GeneNetwork References

Papers and References to GeneNetwork

Highlighted References | Key References | Background References |

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Highlighted References
Please send us citations to articles that we may have missed.

Rietman ML, Sommeijer JP; Neuro-Bsik Mouse Phenomics Consortium, Levelt CN, Heimel JA (2012) Candidate genes in ocular dominance plasticity. Front Neurosci 6:11
From the Abstract: Many studies have been devoted to the identification of genes involved in experience-dependent plasticity in the visual cortex. To discover new candidate genes, we have reexamined data from one such study on ocular dominance (OD) plasticity in recombinant inbred BXD mouse strains. We have correlated the level of plasticity with the gene expression data in the neocortex that have become available for these same strains. PDF version

Moscou MJ, Lauter N, Steffenson B, Wise RP (2011) Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genet 7:e1002208
PDF version

Krebs J, Römer B, Overall RW, Fabel K, Babu H, Brandt MD, Williams RW, Jessberger S, Kempermann G (2011) Adult hippocampal neurogenesis and plasticity in the infrapyramidal bundle of the mossy fiber projection: II. Genetic covariation and identification of Nos1 as linking candidate gene. Front Neurosci 5:106
This study uses QTL mapping methods to define candidate genes, including NOS1, that may modulate both adult neurogenesis in the hippocampus and the volume of the infrapyramidal mossy fiber projection to CA3. The study also tests whether the genetic basis of variation in adult neurogenesis is linked to variation in the size of the mossy fiber projection to basal dendrites of CA3 pyramidal cells. PDF version

Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K (2011) Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease. BMC Genomics 12:610.
The first genetic analysis, as well as comparative analysis, of variation in gene expression in T cell subclasses. Please reference this paper when making use of the BXD T help and T regulatory cell data sets generated by Alberts, Schughart and colleagues.

Yamamoto H, Williams EG, Mouchiroud L, Cantó C, Fan W, Downes M, Héligon C, Barish GD, Desvergne B, Evans RM, Schoonjans K, Auwerx J (2011) NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell 147:827-39
A high impact article on the role of the Ncor1 gene and a high endurance mouse model (see MedKB). The authors made use of expression data sets in GeneNetwork (see Fig 2 and original data from BXD Lung by Alberts et al. (2011), and BH/HB F2 muscle by Lusis and colleagues).

Suwanwela J, Farber CR, Haung B, Song B, Pan C, Lyon KM, Lusis AJ (2011) Systems genetics analysis of mouse chondrocyte differentiation. Journal of Bone and Mineral Research 26:74-760 PDF version
The first analysis of variation in gene expression in cartilage of both the BXD and BXH mouse strain families. These data are now part of GeneNetwork: see UCLA BXD and BXH Cartilage Illumina WG-6 v2.

Jansen R, Timmerman J, Loos M, Spijker S, van Ooyen A, Brussaard AB, Mansvelder HD, The Neuro-Bsik Mouse Phenomics Consortium; Smit AB, de Gunst M, Linkenhaer-Hansen K (2011) Novel candidate genes associated with hippocampal oscillations. PLoS One 6: e26586. HTML and PDF versions

Jackson KJ, Chen X, Miles MF, Harenza J, Damaj MI (2011) The neuropeptide galanin and variants in the GalR1 gene are associated with nicotine dependence. Neuropsychopharmacology 36:2339-2348. PDF version

Krebs J, Römer D, Overall RW, Fabel K. Babu H, Brandt M, Williams RW, Jessberger S, Kempermann G (2011) Adult hippocampal neurogenesis and plasticity in the infrapyramidal bundle of the mossy fiber projection: II. Genetic covariance and identification of Nos1 as a linking candidate gene. Frontiers in Neuroscience 5:106. PDF version

Mozhui K, Wang X, Chen J, Mulligan MK, Li Z, Ingles J, Chen X, Lu L and Williams RW (2011) Genetic regulation of Nrxn1 expression: an integrative cross-species analysis of schizophrenia candidate genes. Transl Psychiatry 1: e25; doi:10.1038/tp.2011.24. PDF version

Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text HTML and PDF versions
The first expression genetic analysis of the BXD mouse retina based on a total of 80 strains of mice: The HEI Retina Illumina V6.2 (April 2010) RankInv database in GeneNetwork. This is a companion study to Geisert and colleagues (2009), but now instead of an analysis of the entire eye, data were generated exclusively for the retina.

Di Curzio DL, Goldowitz D (2011) The genetic basis of adrenal gland weight and structure in BXD recombinant inbred mice. Mammalian Genome 22:209–234 Full Text PDF version
The ultimate histogenetics paper on the adrenal gland of mice. A very high level of variation was pared into a set of strong QTLs using 64 of the BXD strains. Precision of most loci is under +/- 2.5 Mb.

Porcu P, O'Buckley TK, Song SC, Harenza JL, Lu L, Wang X, Williams RW, Miles MF, Morrow AL (2010) Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: Identification of QTLs and downstream gene regulation. PLoS One 6:e18405. Full Text HTML and PDF versions
The first neurogenetic study of deoxycorticosterone, a neuroactive steroid that has a key role in stress biology. Porcu and colleagues detected strong QTLs on Chr 4 and 14 for deoxycorticosterone levels in the brain and circulation.

Alberts R, Schughart K (2010) QTLminer: identifying genes regulating quantitative traits.Full Text PDF version
Innovative new software to help analyze QTL intervals that is currently available at http://genenetwork.helmholtz-hzi.de/ under the Search menu.

