PROTEOME < Library - BIOBASE Biological Databases

User Publications

Disease, Pathway and Human Genomics Publications

Genome regions identified by overlapping clusters of nominally-positive SNPs from genome-wide studies of alcohol and illegal substance dependence.

Johnson C, Drgon T, Walther D, Uhl GR.
PLoS One. 2011;6(7):e19210. Epub 2011 Jul 27.

A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition.

Shimamura T, Imoto S, Shimada Y, Hosono Y, Niida A, Nagasaki M, Yamaguchi R, Takahashi T, Miyano S.
PLoS One. 2011;6(6):e20804. Epub 2011 Jun 7.

Survey of activated FLT3 signaling in leukemia.

Gu TL, Nardone J, Wang Y, Loriaux M, Villen J, Beausoleil S, Tucker M, Komhauser J, Ren J, Macneill J, Gygi SP, Druker BJ, Heinrich MC, Rush J, Polakiewicz RD.
PLoS One. 2011 Apr 28. 6(4):e19169.

Stimulatory effect of Echinacea purpurea extract on the trafficking activity of mouse dendritic cells: revealed by genomic and proteomic analysis.

Yin SY, Wang WH, Wang BX, Aravindaram K, Hwang PI, Wu HM, Yang NS.
BMC Genomics. 2010 Nov 1. 11:612.

The BioPAX community standard for pathway data sharing.

Demir E, Cary MP, Paley S, Fukuda K, Lemur C, Vastrik I, Wu G, D’Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, plus 77 additional authors.
Nat Biotechnol. 2010 Sep 28. 28(9):935-42. Epub 2010 Sep 9.

The normal breast microenvironment of premenopausal women differentially influences the behavior or breast cancer cells in vitro and in vivo.

Fleming JM, Miller TC, Quinones M, Xiao Z, Xu X, Meyer MJ, Ginsburg E, Veenstra TD, Vonderhaar BK.
BMC Med. 2010 May 21. 8:27.

Identifying the hub proteins from complicated membrane protein network systems.

Shen YZ, Ding YS, Gu Q, Chou KC.
Med Chem. 2010 May 1. 6(3):165-73.

Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes.

Qattan AT, Mulvey C, Crawford M, Natale DA, Godovac-Zimmermann J.
J Proteome Res. 2010 Jan;9(1):495-508.

siRNA-mediated knockdown of the melanocortin 2 receptor accessory protein 2 (MRAP2) gene confers resistance to methylmercury on HEK293 cells.

Hwang GW, Oh SE, Takahashi T, Lee JY, Naganuma A.
J Toxicol Sci. 2010. 35(6):947-50.

Expression levels of NF-Y target genes changed by CDKN1B correlate with clinical prognosis in multiple cancers.

Yamanaka K, Mizuarai S, Eguchi T, Itadani H, Hirai H, Kotani H.
Genomics. 2009 Oct. 94(4):219-27. Epub 2009 Jun 25.

In silico method for identification of promising anticancer drug targets.

Koborova ON, Filimonov DA, Zakharov AV, Lagunin AA, Ivanov SM, Kel A, Poroikov VV.
SAR QSAR Environ Res. 2009 Oct. 20_7-8):755-66.

Alternaria alternata TCTP, a novel cross-reactive ascomycete allergen.

Rid R, Onder K, MacDonald S, Lang R, Hawranek T, Ebner C, Hemmer W, Richter K, Simon-Nobbe B, Breitenbach M.
Mol Immunol. 2009 Oct. 46:(16):3476-87. Epub 2009 Aug 15.

Identifying the potential gene targets of microRNAs involved in the metastasis of prostate cancer to bone

Allison Jane Kasmari, Chu Zhang and Mary C. Farach-Carson
Biological Science, University of Delaware, Newark, DE

Coordinated regulation of cell cycle transcripts by p53-inducible microRNAs, miR-192 and miR-215.

Georges SA, Biery MC, Kim SY, Schelter JM, Guo J, Chang AN, Jackson AL, Carleton MO, Linsley PS, Cleary MA, Chau BN.
Cancer Res. 2008 Dec 15. 68(24):10105-12.

Mutual antagonistic relationship between prostaglandin E(2) and IFN-gamma: Implications for rheumatoid arthritis.

Mathieu MC, Lord-Dufour S, Bernier V, Boie Y, Burch JD, Clark P, Denis D, Han Y, Mortimer JR, Therien AG.
Eur J Immunol. 2008 Jul. 8(7):1900-12.

Senescence and apoptosis in yeast mother cell-specific aging and in higher cells: a short review.

