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Additional Resources

Annereau Datasets

  • Analysis of ABC transporter-expression in drug-selected cell lines by a microarray dedicated to multidrug resistance.
    Annereau JP, Szakacs G, Tucker J, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg B, Reinhold W, Weinstein J, Pommier Y, Paules R, Gottesman M.

ILSI Datasets

  • Identification of Putative Gene Based Markers of Renal Toxicity
    Amin RP, Vickers AE, Sistare F, Thompson K, Roman RJ, Lawton M, Kramer J, Hamadeh HK, Collins J, Grissom S, Bennett L, Tucker CJ, Wild S, Oreffo V, Davis J, Curtiss S, Naciff JM, Cunningham M, Tennant R, Stevens J, Car B, Bertram TA, Afshari CA.
    [Individual slide data (txt) (5.1MB)] (Note: Values are on log2 scale)
  • Cross-Site Comparison of Gene Expression Data Reveals High Similarity
    Chu T, Deng S, Wolfinger R, Paules RS, Hamadeh HK, EHP Toxicogenomics
    [Data file (  View Information About ZIP Files (125MB)]

Irofulven Dataset

  • Acquired Irofulven-Resistance is Associated with Unique Transcriptional Alterations and Unchanged Sensitivity to Other Anticancer Agents
    Koeppel F, Annereau JP, Poindessous V, Lemke K, Escargueil A, Szakacs G, Tucker J, Raymond E, Paules R, Gottesman MM, Larsen AK.

Jetten Manuscripts

  • Modulatory role for retinoid-related orphan receptor a (RORa) in allergen-induced lung inflammation.
    Maisa Jaradat, Cliona Stapleton, Darlene Dixon, Christopher J. Erikson, Joshua G. McCaskill, Stephen L. Tilley, Martin Angers, Grace Liao, Jennifer B. Collins, Sherry F. Grissom, Anton M. Jetten.
    [Data File (txt) (5.0MB), xls (  Download Microsoft Excel Viewer (9.4MB), pdf (  Download Adobe Reader (3.7MB) ], [119 WTvsDKO Liver Males (txt) (390KB), xls (  Download Microsoft Excel Viewer (728KB), pdf (  Download Adobe Reader (1.3MB)], [119 WTvsRORalphaKO Liver (txt) (215KB), xls (  Download Microsoft Excel Viewer (408KB), pdf (  Download Adobe Reader (696KB)], [119 WTvsRORgammaKO Liver (txt) (113KB), xls (  Download Microsoft Excel Viewer (221KB), pdf (  Download Adobe Reader (368KB)], [325_OH1STvs4H1ST_001 (  Download Microsoft Excel Viewer (1.8MB), pdf (  Download Adobe Reader (3.5MB)], [325_OH2STvs4H2ST_001 (  Download Microsoft Excel Viewer (2.2MB), pdf (  Download Adobe Reader (4.2MB)]

Janine Hertzog Santos Datasets

  • Telomerase expression sensitizes the mitochondrial genome of mammalian cells to oxidative stress through increased bioavailable iron.
    Janine Hertzog Santos1, Joel Meyer1, Milan Skorvaga1,2, Astrid C. Haugen1, Lois A. Annab3, Cynthia A. Afshari3,4 and Bennett Van Houten1*.
    [Compiled Data (txt) (3.0MB)], [Common genes found by MAPS: Fibroblasts (  Download Microsoft Excel Viewer (50KB), pdf (  Download Adobe Reader (44KB)], [Epithelial Cells (  Download Microsoft Excel Viewer (33KB), pdf (  Download Adobe Reader (35KB)], [Hierarchical Cluster Analysis of MAPS Genes at 95% (  Download Adobe Reader (126KB)] (Note: values are log2 format)

    1Laboratory of Molecular Genetics, 2Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health. 3Currently at Amgen Inc., One Amgen Center Dr., Mailstop 5-1-A Thousand Oaks, CA 91320-1799.

Donghui Zhang Datasets

  • Identification of Potential Target Genes for Transcription Factor RFX4_v3 in the Developing Mouse Brain.
    Zhang D, Stumpo DJ, Graves JP, DeGraff LM, Grissom SF, Collins JB, Li L, Zeldin DC, Blackshear PJ., 2005.
    [Data Set (txt) (64KB)]

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2004 and 2005 Microarray Datasets