Lynch RM, Naswa S, Rogers Jr GL, Kanla SA, Das S, Chesler EJ, Saxton AM, Langston MA, Voy, BH (2010) Identifying genetic loci and spleen gene coexpression networks underlying immunophenotypes in the BXD recombinant inbred mice. Physiological Genomics 41: 244-253 Full Text PDF version
Please cite this publication if you make use of the mouse BXD strain UTK spleen expression databases generated by Voy and colleagues.

Gerrits A, Li Y, Tesson BM, Bystrykh LV, Weersing E, Ausema A, Dontje B, Wang X, Breitling R, Jansen RC, de Haan G (2009) Expression quantitative trait loci are highly sensitive to cellular differentiation state. PLoS Genetics 5: e1000692 Full Text HTML version and PDF Version
Please cite this publication if you make use of any of the hematopoietic stem cell-associated databases for the BXD strains generated by Gerald de Haan and colleagues.

Grisham W, Schottler NA, Valli-Marill J, Beck L, Beatty J (2010) Teaching bioinformatics and neuroinformatics by using free web-based tools. CBE--Life Sciences Education 9: 98-107 Full Text PDF Version
A terrific introduction to a wide range of bioinformatic resources, including GeneNetwork, that have been assembled as a coherent teaching module. A detailed student/instructor’s manual, PDFs of handouts, PowerPoint slides, and sample exams are available for free at http://mdcune.psych.ucla.edu/modules/bioinformatics.
Youtube videos of Dr. William Grisham teaching neurogenetics at UCLA:
Part 1
Part 2
Part 3
Part 4
Part 5

Li D, Mulligan MK, Wang X, Miles MF, Lu L, Williams RW (2010) A transposon in Comt generates mRNA variants and causes widespread expression and behavioral differences among mice. PLoS One. 2010 Aug 17;5(8):e12181. Full Text HTML and PDF Versions
One of the first examples of a sequence variant, in this case a transponson inserted in the 3' UTR of Comt,, that generates both a strong expression QTL and that generates downstream changes in other genes and higher order phenotypes.

Grisham W (2009) Modular digitial course in undergraduate neuroscience education (MDCUNE): A website offering free digital tools for neuroscience educators. Journal of Undergraduate Neuroscience Education 8:A26-A31 Full Text PDF Version
An excellent example of how resources such as GeneNetwork and the Mouse Brain Library can be used in class room labs.

Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, Holmans P, Rohrer K, Zhao A, Marlowe L, Kaleem M, McCorquodale DS 3rd, Cuello C, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV; NACC-Neuropathology Group, Heward CB, Reiman EM, Stephan D, Hardy J, Myers AJ (2009) Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet 84:445-58.
One of the first and certainly best human brain eQTL studies. The focus in on late onset Alzheimer's disease, but the data are split between normal and AD cases. All of these data are in GeneNetwork. The cases can be "decoded" by their identifier numbers (see INFO files).

Gatti DM, Harrill AH, Wright FA, Threadgill DW, Rusyn I (2009) Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mamm Genome 20:437-46.
A extremely interesting comparison of using and combining data sets for common inbred strains (so-called Mouse Diversity Panels) with data sets for recombinant inbred strains such as the BXD set.

Ruden DM, Chen L, Possidente D, Possidente B, Rasouli P, Wang L, Lu X, Garfinkel MD, Hirsch HV, Page GP (2009) Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to lead. Neurotoxicology 30:898-914
A landmark study in toxicogenomics using a drosophila genetic reference populations.

Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Laviviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ (2010) High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. Genes, Brain and Behavior 8:129-159 PMID: 19958391 Full Text HTML Version
A monstrously large (33 pages) and impressive study of many behaviors in more than 60 BXD strains. The design and execution is exemplary; the diversity of data types is unprecedented; the documentation is great. This paper will be a well-spring for a host of other studies on the genetics and epigenetics of behavioral variation in the BXDs for years to come. Over 700 traits (usually in trios of male, female, and combined data) were entered in GeneNetwork. You can read the paper and work with the phenotypes. You can also combine these phenotypes with all of the existing expression data for the BXD strains.

Wu S, Lusis AJ, Drake TA (2009) A systems-based framework for understanding complex metabolic and cardiovascular disorders. J Lipid Res 50 Suppl:S358-63 Full Text PDF

Overall RW, Kempermann G, Peirce J, Lu L, Goldowitz D, Gage FH, Goodwin S, Smit AB, Airey DC, Rosen GD, Schalkwyk LC, Sutter TR, Nowakowski RS, Whatley S, Williams RW (2009) Genetics of the hippocampal transcriptome in mice: a systematic survey and online neurogenomic resource. Frontiers in Neuroscience 3:55 Full Text HTML Version, Full Text PDF Version
A large expression genetic analysis of the mouse hippocampus (99 strains). This paper is the companion to the the BXD Hippocampus Consortium data sets in GeneNetwork.

Tapocik JD, Letwin N, Mayo CL, Frank B, Luu T, Achinike O, House C, Williams R, Elmer GI, Lee NH (2009) Identification of candidate genes and gene networks specifically associated with analgesic tolerance to morphine. J Neurosci 2:5295-307 Full Text HTML
In this study several GeneNetwork data sets were used to study the association of predisposition and tolerance genes with expression QTLs. "The INIA Brain mRNA M430 (Jun06) RMA, VCU BXD PFC Sal M430 2.0 (Dec06) RMA, INIA Brain mRNA M430 (Jun06) RMA, HBP Rosen Striatum M430V2 (Apr05) RMA served as the databases for eQTL searches in the PAG, PFC, TL, and VS, respectively. Significant linkage of eQTL markers to correlated genes was defined by marker regression plots with 1000 permutations. The results from the permutation tests provide LRS (likelihood ratio statistics) scores that are suggestive, significant, or highly significant."

Badea A, Johnson GA, Williams RW (2009) Genetic dissection of the mouse brain using high-field magnetic resonance microscopy. Neuroimaging 45:1067-79
We have generated high field MRIs for a subset of the BXD stains. This paper describes the acquisition and quantitative analysis of many CNS regions and compartments for BXD strains. The summary data are in GeneNetwork and the original MRI data sets are available at the Duke Center for In Vivo Microscopy (CIVM, Al Johnson and colleagues).

Ciobanu DC, Lu L, Mozhui K, Wang X, Morris JA, Taylor WL, Dietz K, Simon P, Williams RW (2010) Detection, validation, and downstream analysis of allelic variation in gene expression. Genetics 184: 119-128 Full Text PDF
Natural allelic variants can cause large differences in gene expression. A problem in microarray-based studies of this phenomenon is that differences in hybridization signal intensity can be due to SNPs in overlapping probes or by isoform variants. The authors develop an approach to this problem that identifies and filters sources of variation and enriches for real differences that can be exploited in downstream functional analyses—essentially reverse complex trait analysis. The authors demonstrate the power of this method by analyzing targets of two validated differences in allelic expression (Stk25 and Rasd2) that segregate in the BXD mouse strains.

Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, Macchiarulo A, Yamamoto H, Mataki C, Pruzanski M, Pellicciari R, Auwerx J, Schoonjans K (2009) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167-77
Schoonjans and colleagues made good use of a liver gene expression data in GeneNetwork (the BXD data set by Gatti et al., 2006) to show a highly significant correlations between expression of TGR5 and COXV1a1 (their figure 1D).

Davies MN, Lawn S, Whatley S, Fernandes C, Williams RW, Schalkwyk LC (2009) To what extent is blood a reasonable surrogate for brain gene expression studies: estimation from mouse hippocampus and spleen. Front. Neurogen. 1:2. doi:10.3389/neuro.15.002.2009 Full Text HTML

Boon AC, deBeauchamp J, Hollmann A, Luke J, Kotb M, Rowe S, Finkelstein D, Neale G, Lu L, Williams RW, Webby RJ (2009) Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol 83:10417-26 PMID: 19706712 Full Text PDF Version
There is about a 10,000-fold variation in the susceptibility of BXD strains to H5N1 infection. Sequence variants in Hc gene contribute to this differential vulnerability.

Geisert EE, Lu L, Freeman-Anderson ME, Wang X, Gu W, Jiao Y, Williams RW (2009) Gene expression landscape of the mammalian eye: A global survey and database of mRNAs of 103 strains of mice. Molecular Vision 15:1730-1763 PMID:19727342 Full Text HTML Version, Full Text PDF Version
This is a comprehensive review of the genetics of gene expression in the mouse eye and includes data for mutant and knockout mice, most of the common strains of mice, and 68 BXD strains. This paper is also serves as an excellent tutorial on almost all major analytic and mapping features of GeneNetwork. Finally, this paper has a useful summary table (Table 2) that provides gene expression signatures (genes and probe sets) for all major ocular cell type.

Koutnikova H, Laakso M, Lu L, Combe R, Paananen J, Kuulasmaa T, Kuusisto J, Häring H, Hansen T, Pedersen,O, Smith U, Hanefel M, Williams RW, Auwerx J (2009) Identification of UBP1 as a critical blood pressure determinant. PLoS Genetics 5:e1000591 Full Text HTML and PDF Versions
A good example of the rapid "translation" of a mouse blood pressure QTL to a human candidate gene, UBP1. This study made use of the new advanced recombinant inbred BXD strains that are now available from JAX and the University of Tennessee.

Carneiro AM, Airey DC, Thompson B, Zhu CB, Lu L, Chesler EJ, Erikson KM, Blakely RD (2009) Functional coding variation in recombinant inbred mouse lines reveals multiple serotonin transporter-associated phenotypes. Proc Natl Acad Sci USA 106:2047-2052 Full Text HTML Version, Full Text PDF Version
A new way to study the impact of sequence variants by exploiting genetic reference populations. In this paper, Blakely and colleagues have analyzed BXD strains that "share specific serotonin receptor (Slc6a4, 5-HT) gene variants against an otherwise randomized genetic background, an advantage over approaches that test allele effects on one or two inbred backgrounds. Perhaps the greatest strength of this approach is the availability of archived, dimensional data across a large number of phenotypes linked to individual BXD lines, including anatomical, neurochemical, and behavioral traits. In this report, we initiate investigation of naturally occurring variation in 5-HT genes via analysis of functional coding polymorphism in mSERT" (Slc6a4).

Rosen GD, Pung CJ, Owens CB, Caplow J, Kim H, Mozhui K, Lu L, Williams RW (2009) Genetic modulation of striatal volume by loci on Chrs 6 and 17 in BXD recombinant inbred mice. Genes Brain Behav. 8: 296–308. Full Text PDF Version.
This paper introduces a comprehensive companion microarray data set for the striatum of the BXD strains (see Mouse BXD Striatum mRNA databases in GeneNetwork).

Whitney IE, Raven MA, Ciobanu DC, Williams RW, Reese BE (2009) Multiple genes on chromosome 7 regulate dopaminergic amacrine cell number in the mouse. Investigative Ophthalmology & Visual Science 50:1996-2003.
In addition to the quantitative genetic analysis of a dopaminergic cell population in the retinas of AXB/BXA strains of mice, this paper also introduces a comprehensive companion microarray data set for the whole eyes of these same strains (see Mouse AXB/BXA Eye mRNA database in GeneNetwork).