Laun P, Heeren G, Rinnerthaler M, Rid R, Kössler S, Koller L, Breitenbach M.
Biochim Biophys Acta. 2008 Jul;1783(7):1328-34. Epub 2008 Mar 4. Review.

The let-7 microRNA represses cell proliferation pathways in human cells.

Johnson CD, Esquela-Kerscher A, Stefani G, Byrom M, Kelnar K, Ovcharenko D, Wilson M, Wang X, Shelton J, Shingara J, Chin L, Brown D, Slack FJ.
Cancer Res. 2007 Aug 15;67(16):7713-22.

Underlying mechanisms of pharmacology and toxicity of a novel PPAR agonist revealed using rodent and canine hepatocytes.

Guo Y, Jolly RA, Halstead BW, Baker TK, Stutz JP, Huffman M, Calley JN, West A, Gao H, Searfoss GH, Li S, Irizarry AR, Qian HR, Stevens JL, Ryan TP.
Toxicol Sci. 2007 Apr. 96(2):294-309. Epub 2007 Jan 25.

A housekeeper with power of attorney: the rRNA genes in robosome biogenesis.

Moss T, Langlois F, Gagnon-Kugler T, Stefanovsky V.
Cell Mol Life Sci. 2007 Jan. 64(1):29-49.

Redox proteomics identification of oxidatively modified hippocampal proteins in mild cognitive impairment: insights into the development of Alzheimer’s disease.

Butterfield DA, Poon HF, StClair D, Keller JN, Pierce WM, Klein JB, Markesbery WR.
Neurobiol Dis. 2006 May. 22(2):223-32. Epub 2006 Feb 8.

Differential global gene expression response patterns of human endothelium exposed to shear stress and intraluminal pressure.

Andersson M, Karlsson L, Svensson PA, Ulfhammer E, Ekman M, Jernås M, Carlsson LM, Jern S.
J Vasc Res. 2005 Sep-Oct;42(5):441-52. Epub 2005 Sep 8.

Microarray profiling of isolated abdominal subcutaneous adipocytes from obese vs non-obese Pima Indians: increased expression of inflammation-related genes.

Lee YH, Nair S, Rousseau E, Allison DB, Page GP, Tataranni PA, Bogardus C, Permana PA.
Diabetologia. 2005 Sep;48(9):1776-83. Epub 2005 Jul 30.

Comparison of the expression profiles induced by genotoxic and nongenotoxic carcinogens in rat liver.

Ellinger-Ziegelbauer H, Stuart B, Wahle B, Bomann W
Ahr HJ. Mutat Res. 2005 Aug 4;575(1-2):61-84.

Intervening sequences in paralogous genes: a comparative genomic approach to study the evolution of X chromosome introns.

Cardazzo B, Bargelloni L, Toffolatti L, Patarnello T.
Mol Biol Evol. 2003 Dec;20(12):2034-41. Epub 2003 Aug 29.

Model systems in drug discovery: chemical genetics meets genomics.

Carroll PM, Dougherty B, Ross-Macdonald P, Browman K, FitzGerald K.
Pharmacol Ther. 2003 Aug;99(2):183-220. Review.

Pneumolysin-dependent and -independent gene expression identified by cDNA microarray analysis of THP-1 human mononuclear cells stimulated by Streptococcus pneumoniae.

Rogers PD, Thornton J, Barker KS, McDaniel DO, Sacks GS, Swiatlo E, McDaniel LS.
Infect Immun. 2003 Apr;71(4):2087-94.

In silico identification of novel therapeutic targets.

Duckworth DM, Sanseau P.
Drug Discov Today. 2002 Jun 1;7(11 Suppl):S64-9.

Strong aggregation and increased toxicity of polyleucine over polyglutamine stretches in mammalian cells.

Dorsman JC, Pepers B, Langenberg D, Kerkdijk H, Ijszenga M, den Dunnen JT, Roos RA, van Ommen GJ.
Hum Mol Genet. 2002 Jun 15;11(13):1487-96.

Yeast Publications

Genome-wide survey of yeast mutations leading to activation of the yeast cell integrity MAPK pathway: Novel insights into diverse MAPK outcomes.

Arias P, Díez-Muñiz S, García R, Nombela C, Rodríguez-Peña JM, Arroyo J.
BMC Genomics. 2011 Aug 2;12:390.

Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using “-omics” techniques.

Piddocke MP, Fazio A, Vongsangnak W, Wong ML, Heldt-Hansen HP, Workman C, Nielsen J, Olsson L.
Microb Cell Fact. 2011 Apr 23;10:27.

