Additional Information

Example Data Sets

Supported Microarrays and Next Generation Sequencing Platforms

ID	Name	Provider	Species
GPL1319	Zebrafish Genome Array	Affymetrix	Danio rerio
GPL1322	Drosophila Genome 2.0 Array	Affymetrix	Drosophila melanogaster
GPL72	Drosophila Genome Array	Affymetrix	Drosophila melanogaster
GPL13158	HT HG-U133+ PM Array Plate	Affymetrix	Homo sapiens
GPL570	Human Genome U133 Plus 2.0 Array	Affymetrix	Homo sapiens
GPL571	Human Genome U133A 2.0 Array	Affymetrix	Homo sapiens
GPL96	Human Genome U133A Array	Affymetrix	Homo sapiens
GPL341	Rat Expression 230A Array	Affymetrix	Homo sapiens
GPL11180	HT MG-430 PM Array Plate	Affymetrix	Mus musculus
GPL16985	HT RG-230 PM Array Plate	Affymetrix	Mus musculus
GPL201	Human HG-Focus Target Array	Affymetrix	Mus musculus
GPL1261	Mouse Genome 430 2.0 Array	Affymetrix	Mus musculus
GPL8321	Mouse Genome 430A 2.0 Array	Affymetrix	Mus musculus
GPL81	Murine Genome U74A 2.0 Array	Affymetrix	Mus musculus
GPL32	Murine Genome U74A Array	Affymetrix	Mus musculus
GPL339	Mouse Expression 430A Array	Affymetrix	Rattus norvegicus
GPL340	Mouse Expression 430B Array	Affymetrix	Rattus norvegicus
GPL342	Rat Expression 230B Array	Affymetrix	Rattus norvegicus
GPL1355	Rat Genome 230 2.0 Array	Affymetrix	Rattus norvegicus
GPL85	Rat Genome U34 Array	Affymetrix	Rattus norvegicus
GPL7300	018972 D. melanogaster Oligo Microarray 4x44K G2519F	Agilent	Drosophila melanogaster
GPL6480	014850 Whole Human Genome Microarray 4x44K G4112F	Agilent	Homo sapiens
GPL14746	028282 Whole Rat Genome Microarray 4x44K v3	Agilent	Homo sapiens
GPL7202	014868 Whole Mouse Genome Microarray 4x44K G4122F	Agilent	Mus musculus
GPL11202	026655 Whole Mouse Genome Microarray 4x44K v2	Agilent	Mus musculus
GPL21163	074809 SurePrint G3 Mouse GE v2 8x60K Microarray	Agilent	Mus musculus
GPL7294	014879 Whole Rat Genome Microarray 4x44K G4131F	Agilent	Rattus norvegicus
GPL14664	026437 D. rerio (Zebrafish) Oligo Microarray V3	Agilent	Rattus norvegicus
EPA_BSP_WholeTranscriptome_170424	EPA_BSP_WholeTranscriptome_170424	BioSpyder	Homo sapiens
S1500_Human	S1500_Human	BioSpyder	Homo sapiens
S1500_Rat	S1500_Rat	BioSpyder	Rattus norvegicus
danRer10_Ensembl	danRer10_Ensembl	Ensembl	Danio rerio
dm6_Ensembl	dm6_Ensembl	Ensembl	Drosophila melanogaster
hg19_Ensembl	hg19_Ensembl	Ensembl	Homo sapiens
mm10_Ensembl	mm10_Ensembl	Ensembl	Mus musculus
rn6_Ensembl	rn6_Ensembl	Ensembl	Rattus norvegicus
GPL10558	HumanHT-12 V4.0 expression beadchip	Illumina	Homo sapiens
GPL6885	MouseRef-8 v2.0 expression beadchip	Illumina	Mus musculus
GPL6887	MouseWG-6 v2.0 expression beadchip	Illumina	Mus musculus
GPL6101	ratRef-12 v1.0 expression beadchip	Illumina	Rattus norvegicus
danRer10_RefSeq	danRer10_RefSeq	RefSeq	Danio rerio
dm6_RefSeq	dm6_RefSeq	RefSeq	Drosophila melanogaster
hg19_RefSeq	hg19_RefSeq	RefSeq	Homo sapiens
mm10_RefSeq	mm10_RefSeq	RefSeq	Mus musculus
rn6_RefSeq	rn6_RefSeq	RefSeq	Rattus norvegicus

Incorporated Software/Databases

JFreeChart. LGPL license.
- JFreeChart Copyright © 2000-2009 by Object Refinery Limited and Contributors.
Reactome Pathway Database. [Creative Common Attribution 4.0 International License](http://www.reactome.org/pages/about/license-agreement/).
Gene Ontology. [Creative Commons Attribution 4.0 Unported License](http://www.geneontology.org/page/use-and-license).
DONLP2 optimizer - DONLP2 and DONLP2_INTV_DYN -- Copyright by P. Spellucci. DONLP2 is restricted to non-commercial use by the author's copyright.
install4j -- BMDExpress 2 installation packages are generated with install4j's multi-platform installer builder.

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.