Tissue compartment analysis for biomarker discovery by gene expression profiling

PLoS ONE

Volumn 4, Issue 11, 2009, Pages

  Disset, Antoine ^a,b   Cheval, Lydie ^a,b   Soutourina, Olga ^c   Van Huyen, Jean Paul Duong ^a   Li, Guorong ^d   Genin, Christian ^d   Tostain, Jacques ^d   Loupy, Alexandre ^a,b   Doucet, Alain ^a,b   Rajerison, Rabary ^a,b  

^a SORBONNE UNIVERSITÉ   (France)

^b CNRS   (France)

^c INSTITUT PASTEUR   (France)

^d UNIVERSITY HOSPITAL OF SAINT ETIENNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALDOLASE B; AQUAPORIN 2; BIOLOGICAL MARKER; COLLAGEN TYPE 4 ALPHA5; CONNECTIVE TISSUE GROWTH FACTOR; DECORIN; DUAL SPECIFICITY PHOSPHATASE 9; FXYD4 PROTEIN; GLUTATHIONE TRANSFERASE A1; MUCIN 1; PEPTIDYLPROPYL ISOMERASE A; PODOCALYXIN LIKE PROTEIN; PODOCIN; PROSTAGLANDIN E RECEPTOR 1; RENAL OUTER MEDULLARY POTASSIUM CHANNEL; RPL19 PROTEIN; RPLP1 PROTEIN; SERPIN PEPTIDASE INHIBITOR H1; SLC12A1 PROTEIN; SLC13A2 PROTEIN; TAMM HORSFALL GLYCOPROTEIN; TRANSIENT RECEPTOR POTENTIAL CHANNEL 6; UNCLASSIFIED DRUG; WT1 PROTEIN; COMPLEMENTARY DNA; MESSENGER RNA;

ARTICLE; CELL COMPOSITION; CONTROLLED STUDY; DNA LIBRARY; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; KIDNEY BIOPSY; KIDNEY PARENCHYMA; MORPHOMETRICS; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TISSUE COMPARTMENT ANALYSIS; BIOLOGY; BIOPSY; GENOMICS; KIDNEY; METABOLISM; METHODOLOGY; PROTEOMICS; REPRODUCIBILITY; STATISTICAL MODEL;

ANIMALIA;

BIOLOGICAL MARKERS; BIOPSY; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; KIDNEY; MODELS, STATISTICAL; PROTEOMICS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 70450175666     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007779     Document Type: Article

References (19)

1. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, et al. (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406: 536-540.
2. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, et al. (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A 94: 2150-2155.
3. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484-487.
4. Lee E, Chuang HY, Kim JW, Ideker T, Lee D (2008) Inferring pathway activity toward precise disease classification. PLoS Comput Biol 4: e1000217.
5. Malarkey DE, Johnson K, Ryan L, Boorman G, Maronpot RR (2005) New insights into functional aspects of liver morphology. Toxicol Pathol 33: 27-34.
6. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503-511.
7. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
8. Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, et al. (2009) A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41: 258-263.
9. Cohen CD, Grone HJ, Grone EF, Nelson PJ, Schlondorff D, et al. (2002) Laser microdissection and gene expression analysis on formaldehyde-fixed archival tissue. Kidney Int 61: 125-132.
10. Fink L, Kwapiszewska G, Wilhelm J, Bohle RM (2006) Laser-microdissection for cell type- and compartment-specific analyses on genomic and proteomic level. Exp Toxicol Pathol 57 Suppl 2: 25-29.
11. Chabardes-Garonne D, Mejean A, Aude JC, Cheval L, Di Stefano A, et al. (2003) A panoramic view of gene expression in the human kidney. Proc Natl Acad Sci U S A 100: 13710-13715.
12. Schmid H, Cohen CD, Henger A, Irrgang S, Schlondorff D, et al. (2003) Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies. Kidney Int 64: 356-360.
13. de Borst MH, Benigni A, Remuzzi G (2008) Primer: strategies for identifying genes involved in renal disease. Nat Clin Pract Nephrol 4: 265-276.
14. Fenton KA, Mjelle JE, Jakobsen S, Olsen R, Rekvig OP (2008) Renal expression of polyomavirus large T antigen is associated with nephritis in human systemic lupus erythematosus. Mol Immunol 45: 3117-3124.
15. Ito Y, Aten J, Bende RJ, Oemar BS, Rabelink TJ, et al. (1998) Expression of connective tissue growth factor in human renal fibrosis. Kidney Int 53: 853-861.
16. Kuroda M, Sasamura H, Kobayashi E, Shimizu-Hirota R, Nakazato Y, et al. (2004) Glomerular expression of biglycan and decorin and urinary levels of decorin in primary glomerular disease. Clin Nephrol 61: 7-16.
17. Razzaque MS, Kumatori A, Harada T, Taguchi T (1998) Coexpression of collagens and collagen-binding heat shock protein 47 in human diabetic nephropathy and IgA nephropathy. Nephron 80: 434-443.
18. Karsten SL, Kudo LC, Geschwind DH (2008) Gene expression analysis of neural cells and tissues using DNA microarrays. Curr Protoc Neurosci Chapter 4: Unit 4 28.
19. Brochier C, Gaillard MC, Diguet E, Caudy N, Dossat C, et al. (2008) Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models. Physiol Genomics 33: 170-179.