An FPT approach for predicting protein localization from yeast genomic data.

Wang J, Li C, Wang E, Wang X.
PLoS One. 2011 Jan 19;6(1):e14449.

The Rpd3L HDAC complex is essential for the heat stress response in yeast.

Ruiz-Roig C, Vieitez C, Posas F, de Nadal E. mol Microbiol. 2010 May. 76(4):1049-62. Epub 2010 Apr 14.

Identification of Candida albicans exposed surface proteins in vivo by a rapid proteomic approach.

Hernaez ML, Ximenez-Embun P, Martinez-Gomariz M, Gutierrez-Blazquez MD, Nombela C, Gil C. J Proteomics. 2010 May 7. 73(7):1404-9. Epub 2010 Feb 16.

Different modulation of the outputs of yeast MAPK-mediated pathways by distinct stimuli and isoforms of the dual-specificity phosphatase Msg5.

Marin MJ, Flandez M, Bermejo C, Arroyo J, Martin H, Molina M.
Mol Genet. Genomics. 2009 Mar. 281(3):345-59. Epub 2009 Jan 4.

Toward a Realistic Model for Gene Network Evolution.

Chen W, Xia T, Jiang T, Gu X.
Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on 14-17 Oct. 2007, page(s): 673-679

Integrated proteomics and genomics strategies bring new insight into Candida albicans response upon macrophage interaction.

Fernández-Arenas E, Cabezón V, Bermejo C, Arroyo J, Nombela C, Diez-Orejas R, Gil C.
Mol Cell Proteomics. 2007 Mar;6(3):460-78. Epub 2006 Dec 12.

Proteome chips for whole-organism assays.

Kung LA, Snyder M.
Nat Rev Mol Cell Biol. 2006 Aug;7(8):617-22. Epub 2006 May 24. Review.

Proteomic analysis of detergent-resistant membranes from Candida albicans.

Insenser M, Nombela C, Molero G, Gil C.
Proteomics. 2006 Apr;6 Suppl 1:S74-81.

A systematic approach to infer biological relevance and biases of gene network structures.

Antonov AV, Tetko IV, Mewes HW.
Nucleic Acids Res. 2006 Jan 10;34(1):e6.

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

Gibbons FD, Proft M, Struhl K, Roth FP.
Genome Biol. 2005;6(11):R96. Epub 2005 Nov 1.

Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways.

Smirnova JB, Selley JN, Sanchez-Cabo F, Carroll K, Eddy AA, McCarthy JE, Hubbard SJ, Pavitt GD, Grant CM, Ashe MP.
Mol Cell Biol. 2005 Nov;25(21):9340-9.

The senescence-accelerated prone mouse (SAMP8): a model of age-related cognitive decline with relevance to alterations of the gene expression and protein abnormalities in Alzheimer’s disease.

Butterfield DA, Poon HF.
Exp Gerontol. 2005 Oct;40(10):774-83. Epub 2005 Jul 18. Review.

A putative dual-specific protein phosphatase encoded by YVH1 controls growth, filamentation and virulence in Candida albicans.

Hanaoka N, Umeyama T, Ueno K, Ueda K, Beppu T, Fugo H, Uehara Y, Niimi M.
Microbiology. 2005 Jul;151(Pt 7):2223-32.

Derivation of genetic interaction networks from quantitative phenotype data.

Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, Galitski T.
Genome Biol. 2005;6(4):R38. Epub 2005 Mar 31.

Reconstruction of microbial transcriptional regulatory networks.

Herrgård MJ, Covert MW, Palsson B.
Curr Opin Biotechnol. 2004 Feb;15(1):70-7. Review.

Predicting co-complexed protein pairs using genomic and proteomic data integration.

Zhang LV, Wong SL, King OD, Roth FP.
BMC Bioinformatics. 2004 Apr 16;5:38.

Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002).

Pitarch A, Sánchez M, Nombela C, Gil C. J Chromatogr B
Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):129-48. Review.

Worm Publications

The Stanford Tissue Microarray Database.

Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA.
Nucleic Acids Res. 2008 Jan;36(Database issue):D871-7. Epub 2007 Nov 7.

Identification and characterization of a novel alternative splice variant of mouse GMx33alpha/GPP34.

Nagano-Ito M, Yoshikawa S, Tamura M, Tsurumaki M, Ichikawa S.
Gene. 2007 Oct 1;400(1-2):82-8. Epub 2007 Jun 19.

Functional analysis of MRG-1: the ortholog of human MRG15 in Caenorhabditis elegans.

