Additional Information

Example Data Sets

Supported Microarrays and Next Generation Sequencing Platforms

ID	Name	Provider	Species
GPL10558	HumanHT-12 v4.0 Expression Beadchip	Illumina	Homo sapiens
GPL11180	HT MG-430 PM Array Plate	Affymetrix	Mus musculus
GPL11202	Mouse Genome Microarray 4x44K 026655	Agilent	Mus musculus
GPL1261	Mouse Genome 430 2.0 Array	Affymetrix	Mus musculus
GPL13158	HT HG-U133+ PM Array Plate	Affymetrix	Homo sapiens
GPL1319	Zebrafish Genome Array	Affymetrix	Danio rerio
GPL1322	Drosophila Genome 2.0 Array	Affymetrix	Drosophila melanogaster
GPL1355	Rat Genome 230 2.0 Array	Affymetrix	Rattus norvegicus
GPL14664	Zebrafish Oligo Microarray 026437 v3	Agilent	Danio rerio
GPL14746	Rat Genome Microarray 4x44K 028282 v3	Agilent	Rattus norvegicus
GPL16985	HT RG-230 PM Array Plate	Affymetrix	Rattus norvegicus
GPL201	HG-Focus Target Array	Affymetrix	Homo sapiens
GPL21163	SurePrint G3 Mouse GE v2 8x60K 074809 Microarray	Agilent	Mus musculus
GPL22145	SurePrint G3 Rat GE v2 8x60K 074036 Microarray	Agilent	Rattus norvegicus
GPL32	Murine Genome U74A Array	Affymetrix	Mus musculus
GPL339	Mouse Expression 430A Array	Affymetrix	Mus musculus
GPL340	Mouse Expression 430B Array	Affymetrix	Mus musculus
GPL341	Rat Expression 230A Array	Affymetrix	Rattus norvegicus
GPL342	Rat Expression 430B Array	Affymetrix	Rattus norvegicus
GPL570	Human Genome U133 Plus 2.0 Array	Affymetrix	Homo sapiens
GPL571	Human Genome U133 2.0 Array	Affymetrix	Homo sapiens
GPL6101	RatRef-12 v1.0 Expression Beadchip	Illumina	Rattus norvegicus
GPL6480	Whole Human Genome Microarray 4x44K 014850 G4112F	Agilent	Homo sapiens
GPL6885	MouseRef-8 v2.0 Expression Beadchip	Illumina	Mus musculus
GPL6887	MouseWG-6 v2.0 Expression Beadchip	Illumina	Mus musculus
GPL72	Drosophila Genome Array	Affymetrix	Drosophila melanogaster
GPL7202	Whole Mouse Genome Microarray 4x44K 014868 G4122F	Agilent	Mus musculus
GPL7294	Whole Rat Genome Microarray 4x44K 014868 G4131F	Agilent	Rattus norvegicus
GPL7300	Fly Oligo Microarray 4x44K 018972 G2519F	Agilent	Drosophila melanogaster
GPL81	Murine Genome U74A v2 Array	Affymetrix	Mus musculus
GPL8321	Mouse Genome430A 2.0 Array	Affymetrix	Mus musculus
GPL85	Rat Genome U34 Array	Affymetrix	Rattus norvegicus
GPL96	Human Genome U133A Array	Affymetrix	Homo sapiens
hg19_RefSeq	hg19_RefSeq	RefSeq	Homo sapiens
hg38_Ensemble	hg38_Ensembl	Ensembl	Homo sapiens
Human_Genie	Human_Genie	Genie	Homo sapiens
mm10_Ensemble	mm10_Ensemble	Ensembl	Mus musculus
mm10_RefSeq	mm10_RefSeq	RefSeq	Mus musculus
Rat_Genie	Rat_Genie	Genie	Homo sapiens

Incorporated Software/Databases

Citations

[1] Fitting of data to the statistical models is performed using source code provided by the U.S. Environmental Protection Agency’s Benchmark Dose Software (BMDS). For more information about the EPA’s BMDS, go to the EPA’s web site.

[2] Benjamini and Hochberg, J. Royal Stat. Soc., Series B 57, 289-300, 1995

[3] Thomas, R.S., et al., A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure. Toxicol Sci, 2007 98(1) pp. 240-8.

[4] Williams DA. A test for differences between treatment means when several dose levels are compared with a zero dose control. Biometrics. 1971 27(1) pp. 103-117.

[5] Peddada S, Harris S, Zajd J, and Harvey E., ORIOGEN: order restricted inference for ordered gene expression data. Bioinformatics. 2005 21(20) pp. 3933-4.