  • Global Uterine Genomics in vivo: Microarray Evaluation of the Estrogen Receptor Alpha-growth Factor Cross-talk Mechanism
    Hewitt SC, Collins J, Grissom S, Deroo B, Korach KS. Molecular Endocrinology 19(3): 657-668, 2005.
    [Individual Slide Data (txt) (4.8MB)] (Noted: Values are on log2 scale)
  • Differential Gene Expression Profiling in Whole Blood During Acute Systemic Inflammation in Lipopolysaccharide-Treated Rats
    Rick D. Fannin, J. Todd Auman, Maribel E. Bruno, Stella O. Sieber, Sandra M. Ward, Charles J. Tucker, B. Alex Merrick and Richard S. Paules.
    [Individual Slide Data (txt) (922KB)], [Averaged experiment data (txt) (658KB)], [Individual Slide Information (  Download Adobe Reader (10KB)]
  • Exploration of Low Dose Estrogen Effects: Identification of No Observed Transcriptional Effect Level (NOTEL)
    Edward K. Lobenhofer, Xiangqin Cui, Lee Bennett, P. LouAnn Cable, B. Alex Merrick, Gary A. Churchill, and Cynthia A. Afshari. Toxicologic Pathology 32(4): 482-492, 2004.
    [Concentration (txt) (491KB)]
  • Integration of Clinical and Gene Expression Endpoints to Explore Furan-Mediated Hepatotoxicity
    Hamadeh, H.K., Jayadev, S., Gaillard, E.T., Huang, Q., Stoll, R., Blanchard, K., Chou, J., Tucker, C.J., Collins, J., Maronpot, R., Bushel, P., Afshari, C.A. Mutation Research 549(1-2): 169-183, 2004.
    [Slide data (txt) (4.3MB)]
  • Unique Patterns of Gene Expression Changes in Liver AfterTreatment of Mice for Two Weeks With Different Known Carcinogens and Non-carcinogens
    Iida M., Anna C.H., Holliday W. M. , Collins J.B., Cunningham M.L., Sills R.C. and Devereux T.R. Carcinogenesis 26(3): 689-699, 2005.
    [All Data (txt) (7.5MB)] (Note: log base 10 values, average of technical replicates)., [Histopath Table (  Download Microsoft Excel Viewer (21KB), pdf (  Download Adobe Reader (33KB)], [Cluster of Individual Animals (gif) (193KB)]
  • A Global Network Model of the Arsenic Response
    Haugen A.C., Kelley R., Collins J.B., Tucker C.J., Deng C., Afshari C.A., Brown J.M., Ideker T. and Van Houten B. Genome Biology 5(12): R95, 2004.
    Supplemental Data(
  • Genome-Wide Analysis of ARS Binding Factor 1 (Abf1p)-Mediated Transcriptional Regulation in Saccharomyces Cerevisiae
    Miyake T., Reese J., Loch C., Auble D., and Li R. Journal of Biological Chemistry, 2004.
    [A1-001 vs. A1-029 (txt) (98KB)] (Note: log base 2 values, average of replicates).
  • Sir Antagonist 1 (San1) is a Ubiquitin Ligase
    Dasgupta A, Ramsey KL, Smith JS, and Auble DT. Journal of Biological Chemistry 279: 26830-26838, 2004.
    [san 1 knockout vs. wildtype (txt) (97KB)] (Note: log base 2 values, average of replicates).
  • Gene Expression Profiling of Rat Livers Reveals Indicators of Potential Adverse Effects
    Heinloth A.N., Irwin R.D., Boorman G.A., Nettesheim P., Fannin R.D., Sieber S.O., Snell M.L., Tucker C.J., Li L., Travlos G.S., Vansant G., Blackshear P.E., Tennant R.W., Cunningham M.L., Paules R.S. Toxicological Sciences 80: 193-202, 2004.
    [Supplemental Summary (  Download Microsoft Excel Viewer (3.3MB), pdf (  Download Adobe Reader (8.7MB)] (Note: log base 2 values, average of replicates)

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2003 Microarray Datasets

  • Estrogen Receptor Dependent Genomic Responses in the Uterus Mirror the Biphasic Physiological Response to Estrogen
    Hewitt SC, Deroo B, Hansen K, Collins J, Grissom S, Afshari CA, Korach KS. Molecular Endocrinology 17(10): 2070-2083, 2003.
    [Individual Slide Data (txt) (5.5MB)] (Note: Values are on log2 scale)
  • ATM-Dependent and -Independent Gene Expression Changes in Response to Oxidative stress, g- and UV-Radiation
    Heinloth AN, Shackelford RE, Innes CL, Bennett L, Li L, Amin RP, Sieber SO, Flores KG, Bushel PR, Paules RS. Radiation Research 2003, in press.
    [Individual slide data (txt) (872KB)] (Note: Values are on log2 scale)
  • Gene Modulation by the Cyclooxygenase Inhibitor Sulindac Sulfide in Human Colorectal Carcinoma Cells: Possible Link to Apoptosis
    Bottone FG, Martinez JM, Collins JB, Afshari CA, and Eling TE. Journal of Biological Chemistry 278(28): 25790-25801, 2003.
    [Individual slide data (txt) (1.6MB)] [Averaged experiment data (txt) (912KB)] (Note: Values are on log2 scale)
  • Genomic profiles and predictive biological networks in oxidant-induced atherogenesis.
    Johnson CD, Balagurunathan Y, Lu KP, Tadesse M, Falahatpisheh MH, Carroll RJ, Dougherty ER, Afshari CA, Ramos KS. Physiol Genomics 13(3): 263-275, 2003.
    [All data (txt) (1.0MB)] [Archived Data (  View Information About ZIP Files (9.5MB)*] (Zip file contains 12 standard intensity raw data files and two corresponding Gene In Plate Order (GIPO) files).
  • Changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens Oxazepam and Wyeth-14,643.
    Iida M, Anna CH, Hartis J, Bruno M, Wetmore B, Dubin JR, Sieber S, Bennett L, Cunningham ML, Paules RS, Tomer KB, Merrick BA, Sills RC, Devereux TR. Carcinogenesis 24(4): 757-770, 2003.
    [2 week data (txt) (1.6MB)] [6 month data (txt) (1.6MB)] [Hierarchical Clustering (.gif) (328K)] [Fraction ids1 (.gif) (34KB)]
  • Gene selection and clustering for time-course and dose response microarray experiments using order-restricted inference.
    Peddada SD, Lobenhofer EK, Li L, Afshari CA, Weinberg CR, Umbach DM. Bioinformatics 19(7): 834-841, 2003.
    [Supplemental information (  Download Adobe Reader (46KB)]
  • Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells.
    Hodges LC, Cook JD, Lobenhofer EK, Martin K, Li L, Bennett L, Bushel PR, Afshari CA, Walker CL. Mol Cancer Res 1(4): 300-311, 2003.
    [Data (txt) (589KB)] [Methods (  Download Adobe Reader (14KB)] [Appendix (  Download Adobe Reader (2.2MB)]

