PhenoGen Informatics
The site for quantitative genetics of the transcriptome.
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If you use PhenoGen HRDP data in your research, please cite the following references:

Networking in Biology: The Hybrid Rat Diversity Panel. Tabakoff B, Smith H, Vanderlinden LA, Hoffman PL,3, Saba LM. Methods Mol. Bio., 2019.
DOI: 10.1007/978-1-4939-9581-3_10


If you use this website in your research, please cite the following references:

Please cite both of the following sources for this website:

(1) The PhenoGen informatics website: Tools for analyses of complex traits.
Sanjiv V Bhave, Cheryl Hornbaker, Tzu L Phang, Laura Saba, Razvan Lapadat, Katherina Kechris, Jeanette Gaydos, Daniel McGoldrick, Andrew Dolbey, Sonia Leach, Brian Soriano, Allison Ellington, Eric Ellington, Kendra Jones, Jonathan Mangion, John K Belknap, Robert W Williams, Lawrence E Hunter, Paula L Hoffman, and Boris Tabakoff, BMC Genetics Aug, 2007   BioMed Central

(2) PhenoGen Website [Internet]. Aurora (CO): University of Colorado Denver Anschutz Medical Campus. PhenoGen Informatics, 2005 - [cited (insert date of access)]. Available from

Resource ID: RRID:SCR_001613

Other Tools available through PhenoGen:


The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Yuanbin Ru, Katerina J. Kechris, Boris Tabakoff, Paula Hoffman, Richard A. Radcliffe, Russell Bowler, Spencer Mahaffey, Simona Rossi, George A. Calin, Lynne Bemis, and Dan Theodorescu. Nucleic Acids Research, 2014.
Paper DOI: 10.1093/nar/gku631
Bioconductor Package DOI: 10.18129/B9.bioc.multiMiR

Promoter (oPOSSUM):

oPOSSUM: Identification of over-represented transcription factor binding sites in co-expressed genes.
Ho-Sui SJ, Mortimer J, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP and Wasserman WW. Nucleic Acids Res. 2005 Jun 2;33(10):3154-64  PubMed

JASPAR: an open access database for eukaryotic transcription factor binding profiles.
Albin Sandelin, Wynand Alkema, Par Engstrom, Wyeth Wasserman and Boris Lenhard Nucleic Acids Res. 2004 Jan; 32(1) Database Issue  PubMed

Promoter (MEME):

Fitting a mixture model by expectation maximization to discover motifs in biopolymers
Timothy L. Bailey and Charles Elkan, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, (28-36), AAAI Press, 1994.  PubMed

INIA West eQTL Data:

QTL Reaper
QTL Reaper Project View

R (used for statistical analysis):

R: A language and environment for statistical computing
R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria, 2005  Website

Bioconductor (used for statistical analysis):

Bioconductor: Open software development for computational biology and bioinformatics
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, and Zhang J (2004). Genome Biology 5:R80  PubMed


Circos: An information aesthetic for comparative genomics
Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, and Marco A Marra Genome Res. Published in Advance June 18, 2009.  PubMed    Website

Allen Brain Atlas:

Genome-wide atlas of gene expression in the adult mouse brain
Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, Jones AR. Nature 445: 168-176 (2007)  PubMed

If you download specific materials from the website, please add the following citation:

(2) Allen Brain Atlas [Internet] Seattle (WA):Allen Institute for Brain Science. � 2004-[cited insert date of access].
Available from: