Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology

Molecular Biotechnology

Volumn 48, Issue 1, 2011, Pages 87-95

  Goel, Renu ^a,b   Muthusamy, Babylakshmi ^a,c   Pandey, Akhilesh ^d   Prasad, T S Keshava ^a,c  

^a Institute of Bioinformatics   (India)

^b KUVEMPU UNIVERSITY   (India)

^c PONDICHERRY UNIVERSITY   (India)

^d JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Bioinformatics; Disease markers; Mass spectrometry; Molecular diagnostics; Signaling pathways

Indexed keywords

BIOLOGICAL DATA; BIOLOGICAL RESEARCH; CELLULAR SYSTEM; COMMUNITY PARTICIPATION; DATA GENERATION; DATA RESOURCES; DATA SHARING; DISEASE MARKERS; GENERATION TECHNOLOGIES; GENOMICS; HIGH THROUGHPUT; HUMAN PROTEINS; MOLECULAR BIOTECHNOLOGY; MOLECULAR DIAGNOSTICS; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN-PROTEIN INTERACTIONS; PROTEOMICS; REFERENCE DATABASE; SENSITIVITY AND SPECIFICITY; SIGNALING PATHWAYS; SMALL SCALE; SUBCELLULAR LOCALIZATIONS; TISSUE EXPRESSION; TRANSCRIPTOMICS;

BIOINFORMATICS; BIOTECHNOLOGY; CLONING; DATA HANDLING; DATABASE SYSTEMS; INFORMATION DISSEMINATION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS; THROUGHPUT; TISSUE;

SCAFFOLDS (BIOLOGY);

PROTEIN;

BIOINFORMATICS; BIOTECHNOLOGY; DATA BASE; HUMAN PROTEIN REFERENCE DATABASE; HUMAN PROTEINPEDIA; REVIEW;

BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MASS SPECTROMETRY; SIGNAL TRANSDUCTION;

EID: 79955917527     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-010-9336-8     Document Type: Review

References (109)

1. H Yu P Braun MA Yildirim I Lemmens K Venkatesan J Sahalie T Hirozane-Kishikawa F Gebreab N Li N Simonis, et al. 2008 High-quality binary protein interaction map of the yeast interactome network Science 322 104 110 1:CAS:528:DC%2BD1cXhtFyhurbM
2. M Kawasumi P Nghiem 2007 Chemical genetics: Elucidating biological systems with small-molecule compounds Journal of Investigative Dermatology 127 1577 1:CAS:528:DC%2BD2sXms1Slur4%3D
3. JS Shim HJ Kwon 2004 Chemical genetics for therapeutic target mining Expert Opinion on Therapeutic Targets 8 653 661 1:CAS:528:DC%2BD2MXmt1ehsw%3D%3D (Pubitemid 40028373)
4. A Dupre L Boyer-Chatenet RM Sattler AP Modi J-H Lee ML Nicolette L Kopelovich M Jasin R Baer TT Paull, et al. 2008 A forward chemical genetic screen reveals an inhibitor of the Mre11-Rad50-Nbs1 complex Nature Chemical Biology 4 119 1:CAS:528:DC%2BD1cXnt1ClsQ%3D%3D
5. H Koga 2006 Establishment of the platform for reverse chemical genetics targeting novel protein-protein interactions Molecular BioSystems 2 159 164 1:CAS:528:DC%2BD28XjvFOjsLg%3D (Pubitemid 43373974)
6. R Chaerkady A Pandey 2008 Applications of proteomics to lab diagnosis Annual Review of Pathology: Mechanisms of Disease 3 485 498 1:CAS:528: DC%2BD1cXjsFersLc%3D (Pubitemid 351488290)
7. R Chaerkady HC Harsha A Nalli M Gucek P Vivekanandan J Akhtar RN Cole J Simmers RD Schulick S Singh, et al. 2008 A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma Journal of Proteome Research 7 4289 4298 1:CAS:528:DC%2BD1cXhtVSrtLbI
8. M Gronborg TZ Kristiansen A Iwahori R Chang R Reddy N Sato H Molina ON Jensen RH Hruban MG Goggins, et al. 2006 Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach Molecular and Cellular Proteomics 5 157 171 1:CAS:528:DC%2BD28Xms1aqsg%3D%3D (Pubitemid 43169348)
9. M Vermeulen NC Hubner M Mann 2008 High confidence determination of specific protein-protein interactions using quantitative mass spectrometry Current Opinion in Biotechnology 19 331 1:CAS:528:DC%2BD1cXhtValsL7I
10. F Leitner M Krallinger C Rodriguez-Penagos J Hakenberg C Plake CJ Kuo CN Hsu RT Tsai HC Hung WW Lau, et al. 2008 Introducing meta-services for biomedical information extraction Genome Biology 9 Suppl 2 S6
11. S Orchard H Hermjakob R Apweiler 2005 Annotating the human proteome Molecular and Cellular Proteomics 4 435 440 1:CAS:528:DC%2BD2MXjtFCisLs%3D (Pubitemid 40590563)
12. M Mueller L Martens R Apweiler 2007 Annotating the human proteome: Beyond establishing a parts list Biochimica et Biophysica Acta (BBA)-Proteins & Proteomics 1774 175 1:CAS:528:DC%2BD2sXhs1Cgsbc%3D
13. S Orchard H Hermjakob 2008 The HUPO proteomics standards initiative-Easing communication and minimizing data loss in a changing world Briefings in Bioinformatics 9 166 173 1:CAS:528:DC%2BD1cXmtFKqsrs%3D (Pubitemid 351517002)
14. S Peri JD Navarro R Amanchy TZ Kristiansen CK Jonnalagadda V Surendranath V Niranjan B Muthusamy TK Gandhi M Gronborg, et al. 2003 Development of human protein reference database as an initial platform for approaching systems biology in humans Genome Research 13 2363 2371 1:CAS:528:DC%2BD3sXps1yls7Y%3D (Pubitemid 37266003)
15. S Peri JD Navarro TZ Kristiansen R Amanchy V Surendranath B Muthusamy TK Gandhi KN Chandrika N Deshpande S Suresh, et al. 2004 Human protein reference database as a discovery resource for proteomics Nucleic Acids Research 32 D497 D501 1:CAS:528:DC%2BD3sXhtVSrurvF
16. GR Mishra M Suresh K Kumaran N Kannabiran S Suresh P Bala K Shivakumar N Anuradha R Reddy TM Raghavan, et al. 2006 Human protein reference database-2006 update Nucleic Acids Research 34 D411 D414 1:CAS:528:DC%2BD28XisFymtg%3D%3D
17. TSK Prasad R Goel K Kandasamy S Keerthikumar S Kumar S Mathivanan D Telikicherla R Raju B Shafreen A Venugopal, et al. 2009 Human protein reference database-2009 update Nucleic Acids Research 37 D767 D772 1:CAS:528: DC%2BD1cXhsFejtLvL
