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.
Lists of differentially expressed genes resulting from MAPS analysis (95% confidence interval):
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/hesi.zip) (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.
Lists of differentially expressed genes resulting from MAPS analysis (95% confidence interval):
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/272jetten.xls) (9.4MB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/272jetten.pdf) (3.7MB) ],
[119 WTvsDKO Liver Males (txt) (390KB),
xls (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/119_WTvsDKO_liver_malesonly_001.xls) (728KB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/119_WTvsDKO_liver_malesonly_001.pdf) (1.3MB)],
[119 WTvsRORalphaKO Liver (txt) (215KB),
xls (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/119_WTvsRORalphaKO_liver_001.xls) (408KB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/119_WTvsRORalphaKO_liver_001.pdf) (696KB)],
[119 WTvsRORgammaKO Liver (txt) (113KB),
xls (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/119_WTvsRORgammaKO_liver_001.xls) (221KB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/119_WTvsRORgammaKO_liver_001.pdf) (368KB)],
[325_OH1STvs4H1ST_001 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/325_OH1STvs4H1ST_001.xls) (1.8MB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/325_OH1STvs4H1ST_001.pdf) (3.5MB)],
[325_OH2STvs4H2ST_001 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/325_OH2STvs4H2ST_001.xls) (2.2MB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/325_OH2STvs4H2ST_001.pdf) (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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/common-genes.xls) (50KB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/common-genes.pdf) (44KB)],
[Epithelial Cells (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/tert.xls) (33KB),
pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/tert.pdf) (35KB)],
[Hierarchical Cluster Analysis of MAPS Genes at 95% (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/query-cluster.pdf) (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)]
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/lsp_blood_si_descrip-1.pdf) (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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/histopath.xls) (21KB), pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/histopath.pdf) (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(http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/index.cfm).
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/heinloth1-04.xls) (3.3MB), pdf (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/heinloth1-04.pdf) (8.7MB)] (Note: log base 2 values, average of replicates)
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/Ramos.zip) (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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/Peddada_SuppTable1.pdf) (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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/Hodges_methods.pdf) (14KB)] [Appendix (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/Hodges_appendix.pdf) (2.2MB)]
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/MolEndo_Table_A.pdf) (21KB)] [Table B (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/MolEndo_Table_B.pdf) (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)]
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/auble_data.pdf) (169KB)] [Methods (txt) (20KB)] [Supplemental information(http://www.people.virginia.edu/~dta4n/auble_lab/Dasgupta_et_al_supplement.html)]
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 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/docs/data1.pdf) (129KB)]
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