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2002 Microarray Datasets

  • Gene Expression Analysis Reveals Chemical-Specific Profiles
    Hamadeh HK, Bushel P, Jayadev S, Martin K, DiSorbo O, Sieber S, Bennett L, Tennant R, Stoll R, Barrett JC, Blanchard K, Paules RS, Afshari CA. Toxicological Sci. 67: 219-231, 2002.
    [1 day (txt) (517KB)] [14 day (txt) (673KB)]
  • Statistical analysis of a gene expression microarray experiment with replication.
    Kerr MK, Afshari CA, Bennett L, Bushel P, Martinez J, Walker NJ, Churchill GA. Statistica Sinica 12(1): 203-217, Jan. 2002.
    [Data (txt) (254KB)] (Note: data consists of log(2) intensity values)
  • Regulation of DNA replication fork genes by 17b-estradiol.
    Lobenhofer EK, Bennett L, Cable PL, Li L, Bushel PR, Afshari CA. Mol. Endocrinology 16(6): 1215-1229, 2002.
    [Data (txt) (813KB)] [Table A (  Download Adobe Reader (21KB)] [Table B (  Download Adobe Reader (8KB)]
  • Coordination of altered DNA repair and damage pathways in arsenite exposed keratinocytes.
    Hamadeh HK, Trouba KJ, Amin RP, Afshari CA, Germolec D. Toxicological Sci 69(2): 306-316, 2002.
    [Data256KB (txt) (256KB)] (Note: Values are on log2 scale)
  • Detection of diluted gene expression alterations using cDNA microarrays.
    Hamadeh HK, Bushel P, Tucker CJ, Martin K, Paules R, Afshari CA. BioTechniques 32(2): 322-329, 2002.
    [Individual slide data (txt) (240KB)] [Averaged experiment data (txt) (180KB)]
  • Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations.
    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. Toxicol. Path. 30: 470-482, 2002.
    [Data (txt) (1.3MB)] [Sample Intensity Files (  View Information About ZIP Files (13.7MB)]
  • Insulin like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells.
    Oh JS, Kucab JE, Bushel PR, Martin K, Bennett L, Collins J, DiAugustine RP, Barrett JC, Afshari CA, Dunn SE. Neoplasia 4(3): 204-217, 2002.
    [Control gene list (txt) (5KB)] [Data (txt) (240KB)]
  • Diverse roles of nuclear orphan receptor CAR in regulating hepatic genes in response to phenobarbital.
    Ueda A, Hamadeh HK, Webb HK, Sueyoshi T, Afshari CA, Lehmann JM, Negishi M. Molecular Pharmacology 61(1): 1-6, 2002.
    [All data (txt) (945KB)]
  • Prediction of compound signature using high density gene expression profiling.
    Hamadeh HK, Bushel P, Jayadev S, Martin K, DiSorbo O, Sieber S, Bennett L, Tennant R, Stoll R, Barrett JC, Blanchard K, Paules R, Afshari CA. Toxicological Sci. 67: 232-240, 2002.
    [1 day (txt) (517KB)] [14 day (txt) (673KB)] [Blinded (txt) (327KB)]
  • MOT1 activates and represses transcription by direct, ATPase-dependent mechanisms.
    Dasgupta A, Darst RP, Martin KJ, Afshari CA, Auble DT. PNAS 99(5): 2666-2671, 2002.
    [Data (txt) (201KB)] [Data (  Download Adobe Reader (169KB)] [Methods (txt) (20KB)] [Supplemental information( Exit NIEHS]

2001 Microarray Datasets

  • Inactivation of DNA mismatch repair by increased expression of yeast MLH1
    Shcherbakova PV, Hall MC, Lewis MS, Bennett SE, Martin KJ, Bushel PR, Afshari CA, Kunkel TA. Mol Cell Biol 21(3):940-51, 2001.
    [Data (txt) (165KB)] [Data (  Download Adobe Reader (129KB)]

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