Additional Information

Example Data Sets

Supported Microarrays and Next Generation Sequencing Platforms

### Platform Annotation Table

ID	Name	Provider	Species
Apis_Mellifera_Genie	Apis_Mellifera_Genie	Genie	Apis mellifera
canFam_ROS_1.0_Ensembl	canFam_ROS_1.0_Ensembl	Ensembl	Canis lupus familiaris
canFam5_RefSeq	canFam5_RefSeq	RefSeq	Canis lupus familiaris
canFam6_RefSeq	canFam6_RefSeq	RefSeq	Canis lupus familiaris
Cyprinodon_variegatus_Genie	Cyprinodon_variegatus_Genie	Genie	Cyprinodon variegatus
danRer10_RefSeq	danRer10_RefSeq	RefSeq	Danio rerio
danRer11_Ensembl	danRer11_Ensembl	Ensembl	Danio rerio
danRer11_RefSeq	danRer11_RefSeq	RefSeq	Danio rerio
Daphnia_magna_Genie	Daphnia_magna_Genie	Genie	Daphnia magna
dm3_RefSeq	dm3_RefSeq	RefSeq	Drosophila melanogaster
dm6_Ensembl	dm6_Ensembl	Ensembl	Drosophila melanogaster
dm6_RefSeq	dm6_RefSeq	RefSeq	Drosophila melanogaster
EUToxRisk_Human	BioSpyder EU_ToxRisk_Human	BioSpyder	Homo sapiens
GPL32	Affymetrix Murine Genome U74A Array	Affymetrix	Mus musculus
GPL72	Affymetrix Drosophila Genome Array	Affymetrix	Drosophila melanogaster
GPL81	Affymetrix Murine Genome U74A Version 2 Array	Affymetrix	Mus musculus
GPL85	Affymetrix Rat Genome U34 Array	Affymetrix	Rattus norvegicus
GPL96	Affymetrix Human Genome U133A Array	Affymetrix	Homo sapiens
GPL201	Affymetrix Human HG-Focus Target Array	Affymetrix	Homo sapiens
GPL339	Affymetrix Mouse Expression 430A Array	Affymetrix	Mus musculus
GPL340	Affymetrix Mouse Expression 430B Array	Affymetrix	Mus musculus
GPL341	Affymetrix Rat Expression 230A Array	Affymetrix	Rattus norvegicus
GPL342	Affymetrix Rat Expression 230B Array	Affymetrix	Rattus norvegicus
GPL570	Affymetrix Human Genome U133 Plus 2.0 Array	Affymetrix	Homo sapiens
GPL571	Affymetrix Human Genome U133A 2.0 Array	Affymetrix	Homo sapiens
GPL1261	Affymetrix Mouse Genome 430 2.0 Array	Affymetrix	Mus musculus
GPL1319	Affymetrix Zebrafish Genome Array	Affymetrix	Danio rerio
GPL1322	Affymetrix Drosophila Genome 2.0 Array	Affymetrix	Drosophila melanogaster
GPL1355	Affymetrix Rat Genome 230 2.0 Array	Affymetrix	Rattus norvegicus
GPL6101	Illumina RatRef-12 v1.0 Expression Beadchip	Illumina	Rattus norvegicus
GPL6480	Agilent-014850 Whole Human Genome Microarray 4x44K G4112F	Agilent	Homo sapiens
GPL6885	Illumina MouseRef-8 v2.0 Expression Beadchip	Illumina	Mus musculus
GPL6887	Illumina MouseWG-6 v2.0 Expression Beadchip	Illumina	Mus musculus
GPL7202	Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F	Agilent	Mus musculus
GPL7294	Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F	Agilent	Rattus norvegicus
GPL7300	Agilent-018972 D. melanogaster (FruitFly) Oligo Microarray 4x44K G2519F	Agilent	Drosophila melanogaster
GPL8321	Affymetrix Mouse Genome 430A 2.0 Array	Affymetrix	Mus musculus
GPL10558	Illumina HumanHT-12 v4.0 Expression Beadchip	Illumina	Homo sapiens
GPL11180	Affymetrix HT MG-430 PM Array Plate	Affymetrix	Mus musculus
GPL11202	Agilent-026655 Whole Mouse Genome Microarray 4x44K v2_GPL11202	Agilent	Mus musculus
GPL13158	Affymetrix HT HG-U133+ PM Array Plate	Affymetrix	Homo sapiens
GPL13667	Affymetrix Human Genome U219 Array	Affymetrix	Homo sapiens
GPL14664	Agilent-026437 D. rerio (Zebrafish) Oligo Microarray V3	Agilent	Danio rerio
GPL14746	Agilent-028282 Whole Rat Genome Microarray 4x44K v3	Agilent	Rattus norvegicus
GPL16985	Affymetrix HT RG-230 PM Array Plate	Affymetrix	Rattus norvegicus
GPL21163	Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray	Agilent	Mus musculus
GPL22145	Agilent-074036 SurePrint G3 Rat GE v2 8x60K Microarray	Agilent	Rattus norvegicus
GPL24324	Affymetrix Clariom S Assay HT	Affymetrix	Homo sapiens
hg19_RefSeq	hg19_RefSeq	RefSeq	Homo sapiens
hg38_Ensembl	hg38_Ensembl	Ensembl	Homo sapiens
hg38_RefSeq	hg38_RefSeq	RefSeq	Homo sapiens
Human_Genie	Human_Genie	Genie	Homo sapiens
Hyalella_azteca_Genie	Hyalella_azteca_Genie	Genie	Hyalella azteca
Macaca_fascicularis_Genie	Macaca_fascicularis_Genie	Genie	Macaca fascicularis
mm10_Ensembl	mm10_Ensembl	Ensembl	Mus musculus
mm10_RefSeq	mm10_RefSeq	RefSeq	Mus musculus
mm39_RefSeq	mm39_RefSeq	RefSeq	Mus musculus
Mouse_Genie	Mouse_Genie	Genie	Mus musculus
Oncorhynchus_mykiss_Genie	Oncorhynchus_mykiss_Genie	Genie	Oncorhynchus mykiss
Pimephales_promelas_Genie	Pimephales_promelas_Genie	Genie	Pimephales promelas
Rat_Genie	Rat_Genie	Genie	Rattus norvegicus
rn6_RefSeq	rn6_RefSeq	RefSeq	Rattus norvegicus
rn7_Ensembl	rn7_Ensembl	Ensembl	Rattus norvegicus
rn7_RefSeq	rn7_RefSeq	RefSeq	Rattus norvegicus
S1500_Plus_Human	BioSpyder S1500_Human	BioSpyder	Homo sapiens
S1500_Plus_Mouse	BioSpyder S1500_Mouse	BioSpyder	Mus musculus
S1500_Plus_Plus_Human	BioSpyder S1500_Plus_Plus_Human_2.0 191113	BioSpyder	Homo sapiens
S1500_Plus_Rat	BioSpyder S1500_Rat	BioSpyder	Rattus norvegicus
WT_Human	BioSpyder WT_Human	BioSpyder	Homo sapiens
WT_Human_21	BioSpyder WT_Human_21 revB 100739	BioSpyder	Homo sapiens
WT_Human_v2	BioSpyder WT_Human_v2	BioSpyder	Homo sapiens
WT_Mouse	BioSpyder WT_Mouse	BioSpyder	Mus musculus
WT_Rat	BioSpyder WT_Rat	BioSpyder	Rattus norvegicus

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.