18. DL Wheeler T Barrett DA Benson SH Bryant K Canese V Chetvernin DM Church M Dicuccio R Edgar S Federhen, et al. 2008 Database resources of the National Center for Biotechnology Information Nucleic Acids Research 36 D13 D21 1:CAS:528:DC%2BD1cXhtVSqtL8%3D (Pubitemid 351149689)
19. S Mathivanan B Periaswamy TK Gandhi K Kandasamy S Suresh R Mohmood YL Ramachandra A Pandey 2006 An evaluation of human protein-protein interaction data in the public domain BMC Bioinformatics 7 Suppl 5 S19
20. A Ceol A Chatr Aryamontri L Licata D Peluso L Briganti L Perfetto L Castagnoli G Cesareni 2010 MINT, the molecular interaction database: 2009 update Nucleic Acids Research 38 D532 D539 1:CAS:528:DC%2BC3cXktlOqug%3D%3D
21. B Aranda P Achuthan Y Alam-Faruque I Armean A Bridge C Derow M Feuermann AT Ghanbarian S Kerrien J Khadake, et al. 2010 The IntAct molecular interaction database in 2010 Nucleic Acids Research 38 D525 D531 1:CAS:528: DC%2BC3cXktlKkuw%3D%3D
22. C Alfarano CE Andrade K Anthony N Bahroos M Bajec K Bantoft D Betel B Bobechko K Boutilier E Burgess, et al. 2005 The biomolecular interaction network database and related tools 2005 update Nucleic Acids Research 33 D418 D424 1:CAS:528:DC%2BD2MXisVChsw%3D%3D (Pubitemid 40207907)
23. L Salwinski CS Miller AJ Smith FK Pettit JU Bowie D Eisenberg 2004 The database of interacting proteins: 2004 update Nucleic Acids Research 32 D449 D451 1:CAS:528:DC%2BD3sXhtVSrurnJ (Pubitemid 38081696)
24. P Pagel S Kovac M Oesterheld B Brauner I Dunger-Kaltenbach G Frishman C Montrone P Mark V Stumpflen H-W Mewes, et al. 2005 The MIPS mammalian protein-protein interaction database Bioinformatics 21 832 834 1:CAS:528:DC%2BD2MXit1Knt7s%3D (Pubitemid 40439425)
25. T Beuming L Skrabanek MY Niv P Mukherjee H Weinstein 2005 PDZBase: A protein-protein interaction database for PDZ-domains Bioinformatics 21 827 828 1:CAS:528:DC%2BD2MXit1Knt78%3D (Pubitemid 40439423)
26. H Hermjakob L Montecchi-Palazzi G Bader J Wojcik L Salwinski A Ceol S Moore S Orchard U Sarkans C von Mering, et al. 2004 The HUPO PSI's molecular interaction format[mdash]a community standard for the representation of protein interaction data Nature Biotechnology 22 177 1:CAS:528:DC%2BD2cXnvFeisA%3D%3D
27. S Kerrien S Orchard L Montecchi-Palazzi B Aranda AF Quinn N Vinod GD Bader I Xenarios J Wojcik D Sherman, et al. 2007 Broadening the horizon-Level 2.5 of the HUPO-PSI format for molecular interactions BMC Biology 5 44
28. SG John 2004 The RESID database of protein modifications as a resource and annotation tool Proteomics 4 1527 1533
29. M Ashburner CA Ball JA Blake D Botstein H Butler JM Cherry AP Davis K Dolinski SS Dwight JT Eppig, et al. 2000 Gene ontology: Tool for the unification of biology Nature Genetics 25 25 1:CAS:528:DC%2BD3cXjtFSlsbc%3D
30. J Kelso J Visagie G Theiler A Christoffels S Bardien D Smedley D Otgaar G Greyling CV Jongeneel MI McCarthy, et al. 2003 eVOC: A controlled vocabulary for unifying gene expression data Genome Research 13 1222 1230 1:CAS:528:DC%2BD3sXksFegsrc%3D (Pubitemid 36764202)
31. TK Gandhi J Zhong S Mathivanan L Karthick KN Chandrika SS Mohan S Sharma S Pinkert S Nagaraju B Periaswamy, et al. 2006 Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets Nature Genetics 38 285 293 1:CAS:528:DC%2BD28XhslCjt70%3D
32. DR Rhodes SA Tomlins S Varambally V Mahavisno T Barrette S Kalyana-Sundaram D Ghosh A Pandey AM Chinnaiyan 2005 Probabilistic model of the human protein-protein interaction network Nature Biotechnology 23 951 959 1:CAS:528:DC%2BD2MXntVSrtr8%3D (Pubitemid 41114028)
33. W Ali CM Deane 2009 Functionally guided alignment of protein interaction networks for module detection Bioinformatics 25 3166 3173 1:CAS:528: DC%2BD1MXhsVGlsLbF