Mozhui RT, Ciobanu DC, Schikorski T, Wang XS, Lu L, Williams RW (2008) Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genetics 4: e1000260. doi:10.1371/journal.pgen.1000260 Full Text HTML Version.
A fine-grained analysis of one of the most intriguing parts of the mouse genome that controls a wide variety of traits. This study highlights sequence variants in formin 2 (Fmn2) as important in translation of mRNA and protein in neurons.

Key References

The first section lists key technical papers that are appropriate references when citing GeneNetwork and WebQTL. The second section lists publications and other resources that have made use of GeneNetwork.

Wang J, Williams RW, Manly KF (2003) WebQTL: Web-based complex trait analysis. Neuroinformatics 1: 299-308 Full Text PDF Version. [A good technical reference to WebQTL and GeneNetwork]
Chesler EJ, Wang J, Lu L, Qu Y, Manly KF, Williams RW (2003) Genetic correlates of gene expression in recombinant inbred strains: a relational model to explore for neurobehavioral phenotypes. Neuroinformatics 1: 343-357. Full Text PDF Version. [Best reference regarding interpretation of genetic correlations.]
Chesler EJ, Lu L, Wang J, Williams RW, Manly KF (2004) WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nature Neuroscience 7: 485-486. Full Text PDF Version [A short review]
Chesler EJ, Williams RW (2004) Brain gene expression: genomics and genetics. International Review of Neurobiology 60:59-95. (DNA Arrays in Neurobiology, edited by MF Miles, Elsevier, Amsterdam). [A longer discussion, both statistical and conceptual, on the genetic analysis of gene expression and relations to higher order behavioral phenotypes]
Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke M, de Haan G (2005) Uncovering regulatory pathways affecting hematopoietic stem cell function using "genetical genomics." Nature Genetics 37:225-232. [Please cite this article if you have used the GNF-Groningen hematopoietic stem cell data set.]
Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin N, Langston MA, Threadgill DW, Manly KF, Williams RW (2005) Genetic dissection of gene expression reveals polygenic and pleiotropic networks modulating brain structure and function. Nature Genetics 37: 233-242. [Please cite this article if you have used one of the UTHSC brain data sets.]
Damerval C, Maurice A, Josse JM, de Vienne D (1994) Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137: 289-301 Full Text PDF Version [The first published paper on system genetics. Impressive; before its time.]
[Damerval et al., 1994 abstract] A methodology to dissect the genetic architecture of quantitative variation of numerous gene products simultaneously is proposed. For each individual of a segregating progeny, proteins extracted from a given organ are separated using two-dimensional electrophoresis, and their amounts are estimated with a computer-assisted system for spot quantification. Provided a complete genetic map is available, statistical procedures allow determination of the number, effects and chromosomal locations of factors controlling the amounts of individual proteins. This approach was applied to anonymous proteins of etiolated coleoptiles of maize, in an F(2) progeny between two distant lines. The genetic map included both restriction fragment length polymorphism and protein markers. Minimum estimates of one to five unlinked regulatory factors were found for 42 of the 72 proteins analyzed, with a large diversity of effects. Dominance and epistasis interactions were involved in the control of 38% and 14% of the 72 proteins, respectively. Such a methodology might help understanding the architecture of regulatory networks and the possible adaptive or phenotypic significance of the polymorphism of the genes involved.

Hübner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Muller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics 37: 243-253. [Please cite this article if you have used one of the rat HXB kidney or peritoneal fat data sets.]
Kang HM, Ye C, Eskin E (2008) Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics 180:1909-1925 Full Text PDF Version. [An important method that can greatly improve the ability to resolve true genetic interactions in expression genetic studies.]
Ljungberg K, Holmgren S, Carlborg O (2004) Simultaneous search for multiple QTL using the global optimization algorithm DIRECT. Bioinformatics 20:1887-1895. [Please review and cite this article if you have exploited the DIRECT pair-scan tool and output graphs in WebQTL.]
Manly KF, Wang J, Williams RW (2005) Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression. Genome Biology 6: R27 Full Text HTML and PDF Version. [Please cite this article if you have used one of the HWT (Heritability Weighted Transform) data sets.]
Manly K, Williams RW (2001) WEBQTL—WWW service for mapping quantitative trait loci. International Mouse Genome Conference 15: 74. [First published abstract on WebQTL, presented Oct 2001, Edinburgh; also see 2002 CTC abstract]
Taylor BA, Heiniger HJ, Meier H (1973) Genetic analysis of resistance to cadmium-induced teticular damage in mice. Proc Soc Exp Biol Med 143:629-33 [This is one of the first full paper on the use of recombinant inbred strains in biomedical research and the first paper to use BXD lines of mice. Full text
Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, Holmans P, Rohrer K, Zhao A, Marlowe L, Kaleem M, McCorquodale DS 3rd, Cuello C, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV; NACC-Neuropathology Group, Heward CB, Reiman EM, Stephan D, Hardy J, Myers AJ (2009) Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet 84:445-58. [Please review and cite this article if you have used the HUMAN data set by Myers and colleagues in GeneNetwork.]
Williams RW, Shou S, Lu L, Wang J, Manly KF, Hsu HC, Mountz J, Threadgill DW (2002) Genomic analysis of transcriptional networks: combining microarrays with complex trait analysis. Complex Trait Consortium 1 [One of the first published abstracts on system genetic analysis of microarray data sets, presented May 2002.]
Zhang B, Schmoyer D, Kirov S, Snoddy J (2004) GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 5:16. [This reference describes GOTM--the predecessor of WebGestalt that is now used to analyze sets of covarying transcripts.]

