Application of Visualization Tools to the Analysis of Histopathological Data Enhances Biological Insight and Interpretation

Toxicologic Pathology

Volumn 34, Issue 7, 2006, Pages 921-928

  Lobenhofer, Edward K ^a   Boorman, Gary A ^b   Phillips, Kenneth L ^a   Heinloth, Alexandra N ^b   Malarkey, David E ^b   Blackshear, Pamela E ^c   Houle, Christopher ^d   Hurban, Patrick ^a  

^a A Division of Clinical Data ^*  (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c INTEGRATED LABORATORY SYSTEMS   (United States)

^d EXPERIMENTAL PATHOLOGY LABORATORIES INC   (United States)

Author keywords

acute hepatocyte toxicity; gene expression; histopathology; Information visualization; phenotypic anchor

Indexed keywords

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION PROFILING; HISTOPATHOLOGY; INTROSPECTION; LIVER CELL DAMAGE; MALE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RAT; SCORING SYSTEM; TOXICOGENETICS; VALIDITY;

ANIMALS; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; HEPATOCYTES; HYPERPLASIA; LIVER; MALE; NECROSIS; PATHOLOGY; RATS; RATS, INBRED F344; REGENERATION; TOXICOGENETICS;

EID: 33845781014     PISSN: 01926233     EISSN: None     Source Type: Journal    
DOI: 10.1080/01926230601072319     Document Type: Article

References (19)

1. Aldenderfer MS Blashfield RK Cluster Analysis 1984 Beverly Hills, CA Sage Publications
2. Boorman GA Haseman JK Waters MD Hardisty JF Sills RC Quality review procedures necessary for rodent pathology databases and toxicogenomic studies: the National Toxicology Program experience Toxicol Pathol 2002 30 88 92
3. Causton HC Quackenbush J Brazma A Microarray Gene Expressions Data Analysis: A Beginner's Guide 2003 Malden, MA Blackwell Publishers
4. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998 95 14863 8
5. Hamadeh HK Jayadev S Gaillard ET Huang Q Stoll R Blanchard K Chou J Tucker CJ Collins J Maronpot R Bushel P Afshari CA Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity Mutat Res 2004 549 169 83
6. Hamadeh HK Knight BL Haugen AC Sieber S Amin RP Bushel PR Stoll R Blanchard K Jayadev S Tennant RW Cunningham ML Afshari CA Paules RS Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations Toxicol Pathol 2002 30 470 82
7. Livasy CA Karaca G Nanda R Tretiakova MS Olopade OI Moore DT Perou CM Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma Mod Pathol 2006 19 264 71
8. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H Brown EL Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996 14 1675 80
9. Luo W Fan W Xie H Jing L Ricicki E Vouros P Zhao LP Zarbl H Phenotypic anchoring of global gene expression profiles induced by N-hydroxy-4-acetylaminobiphenyl and benzo[a]pyrene diol epoxide reveals correlations between expression profiles and mechanism of toxicity Chem Res Toxicol 2005 18 619 29
10. Moggs JG Tinwell H Spurway T Chang HS Pate I Lim FL Moore DJ Soames A Stuckey R Currie R Zhu T Kimber I Ashby J Orphanides G Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth Environ Health Perspect 2004 112 1589 606
11. National Research Council (NRC) Guide for the Care and Use of Laboratory Animals 1996 Washington, DC National Academy Press
12. Nielsen TO Hsu FD Jensen K Cheang M Karaca G Hu Z Hernandez-Boussard T Livasy C Cowan D Dressler L Akslen LA Ragaz J Gown AM Gilks CB van de Rijn M Perou CM Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma Clin Cancer Res 2004 10 5367 74
13. Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995 270 467 70
14. Schwabe RF Brenner DA Mechanisms of Liver Injury. I. TNF-alpha-induced liver injury: role of IKK, JNK, and ROS pathways Am J Physiol Gastrointest Liver Physiol 2006 290 G583 9
15. Weinstein JN Myers TG O’Connor PM Friend SH Fornace AJ Jr Kohn KW Fojo T Bates SE Rubinstein LV Anderson NL Buolamwini JK van Osdol WW Monks AP Scudiero DA Sausville EA Zaharevitz DW Bunow B Viswanadhan VN Johnson GS Wittes RE Paull KD An information-intensive approach to the molecular pharmacology of cancer Science 1997 275 343 9
16. Weng L Dai H Zhan Y He Y Stepaniants SB Bassett DE Rosetta error model for gene expression analysis Bioinformatics 2006 22 1111 21
17. Whitton PD Hems DA Actions of vasopressin-related peptides on glycogen metabolism in the perfused rat liver Biochem Pharmacol 1976 25 405 7
18. Zeeberg BR Feng W Wang G Wang MD Fojo AT Sunshine M Narasimhan S Kane DW Reinhold WC Lababidi S Bussey KJ Riss J Barrett JC Weinstein JN GoMiner: a resource for biological interpretation of genomic and proteomic data Genome Biol 2003 4 R28
19. Zeeberg BR Qin H Narasimhan S Sunshine M Cao H Kane DW Reimers M Stephens RM Bryant D Burt SK Elnekave E Hari DM Wynn TA Cunningham-Rundles C Stewart DM Nelson D Weinstein JN High-Throughput GoMiner, an ‘industrial-strength’ integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID) BMC Bioinformatics 2005 6 168