34. Fernandes, L. P., Annibale, A., Kleinjung, J., Coolen, A. C. & Fraternali, F. (2010). Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. PLoS One, 5, e12083.
35. A Ozgur Z Xiang DR Radev Y He 2010 Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks Journal of Biomedicine and Biotechnology 2010 426479
36. JF Rual K Venkatesan T Hao T Hirozane-Kishikawa A Dricot N Li GF Berriz FD Gibbons M Dreze N Ayivi-Guedehoussou, et al. 2005 Towards a proteome-scale map of the human protein-protein interaction network Nature 437 1173 1178 1:CAS:528:DC%2BD2MXhtFahtLzP (Pubitemid 41509356)
37. U Stelzl U Worm M Lalowski C Haenig FH Brembeck H Goehler M Stroedicke M Zenkner A Schoenherr S Koeppen, et al. 2005 A human protein-protein interaction network: A resource for annotating the proteome Cell 122 957 968 1:CAS:528:DC%2BD2MXhtVOrurbK (Pubitemid 41345212)
38. MA Pujana JD Han LM Starita KN Stevens M Tewari JS Ahn G Rennert V Moreno T Kirchhoff B Gold, et al. 2007 Network modeling links breast cancer susceptibility and centrosome dysfunction Nature Genetics 39 1338 1349 1:CAS:528:DC%2BD2sXht1aqurbJ (Pubitemid 350035000)
39. S Navlakha C Kingsford 2010 The power of protein interaction networks for associating genes with diseases Bioinformatics 26 1057 1063 1:CAS:528:DC%2BC3cXkvVOqsr0%3D
40. S Suthram JT Dudley AP Chiang R Chen TJ Hastie AJ Butte 2010 Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets PLoS Computational Biology 6 e1000662
41. S Zhao S Li 2010 Network-based relating pharmacological and genomic spaces for drug target identification PLoS One 5 e11764
42. R Sompallae S Callegari SA Kamranvar MG Masucci 2010 Transcription profiling of Epstein-Barr virus nuclear antigen (EBNA)-1 expressing cells suggests targeting of chromatin remodeling complexes PLoS One 5 e12052
43. D van Dijk G Ertaylan CA Boucher PM Sloot 2010 Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks BMC Systems Biology 4 96
44. JA Miller S Horvath DH Geschwind 2010 Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways Proceedings of the National Academy of Sciences USA 107 12698 12703 1:CAS:528:DC%2BC3cXpt1Shuro%3D
45. SK Yang YC Wang CC Chao YJ Chuang CY Lan BS Chen 2010 Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFalpha-induced inflammatory responses BMC Medical Genomics 3 19
46. AH Qureshi V Chaoji D Maiguel MH Faridi CJ Barth SM Salem M Singhal D Stoub B Krastins M Ogihara, et al. 2009 Proteomic and phospho-proteomic profile of human platelets in basal, resting state: Insights into integrin signaling PLoS One 4 e7627
47. E Mosca G Bertoli E Piscitelli L Vilardo RA Reinbold I Zucchi L Milanesi 2009 Identification of functionally related genes using data mining and data integration: A breast cancer case study BMC Bioinformatics 10 Suppl 12 S8
48. SA Cain A McGovern E Small LJ Ward C Baldock A Shuttleworth CM Kielty 2009 Defining elastic fiber interactions by molecular fishing: An affinity purification and mass spectrometry approach Molecular and Cellular Proteomics 8 2715 2732 1:CAS:528:DC%2BD1MXhsFOgsL7O
49. S Keerthikumar S Bhadra K Kandasamy R Raju YL Ramachandra C Bhattacharyya K Imai O Ohara S Mohan A Pandey 2009 Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach DNA Research 16 345 351 1:CAS:528:DC%2BD1MXhsV2jsbzK
50. Y Liu A Tozeren 2010 Modular composition predicts kinase/substrate interactions BMC Bioinformatics 11 349 1:CAS:528:DC%2BC3cXht1KgsbfJ
51. H Blankenburg RD Finn A Prlic AM Jenkinson F Ramirez D Emig SE Schelhorn J Buch T Lengauer M Albrecht 2009 DASMI: Exchanging, annotating and assessing molecular interaction data Bioinformatics 25 1321 1328 1:CAS:528: DC%2BD1MXlslGgt7Y%3D