GeneNetwork (2011)

Alberts R, Lu L, Williams RW, Schughart K. (2011) Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures. Respir Res 12:61 Full Text version
Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K (2011) Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease. BMC Genomics 12:610. Full Text version
Di Curzio DL, Goldowitz D (2011) The genetic basis of adrenal gland weight and structure in BXD recombinant inbred mice. Mammalian Genome 22:209–234 Full Text PDF version
Gatti DM, Lu L, Williams RW, Sun W, Wright FA, Threadgill DW, Rusyn I (2011) MicroRNA expression in the livers of inbred mice. Mutat Res 714:126-133
Gibson JN, Jellen LC, Unger EL, Morahan G, Mehta M, Earley CJ, Allen RP, Lu L, Jones BC (2011) Genetic analysis of iron-deficiency effects on the mouse spleen. Mamm Genome, in press
Hakvoort TB, Moerland PD, Frijters R, Sokolovic A, Labruyère WT, Vermeulen JL, Ver Loren van Themaat E, Breit TM, Wittink FR, van Kampen AH, Verhoeven AJ, Lamers WH, Sokolovic M (2011) Interorgan coordination of the murine adaptive response to fasting. J Biol Chem 286:16332-43
Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text HTML and PDF versions
Jablonski MM, Freeman NE, Orr WE, Templeton JP, Lu L, Williams RW, Geisert EE (2011) Genetic pathways regulating glutamate levels in retinal Müller cells. Neurochem Res 36:594-603
Jackson KJ, Chen X, Miles MF, Harenza J, Damaj MI (2011) The neuropeptide galanin and variants in the GalR1 gene are associated with nicotine dependence. Neuropsychopharmacology 36:2339-2348
Jansen R, Timmerman J, Loos M, Spijker S, van Ooyen A, Brussaard AB, Mansvelder HD, The Neuro-Bsik Mouse Phenomics Consortium; Smit AB, de Gunst M, Linkenhaer-Hansen K (2011) Novel candidate genes associated with hippocampal oscillations. PLoS One 6: e26586. HTML and PDF versions
Jiao Y, Jiao F, Yan J, Xiong Q, Shriner D, Hasty K, Stuart J, Gu W (2011) Identifying a major locus that regulates spontaneous arthritis in IL-1ra-deficient mice and analysis of potential candidates. Genet Res (Camb) 18:1-9
Krebs J, Römer D, Overall RW, Fabel K. Babu H, Brandt M, Williams RW, Jessberger S, Kempermann G (2011)) Adult hippocampal neurogenesis and plasticity in the infrapyramidal bundle of the mossy fiber projection: II. Genetic covariance and identification of Nos1 as a linking candidate gene. Frontiers in Neuroscience 5:106 PDF version
Jansen R, Timmerman J, Loos M, Spijker S, van Ooyen A, Brussaard AB, Mansvelder HD, The Neuro-Bsik Mouse Phenomics Consortium; Smit AB, de Gunst M, Linkenhaer-Hansen K (2011) Novel candidate genes associated with hippocampal oscillations. PLoS One 6: e26586 PDF
Krebs J, Römer B, Overall RW, Fabel K, Babu H, Brandt MD, Williams RW, Jessberger S, Kempermann G (2011) Adult hippocampal neurogenesis and plasticity in the infrapyramidal bundle of the mossy fiber projection: II. Genetic covariation and identification of Nos1 as linking candidate gene. Front Neurosci 5:106 PDF version
Laughlin RE, Grant TL, Williams RW, Jentsch JD (2011) Genetic dissection of behavioral flexibility: reversal learning in mice. Biol Psychiatry 69:1109-16
Lu H, Wang X, Pullen M, Guan H, Chen H, Sahu S, Zhang B, Chen H, Williams RW, Geisert EE, Lu L, Jablonski MM (2011) Genetic dissection of the Gpnmb network in the eye. Invest Ophthalmol Vis Sci. 52:4132-42
McLachlan SM, Aliesky HA, Chen CR, Williams RW, Rapoport B (2011) Exceptional Hyperthyroidism and a role for both major histocompatibility class I and class II genes in a murine model of Graves' disease. PLoS One 6:e21378
McLachlan SM, Lu L, Aliesky HA, Williams RW, Rapoport B (2011) Distinct genetic signatures for variability in total and free serum thyroxine levels in four sets of recombinant inbred mice. Endocrinology 152:1172-9
McCall RD (2011) HPNS seizure risk: a role for the Golgi-associated retrograde protein complex? Undersea Hyperb Med. 38:3-9
Moscou MJ, Lauter N, Steffenson B, Wise RP (2011) Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genet 7:e1002208
PDF version
Mozhui K, Wang X, Chen J, Mulligan MK, Li Z, Ingles J, Chen X, Lu L and Williams RW (2011) Genetic regulation of Nrxn1 expression: an integrative cross-species analysis of schizophrenia candidate genes. Transl Psychiatry 1: e25; doi:10.1038/tp.2011.24. PDF version
Porcu P, O'Buckley TK, Song SC, Harenza JL, Lu L, Wang X, Williams RW, Miles MF, Morrow AL (2010) Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: Identification of QTLs and downstream gene regulation. PLoS One 6:e18405 Full Text HTML and PDF versions
Suwanwela J, Farber CR, Haung B, Song B, Pan C, Lyon KM, Lusis AJ (2011) Systems genetics analysis of mouse chondrocyte differentiation. Journal of Bone and Mineral Research 26:74-760 PDF version
Whitney IE, Raven MA, Lu L, Williams RW, Reese BE (2011) A QTL on chromosome 10 modulates cone photoreceptor number in the mouse retina. Invest Ophthalmol Vis Sci. 52:3228-36
Whitney IE, Raven MA, Ciobanu DC, Poché RA, Ding Q, Elshatory Y, Gan L, Williams RW, Reese BE (2011) Genetic modulation of horizontal cell number in the mouse retina. Proc Natl Acad Sci USA 108:9697-702
Yadav JS, Pradhan S, Kapoor R, Bangar H, Burzynski BB, Prows DR, Levin L (2011) Multigenic control and sex-bias in host susceptibility to spore-induced pulmonary anthrax in mice. Infect Immun in press.
Yamamoto H, Williams EG, Mouchiroud L, Cantó C, Fan W, Downes M, Héligon C, Barish GD, Desvergne B, Evans RM, Schoonjans K, Auwerx J (2011) NCoR1 is a conserved physiological modulator of muscle mass and oxidative function. Cell 147:827-39

