V IPI00020071IPI00215922 NPM
12、1 NR2E3 152.9 X X V X X X IPI00000144IPI00218158 OXT ESR2 5.9e-001 X X X X X X IPI00299399IPI00465084 S100B DES 454.2 V X V V X V IPI00184584IPI00414264 PSEN2 SRI 152.9 X X V X X X IPI00010320IPI00031519 CBX1 DNMT1 420911.2 V X V V X V IPI00017292IPI00020070 CTNNB1 AR 249.5 X X V V X X IPI00006451IP
13、I00336017 NSF ARRB1 5.9e-001 X X X X X X IPI00006451IPI00031583 NSF VDP 719.7 V X X V X V IPI00005040IPI00395811 ACADM DAZL 2.0e-001 V X X X X X 说明：除了给出蛋白质相互作用的可信度打分，还提供蛋白质相互作用在公共数据库中的信息、相互作用结构域、基因本体共注释等。说明：除了给出蛋白质相互作用的可信度打分，还提供蛋白质相互作用在公共数据库中的信息、相互作用结构域、基因本体共注释等。Statistics Evidence Interactions Subm
14、itted HighConfLR2.0 PPI_DatabaseInterologInteracting_DomainGO_Coannotation#interaction14 9 6 1 7 7 附件信息：在附件信息中详细标出每对蛋白质的相互作用可信度评分，这对蛋白质相互作用的相关数据库参考信息，相互作用结构域等等。（二）蛋白质相互作用网络深入分析（包括拓扑性质、相互作用结构域、重要节点以及网络模块化等）。下图展示了蛋白质相互作用网络模块以及模块间的 crosstalk 节点，这些节点相当于不同生物网络之间通讯的重要“关塞”，可以直观地显现其在药物靶标挖掘方面的潜力。Figure 3 Pathway crosstalks and functional moduls
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