Olgun A, Aleksenko T, Pereira-Smith OM, Vassilatis DK. J Gerontol A
Biol Sci Med Sci. 2005 May;60(5):543-8.

A map of the interactome network of the metazoan C. elegans.

Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M.
Science. 2004 Jan 23;303(5657):540-3. Epub 2004 Jan 2.

Cloning and comparative sequence analysis of PUM1 and PUM2 genes, human members of the Pumilio family of RNA-binding proteins.

Spassov DS, Jurecic R.
Gene. 2002 Oct 16;299(1-2):195-204.

AGEID: a database of aging genes and interventions.

Kaeberlein M, Jegalian B, McVey M.
Mech Ageing Dev. 2002 Apr 30;123(8):1115-9.

BIOBASE Publications

HumanPSD, GPCR-PD and TRANSPATH

Molecular mechanistic associations of human diseases.

Stegmaier P, Krull M, Voss N, Kel A, Wingender E.
BMC Syst Biol. 2010 Sep 6;4(1):124.

Integrating pathway data for systems pathology.

Wingender E, Hogan J, Schacherer F, Potapov AP, Kel-Margoulis O.
In Silico Biol. 2007;7(2 Suppl):S17-25.

Beyond microarrays: find key transcription factors controlling signal transduction pathways.

Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E.
BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S13.

TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations.

Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D, Michael H, Schwarzer K, Potapov A, Choi C, Kel-Margoulis O, Wingender E.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D546-51.

Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database.
Choi C, Crass T, Kel A, Kel-Margoulis O, Krull M, Pistor S, Potapov A, Voss N, Wingender E.
Genome Inform. 2004;15(2):244-54.

TRANSPATH – a high quality database focused on signal transduction.

Choi C, Krull M, Kel A, Kel-Margoulis O, Pistor S, Potapov A, Voss N, Wingender E.
Comp Funct Genomics. 2004;5(2):163-8.

TRANSPATH: an integrated database on signal transduction and a tool for array analysis.

Krull M, Voss N, Choi C, Pistor S, Potapov A, Wingender E.
Nucleic Acids Res. 2003 Jan 1;31(1):97-100.

Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics.

Hodges, P. E., Carrico, P. M., Hogan, J. D., O’Neill, K. E., Owen, J. J., Mangan, M., Davis, B. P., Brooks, J. E., Garrels, J. I.
Nucleic Acids Res. 30, 137-41 (2002).

The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.

Schacherer F, Choi C, Götze U, Krull M, Pistor S, Wingender E.
Bioinformatics. 2001 Nov;17(11):1053-7.

YPD, PombePD, and MycoPath

Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002)
Pitarch, A., Sanchez, M., Nombela, C., Gil, C. J Chromatogr B
Analyt Technol Biomed Life Sci 787, 129-48 (2003).

Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD)
Csank, C., Costanzo, M. C., Hirschman, J., Hodges, P., Kranz, J. E., Mangan, M., O’Neill, K., Robertson, L. S., Skrzypek, M. S., Brooks, J., Garrels, J. I.
Methods Enzymol 350, 347-73 (2002).

YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information
Costanzo, M. C., Crawford, M. E., Hirschman, J. E., Kranz, J. E., Olsen, P., Robertson, L. S., Skrzypek, M. S., Braun, B. R., Hopkins, K. L., Kondu, P., Lengieza, C., Lew-Smith, J. E., Tillberg, M., Garrels, J. I.
Nucleic Acids Res. 29, 75-79 (2001). PMID: 11125054

The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.

Costanzo, M. C., Hogan, J. D., Cusick, M. E., Davis, B. P., Fancher, A. M., Hodges, P. E., Kondu, P., Lengieza, C., Lew-Smith, J. E., Lingner, C., Roberg-Perez, K. J., Tillberg, M., Brooks, J. E., Garrels, J. I. Nucleic Acids Res. 28, 73-76 (2000).

The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data.

Hodges, P.E., McKee, A.H., Davis, B.P., Payne, W.E., Garrels, J. I.
Nucleic Acids Res. 27, 69-73 (1999).

The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae.

Hodges, P. E., Payne, W. E., Garrels, J. I.
Nucleic Acids Res. 26, 68-72 (1998).

WormPD

YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information.

Costanzo, M. C., Crawford, M. E., Hirschman, J. E., Kranz, J. E., Olsen, P., Robertson, L. S., Skrzypek, M. S., Braun, B. R., Hopkins, K. L., Kondu, P., Lengieza, C., Lew-Smith, J. E., Tillberg, M., Garrels, J. I.
Nucleic Acids Res. 29, 75-79 (2001).

The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.