52. H Blankenburg F Ramirez J Buch M Albrecht 2009 DASMIweb: Online integration, analysis and assessment of distributed protein interaction data Nucleic Acids Research 37 W122 W128 1:CAS:528:DC%2BD1MXosFSrsL4%3D
53. Sun, C. H., Hwang, T., Oh, K. & Yi, G. S. (2010). DynaMod: Dynamic functional modularity analysis. Nucleic Acids Research, 38 Suppl, W103-W108.
54. U Dogrusoz A Cetintas E Demir O Babur 2009 Algorithms for effective querying of compound graph-based pathway databases BMC Bioinformatics 10 376
55. SA Lee CH Chan TC Chen CY Yang KC Huang CH Tsai JM Lai FS Wang CY Kao CY Huang 2009 POINeT: Protein interactome with sub-network analysis and hub prioritization BMC Bioinformatics 10 114
56. M Klammer K Godl A Tebbe C Schaab 2010 Identifying differentially regulated subnetworks from phosphoproteomic data BMC Bioinformatics 11 351
57. D Banky R Ordog V Grolmusz 2009 NASCENT: An automatic protein interaction network generation tool for non-model organisms Bioinformation 3 361 363
58. A Kamburov C Wierling H Lehrach R Herwig 2008 ConsensusPathDB-A database for integrating human functional interaction networks Nucleic Acids Research 37 D623 D628
59. Z Hu ES Snitkin C DeLisi 2008 VisANT: An integrative framework for networks in systems biology Briefings in Bioinformatics 9 317 325 1:CAS:528:DC%2BD1cXpt1artrY%3D (Pubitemid 351890828)
60. SI Berger JM Posner A Ma'ayan 2007 Genes2Networks: Connecting lists of gene symbols using mammalian protein interactions databases BMC Bioinformatics 8 372
61. A Barsky JL Gardy RE Hancock T Munzner 2007 Cerebral: A cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation Bioinformatics 23 1040 1042 1:CAS:528: DC%2BD2sXmtVKqtbg%3D (Pubitemid 47050596)
62. I Avila-Campillo K Drew J Lin DJ Reiss R Bonneau 2007 BioNetBuilder: Automatic integration of biological networks Bioinformatics 23 392 393 1:CAS:528:DC%2BD2sXhtlOlur8%3D (Pubitemid 46323169)
63. T Obayashi S Hayashi M Shibaoka M Saeki H Ohta K Kinoshita 2008 COXPRESdb: A database of coexpressed gene networks in mammals Nucleic Acids Research 36 D77 D82 1:CAS:528:DC%2BD1cXhtVSrsL0%3D
64. LJ Jensen M Kuhn M Stark S Chaffron C Creevey J Muller T Doerks P Julien A Roth M Simonovic, et al. 2008 STRING 8-A global view on proteins and their functional interactions in 630 organisms Nucleic Acids Research 37 D412 D416
65. G Chaurasia Y Iqbal C Hanig H Herzel EE Wanker ME Futschik 2007 UniHI: An entry gate to the human protein interactome Nucleic Acids Research 35 D590 D594 1:CAS:528:DC%2BD2sXivFGltw%3D%3D
66. R Zaidel-Bar S Itzkovitz A Ma'ayan R Iyengar B Geiger 2007 Functional atlas of the integrin adhesome Nature Cell Biology 9 858 867 1:CAS:528:DC%2BD2sXosVSlt7g%3D (Pubitemid 47190436)
67. A Subramanian P Tamayo VK Mootha S Mukherjee BL Ebert MA Gillette A Paulovich SL Pomeroy TR Golub ES Lander, et al. 2005 Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proceedings of the National Academy of Sciences USA 102 15545 15550 1:CAS:528:DC%2BD2MXht1ShtrnO (Pubitemid 41528093)
68. Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T. et al. (2010). The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research, 38 Suppl, W214-W220.
69. AM Newman JB Cooper 2010 AutoSOME: A clustering method for identifying gene expression modules without prior knowledge of cluster number BMC Bioinformatics 11 117
70. CM Gould F Diella A Via P Puntervoll C Gemund S Chabanis-Davidson S Michael A Sayadi JC Bryne C Chica, et al. 2010 ELM: The status of the 2010 eukaryotic linear motif resource Nucleic Acids Research 38 D167 D180 1:CAS:528:DC%2BC3cXktlyjuw%3D%3D
71. RJ Edwards NE Davey DC Shields 2008 CompariMotif: Quick and easy comparisons of sequence motifs Bioinformatics 24 1307 1309 1:CAS:528: DC%2BD1cXlslylurg%3D (Pubitemid 351659630)
72. RJ Edwards NE Davey DC Shields 2007 SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins PLoS ONE 2 e967