GeneNetwork (2010)

Alberts R, Schughart K (2010) QTLminer: identifying genes regulating quantitative traits.Full Text PDF version
Ciobanu DC, Lu L, Mozhui K, Wang X, Morris JA, Taylor WL, Dietz K, Simon P, Williams RW (2010) Detection, validation, and downstream analysis of allelic variation in gene expression. Genetics 184: 119-128 Full Text PDF
Downing C, Marks MJ, Larson C, Johnson TE (2010) The metabotropic glutamate receptor subtype 5 mediates sensitivity to the sedative properties of ethanol. Pharmacogenet Genomics 20:553-64
Gatti DM, Zhao N, Chesler EJ, Bradford BU, Shabalin AA, Yordanova R, Lu L, Rusyn I (2010) Sex-specific gene expression in the BXD mouse liver. Physiol Genomics 42:456-68 Full Text PDF Version
Grisham W, Schottler NA, Valli-Marill J, Beck L, Beatty J (2010) Teaching bioinformatics and neuroinformatics by using free web-based tools. CBE--Life Sciences Education 9: 98-107 Full Text PDF Version
Hoffman PL, Bennett B, Saba LM, Bhave SV, Carosone-Link PJ, Hornbaker CK, Kechris KJ, Williams RW, Tabakoff B 2010 Using the Phenogen website for 'in silico' analysis of morphine-induced analgesia: identifying candidate genes. Addiction Biology, doi: 10.1111/j.1369-1600.2010.00254.x
Li D, Mulligan MK, Wang X, Miles MF, Lu L, Williams RW (2010) A transposon in Comt generates mRNA variants and causes widespread expression and behavioral differences among mice. PLoS One. 2010 Aug 17;5(8):e12181. Full Text HTML and PDF Versions
Lionikas A, Carlborg O, Lu L; Peirce JL, Williams RW, Yu F, Vogler GP, McClearn GE, Blizard DA 2010 Genomic analysis of variation in hindlimb musculature of mice from the C57BL/6J and DBA/2J lineage. Journal of Heredity 2010; doi: 10.1093/jhered/esq023. Full Text PDF Version
Loguercio S, Overall RW, Michaelson JJ, Wiltshire T, Pletcher MT, Miller BH, Walker JR, Kempermann G, Su AI, Beyer A 2010 Integrative analysis of low- and high-resolution eQTL. PLoS One. 2010 Nov 10;5(11):e13920 Full Text PDF Version
Lynch RM, Naswa S, Rogers Jr GL, Kanla SA, Das S, Chesler EJ, Saxton AM, Langston MA, Voy, BH (2010) Identifying genetic loci and spleen gene coexpression networks underlying immunophenotypes in the BXD recombinant inbred mice. Physiological Genomics 41: 244-253 Full Text PDF version
Malkki HA, Donga LA, de Groot SE, Battaglia FP; NeuroBSIK Mouse Phenomics Consortium, Pennartz CM (2010) Appetitive operant conditioning in mice: heritability and dissociability of training stages. Front Behav Neuroscience 4:171 Full Text PDF version
Mulligan MK, Lu L, Overall RW, Kempermann G, Rogers GL, Langston MA, Williams RW (2010) Genetic analysis of BDNF expression cliques and adult neurogenesis in the hippocampus. Biomedical Sciences and Engineering Conference (BSEC) DOI: 10.1109/BSEC.2010.5510848 Full Text PDF version
Peidis P, Giannakouros T, Burow ME, Williams RW, Scott RE (2010) Systems genetics analyses predict a transcription role for P2P-R: molecular confirmation that P2P-R is a transcriptional co-repressor. BMC Systems Biology 4:14 Full Text PDF version and
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Laviviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ (2010) High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. Genes, Brain and Behavior 8:129-159 Full Text HTML Version
Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E. (2010) Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse. BMC Genomics. 2010 Nov 3;11:614 Full Text HTML Version
Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV (2010) Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Genes, Brain and Behavior 5:257-73. Full Text HTML Version
Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ (2010) Systems genetics analysis of mouse chondrocyte differentiation. JBMR, in press Full Text PDF version
Wang X, Chen Y, Wang X, Lu L. (2010) Genetic regulatory network analysis for App based on genetical genomics approach. Exp Aging Res 36:79-93

GeneNetwork (2009)