73. CY Yang CH Chang YL Yu TC Lin SA Lee CC Yen JM Yang JM Lai YR Hong TL Tseng, et al. 2008 PhosphoPOINT: A comprehensive human kinase interactome and phospho-protein database Bioinformatics 24 i14 i20
74. W Gong D Zhou Y Ren Y Wang Z Zuo Y Shen F Xiao Q Zhu A Hong X Zhou, et al. 2008 PepCyber:P PEP: A database of human protein-protein interactions mediated by phosphoprotein-binding domains Nucleic Acids Research 36 D679 D683 1:CAS:528:DC%2BD1cXhtVWjurY%3D (Pubitemid 351149806)
75. Y Xue J Ren X Gao C Jin L Wen X Yao 2008 GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy Molecular and Cellular Proteomics 7 1598 1608 1:CAS:528:DC%2BD1cXhtFantL%2FP
76. S Keerthikumar R Raju K Kandasamy A Hijikata S Ramabadran L Balakrishnan M Ahmed S Rani LDN Selvan DS Somanathan, et al. 2008 RAPID: Resource of Asian primary immunodeficiency diseases Nucleic Acids Research 37 D863 D867
77. AS Syed M D'Antonio FD Ciccarelli 2010 Network of cancer genes: A web resource to analyze duplicability, orthology and network properties of cancer genes Nucleic Acids Research 38 D670 D675 1:CAS:528:DC%2BC3cXktlKjtQ%3D%3D
78. L Wang Y Xiong Y Sun Z Fang L Li H Ji T Shi 2010 HLungDB: An integrated database of human lung cancer research Nucleic Acids Research 38 D665 D669 1:CAS:528:DC%2BC3cXktlKlsA%3D%3D
79. X Gong R Wu Y Zhang W Zhao L Cheng Y Gu L Zhang J Wang J Zhu Z Guo 2010 Extracting consistent knowledge from highly inconsistent cancer gene data sources BMC Bioinformatics 11 76
80. E Chautard L Ballut N Thierry-Mieg S Ricard-Blum 2009 MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions Bioinformatics 25 690 691 1:CAS:528:DC%2BD1MXisFeksrg%3D
81. JO Yang WY Kim SY Jeong JH Oh S Jho J Bhak NS Kim 2009 PDbase: A database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs BMC Genomics 10 Suppl 3 S32
82. R Nogales-Cadenas F Abascal J Diez-Perez JM Carazo A Pascual-Montano 2008 CentrosomeDB: A human centrosomal proteins database Nucleic Acids Research 37 D175 D180
83. CJ Richardson Q Gao C Mitsopoulous M Zvelebil LH Pearl FMG Pearl 2008 MoKCa database-Mutations of kinases in cancer Nucleic Acids Research 37 D824 D831
84. Y Igarashi A Eroshkin S Gramatikova K Gramatikoff Y Zhang JW Smith AL Osterman A Godzik 2007 CutDB: A proteolytic event database Nucleic Acids Research 35 D546 D549 1:CAS:528:DC%2BD2sXivFGlsw%3D%3D
85. T Shtatland D Guettler M Kossodo M Pivovarov R Weissleder 2007 PepBank-A database of peptides based on sequence text mining and public peptide data sources BMC Bioinformatics 8 280
86. C-Y Li Q-R Liu P-W Zhang X-M Li L Wei GR Uhl 2008 OKCAM: An ontology-based, human-centered knowledgebase for cell adhesion molecules Nucleic Acids Research 37 D251 D260
87. EM Hulbert LJ Smink EC Adlem JE Allen DB Burdick OS Burren VM Cassen CC Cavnor GE Dolman D Flamez, et al. 2007 T1DBase: Integration and presentation of complex data for type 1 diabetes research Nucleic Acids Research 35 D742 D746 1:CAS:528:DC%2BD2sXivFKgtg%3D%3D (Pubitemid 46056302)
88. A Hijikata R Raju S Keerthikumar S Ramabadran L Balakrishnan SK Ramadoss A Pandey S Mohan O Ohara 2010 Mutation@A Glance: An integrative web application for analysing mutations from human genetic diseases DNA Research 17 197 208 1:CAS:528:DC%2BC3cXns1yltr8%3D
89. K Kandasamy SS Mohan R Raju S Keerthikumar GS Kumar AK Venugopal D Telikicherla JD Navarro S Mathivanan C Pecquet, et al. 2010 NetPath: A public resource of curated signal transduction pathways Genome Biology 11 R3
90. R Amanchy B Periaswamy S Mathivanan R Reddy SG Tattikota A Pandey 2007 A curated compendium of phosphorylation motifs Nature Biotechnology 25 285 286 1:CAS:528:DC%2BD2sXisFynsro%3D