Badea A, Johnson GA, Williams RW (2009) Genetic dissection of the mouse brain using high-field magnetic resonance microscopy. Neuroimaging 45:1067-79
Boon AC, deBeauchamp J, Hollmann A, Luke J, Kotb M, Rowe S, Finkelstein D, Neale G, Lu L, Williams RW, Webby RJ (2009) Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol 83:10417-26 PMID: 19706712 Full Text PDF Version
Brigman JL, Mathur P, Lu L, Williams RW, Holmes A (2009) Genetic relationship between anxiety- and fear-related behaviors in BXD recombinant inbred mice. Behavioral Pharmacology 20:204-209 Full Text HTML Version,
Carneiro AM, Airey DC, Thompson B, Zhu CB, Lu L, Chesler EJ, Erikson KM, Blakely RD (2009) Functional coding variation in recombinant inbred mouse lines reveals multiple serotonin transporter-associated phenotypes. Proc Natl Acad Sci USA 106:2047-2052 Full Text HTML Version, Full Text PDF Version
Cowley MJ, Cotsapas CJ, Williams RB, Chan EK, Pulvers JN, Liu MY, Luo OJ, Nott DJ, Little PF (2009) Intra- and inter-individual genetic differences in gene expression. Mamm Genome 20:281-295 Full Text HTML Version
Davies MN, Lawn S, Whatley S, Fernandes C, Williams RW, Schalkwyk LC (2009) To what extent is blood a reasonable surrogate for brain gene expression studies: estimation from mouse hippocampus and spleen. Front. Neurogen. 1:2. doi:10.3389/neuro.15.002.2009
Foreman JE, Lionikas A, Lang DH, Gyekis JP, Krishnan M, Sharkey NA, Gerhard GS, Grant MD, Vogler GP, Mack HA, Stout JT, Griffith JW, Lakoski JM, Hofer SM, McClearn GE, Vandenbergh DJ, Blizard DA (2009) Genetic architecture for hole-board behaviors across substantial time intervals in young, middle-aged and old mice. Genes Brain Behav 8:714-27
Gaglani SM, Lu L, Williams RW, Rosen GD (2009) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 Full Text HTML Version, Full Text PDF Version
Gatti DM, Harrill AH, Wright FA, Threadgill DW, Rusyn I. (2009) Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mamm Genome 20:437-46.
Geisert EE, Lu L, Freeman-Anderson ME, Wang X, Gu W, Jiao Y, Williams RW (2009) Gene expression landscape of the mammalian eye: A global survey and database of mRNAs of 103 strains of mice. Molecular Vision 15:1730-1763 PMID:19727342 Full Text HTML Version, Full Text PDF Version
Grisham W (2009) Modular digitial course in undergraduate neuroscience education (MDCUNE): A website offering free digital tools for neuroscience educators. Journal of Undergraduate Neuroscience Education 8:A26-A31 Full Text PDF Version
An excellent example of how resources such as GeneNetwork and the Mouse Brain Library can be used in class room labs.
Jellen LC, Beard JL, Jones BC (2009) Systems genetics analysis of iron regulation. Biochemie in press. 19393285
Koutnikova H, Markku L, Lu L, Combe R, Paananen J, Kuulasmaa T, Kuusisto J, Häring H, Hansen T, Pedersen,O, Smith U, Hanefel M, Williams RW, Auwerx J (2009) Identification of UBP1 as a critical blood pressure determinant. PLoS Genetics 5:e1000591 Full Text HTML Version, Full Text PDF Version
Michaelson JJ, Loguercio S, Beyer A (2009) Detection and interpretation of expression quantitative trait loci (eQTL). Methods 48:265-276 Full Text HTML Version
Overall RW, Kempermann G, Peirce J, Lu L, Goldowitz D, Gage FH, Goodwin S, Smit AB, Airey DC, Rosen GD, Schalkwyk LC, Sutter TR, Nowakowski RS, Whatley S, Williams RW (2009) Genetics of the hippocampal transcriptome in mice: a systematic survey and online neurogenomic resource. Frontiers in Neuroscience 3:55 Full Text HTML Version, Full Text PDF Version
Overton JD, Adams GS, McCall RD, Kinsey ST (2009)High energy phosphate concentrations and AMPK phosphorylation in skeletal muscle from mice with inherited differences in hypoxic exercise tolerance. Comp Biochem Physiol A Mol Integr Physiol 152:478-85
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Laviviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ (2009) High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. Genes, Brain and Behavior 8:in press PMID: 19958391 Full Text HTML Version
Ruden DM, Chen L, Possidente D, Possidente B, Rasouli P, Wang L, Lu X, Garfinkel MD, Hirsch HV, Page GP (2009) Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to lead. Neurotoxicology 30:898-914
Rosen GL, Pung C, Owens C, Caplow J, Kim H, Lu L, Williams RW (2009) Genetic modulation of striatal volume in BXD recombinant inbred mice. Genes, Brain & Behavior 8:296-308
Saccone SF, Bierut LJ, Chesler EJ, Kalivas PW, Lerman C, Saccone NL, Uhl GR, Li CY, Philip VM, Edenberg HJ, Sherry ST, Feolo M, Moyzis RK, Rutter JL (2009) Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. PLoS ONE 4:e5225. Full Text HTML Version, Full Text PDF Version. [Supplementary table 1 provides links to many transcripts and genes, some of which were mined from an analysis of GeneNetwork data sets.]
Silva GL, Junta CM, Sakamoto-Hojo ET, Donadi EA, Louzada-Junior P, Passos GA (2009) Genetic susceptibility loci in rheumatoid arthritis establish transcriptional regulatory networks with other genes. Ann N Y Acad Sci 1173:521-37
Tapocik JD, Letwin N, Mayo CL, Frank B, Luu T, Achinike O, House C, Williams R, Elmer GI, Lee NH (2009) Identification of candidate genes and gene networks specifically associated with analgesic tolerance to morphine. J Neurosci 2:5295-307 Full Text HTML
Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, Macchiarulo A, Yamamoto H, Mataki C, Pruzanski M, Pellicciari R, Auwerx J, Schoonjans K (2009) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167-77 Full Text PDF
Webb BT, McClay JL, Vargas-Irwin C, York TP, van den Oord EJCG (2009) In silico whole genome association scan for murine prepulse inhibition. PLoS ONE 4: e5246. doi:10.1371/journal.pone.0005246 Full Text HTML, Full Text HTML
Weng J, Symons MN, Singh SM (2009) Studies on syntaxin 12 and alcohol preference involving C57BL/6J and DBA/2J strains of mice. Behav Genet. 39:183-191 Full Text HTML Version
Whitney IE, Raven MA, Ciobanu DC, Williams RW, Reese BE (2009) Multiple genes on chromosome 7 regulate dopaminergic amacrine cell number in the mouse. Investigative Ophthalmology & Visual Science 50:1996-2003. Full Text HTML Version.
Wu S, Lusis AJ, Drake TA (2009) A systems-based framework for understanding complex metabolic and cardiovascular disorders. Journal of Lipid Research, in press Full Text PDF
Zheng QY, Ding D, Yu H, Salvi RJ, Johnson KR (2009) A locus on distal chromosome 10 (ahl4) affecting age-related hearing loss in A/J mice. Neurobiol Aging. 2009 Oct;30(10):1693-705.