91. S Mathivanan M Ahmed NG Ahn H Alexandre R Amanchy PC Andrews JS Bader BM Balgley M Bantscheff KL Bennett, et al. 2008 Human Proteinpedia enables sharing of human protein data Nature Biotechnology 26 164 167 1:CAS:528: DC%2BD1cXhs1KhtLs%3D (Pubitemid 351225942)
92. K Kandasamy S Keerthikumar R Goel S Mathivanan N Patankar B Shafreen S Renuse H Pawar YL Ramachandra PK Acharya, et al. 2009 Human Proteinpedia: A unified discovery resource for proteomics research Nucleic Acids Research 37 D773 D781 1:CAS:528:DC%2BD1cXhsFejt7bM
93. TS Prasad K Kandasamy A Pandey 2009 Human protein reference database and human proteinpedia as discovery tools for systems biology Methods in Molecular Biology 577 67 79 1:CAS:528:DC%2BC3cXjvVOrsg%3D%3D
94. M Krzywinski J Schein I Birol J Connors R Gascoyne D Horsman SJ Jones MA Marra 2009 Circos: An information aesthetic for comparative genomics Genome Research 19 1639 1645 1:CAS:528:DC%2BD1MXhtFCjsLvJ
95. B Kuster M Schirle P Mallick R Aebersold 2005 Scoring proteomes with proteotypic peptide probes Nature Reviews Molecular Cell Biology 6 577 1:CAS:528:DC%2BD2MXmtFOhs7o%3D
96. R Craig JP Cortens RC Beavis 2005 The use of proteotypic peptide libraries for protein identification Rapid Communications in Mass Spectrometry 19 1844 1850 1:CAS:528:DC%2BD2MXmtVegt7c%3D (Pubitemid 40886710)
97. A Wolf-Yadlin S Hautaniemi DA Lauffenburger FM White 2007 Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks Proceedings of the National Academy of Sciences USA 104 5860 5865 1:CAS:528:DC%2BD2sXkt1Kgt7w%3D (Pubitemid 47175624)
98. L Anderson CL Hunter 2006 Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins Molecular and Cellular Proteomics 5 573 588 1:CAS:528:DC%2BD28XjsVCmtb8%3D
99. H Koc JA Swenberg 2002 Applications of mass spectrometry for quantitation of DNA adducts Journal of Chromatography B 778 323 1:CAS:528: DC%2BD38XovF2nt7g%3D
100. M Thevis G Opfermann W Schanzer 2001 High speed determination of beta-receptor blocking agents in human urine by liquid chromatography/tandem mass spectrometry Biomedical Chromatography 15 393 402 1:CAS:528: DC%2BD3MXnt1yjtbk%3D (Pubitemid 32895619)
101. ENM Ho DKK Leung TSM Wan NH Yu 2006 Comprehensive screening of anabolic steroids, corticosteroids, and acidic drugs in horse urine by solid-phase extraction and liquid chromatography-mass spectrometry Journal of Chromatography A 1120 38 1:CAS:528:DC%2BD28XmtV2qtbk%3D
102. G Herrin HHH McCurdy WH Wall 2005 Investigation of an LCMSMS (QTrap) method for the rapid screening and identification of drugs in postmortem toxicology whole blood samples Journal of Analytical Toxicology 29 599 1:CAS:528:DC%2BD2MXhtFChsL7M
103. F Guan CE Uboh LR Soma Y Luo J Rudy T Tobin 2005 Detection, quantification and confirmation of anabolic steroids in equine plasma by liquid chromatography and tandem mass spectrometry Journal of Chromatography B 829 56 1:CAS:528:DC%2BD2MXhtlags7jN
104. L Hua W Jiang K Eric C Wendy C Betty DJ Michael ON Steve RC Karl K Johann H Fritz, et al. 2004 Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis Arthritis and Rheumatism 50 3792 3803
105. MK Gupta JW Jung SJ Uhm H Lee HT Lee KP Kim 2009 Combining selected reaction monitoring with discovery proteomics in limited biological samples Proteomics 9 4834 4836 1:CAS:528:DC%2BD1MXhtleqtbnE
106. MA Kuzyk D Smith J Yang TJ Cross AM Jackson DB Hardie NL Anderson CH Borchers 2009 Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma Molecular and Cellular Proteomics 8 1860 1877 1:CAS:528:DC%2BD1MXhtVSjtbjM
107. P Picotti O Rinner R Stallmach F Dautel T Farrah B Domon H Wenschuh R Aebersold 2010 High-throughput generation of selected reaction-monitoring assays for proteins and proteomes Nature Methods 7 43 46 1:CAS:528:DC%2BD1MXhsFWksb7K
108. Editorial 2007 Democratizing proteomics data Nature Biotechnology 25 262
109. Editorial 2008 Thou shalt share your data Nature Methods 5 209