GeneNetwork (2008)

Abdeltawab NF, Aziz RK, Kansal R, Rowe SL, Su Y, Gardner L, Brannen C, Nooh MM, Attia RR, Abdelsamed HA, Taylor WL, Williams RW, Kotb M (2008) An unbiased systems genetics approach to mapping genetic loci modulating susceptibility to severe streptococcal sepsis. PLoS Pathogens 4:e1000042 Full Text HTML Version, Full Text PDF Version
Bertrand L, Fan Y, Nissanov J, Rioux L (2008) Genetic regulation of the anatomy of the olfactory bulb. Society for Neuroscience 2008
Bhoumik A, Singha N, O'Connell MJ, Ronai ZA (2008) Regulation of TIP60 by ATF2 modulates ATM activation. J Biol Chem 283:17605-14 Full Text HTML Version, Full Text PDF Version
Bjork K, Rimondini R, Hansson AC, Terasmaa A, Hyytiä P, Heilig M, Sommer WH (2008) Modulation of voluntary ethanol consumption by beta-arrestin 2. FASEB J 22:2552-60 Full Text HTML Version, Full Text PDF Version
Boone EM, Hawks BW, Li W, Garlow SJ (2008) Genetic regulation of hypothalamic cocaine and amphetamine-regulated transcript (CART) in BxD inbred mice. Brain Res 1194:1-7
Crawford NP, Alsarraj J, Lukes L, Walker RC, Officewala JS, Yang HH, Lee MP, Ozato K, Hunter KW (2008) Bromodomain 4 activation predicts breast cancer survival. Proc Natl Acad Sci USA 105:6380-6385 Full Text HTML Version
Crawford NP, Walker RC, Lukes L, Officewala JS, Williams RW, Hunter KW (2008) The Diasporin Pathway: a tumor progression-related transcriptional network that predicts breast cancer survival. Clin Exp Metastasis 25:357-69 Full Text HTML Version
Danciger M, Ogando D, Yang H, Matthes MT, Yu N, Ahern K, Yasumura D, Williams RW, Lavail MM (2008) Genetic modifiers of retinal degeneration in the rd3 mouse. Invest Ophthalmol Vis Sci 49:2863-2869 Full Text HTML Version
Druka A, Druka I, Centeno AG, Li H, Sun Z, Thomas WT, Bonar N, Steffenson BJ, Ullrich SE, Kleinhofs A, Wise RP, Close TJ, Potokina E, Luo Z, Wagner C, Schweizer GF, Marshall DF, Kearsey MJ, Williams RW, Waugh R (2008) Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genet 9:73 Full Text HTML Version
Dykstra B, de Haan G (2008) Hematopoietic stem cell aging and self-renewal. Cell Tissue Res 331:91-101
Ferrara CT, Wang P, Neta EC, Stevenes RD, Bain JR, Wenner BR, Ilkayeva OR, Keller MP, Blasiole DA, Kendziorski C, Yandell BS, Newgard CB, Attie AD (2008) Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. PLoS Genetics 4: e1000034. doi:10.1371/journal.pgen.1000034 Full Text HTML Version
Gerrits A, Dykstra B, Otten M, Bystrykh L, de Haan G (2008) Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny. Immunogenetics. 60:411-22.
Grieve IC, Dickens NJ, Pravenec M, Kren V, Hubner N, Cook SA, Aitman TJ, Petretto E, Mangion J (2008) Genome-wide co-expression analysis in multiple tissues. PLoS One. 3:e4033. PMID: 19706712 Full Text HTML Version, Full Text PDF Version
Hall R, Hillebrandt S, Hochrath K, Gruenhage F, Weber S, Schwartz S, Yildiz Y , Sauerbruch T, Lammert F (2008) BXD recombinant inbred mouse lines–a genetic reference population for dissection of the complex genetics of liver fibrosis. Zeitschrift fur Gastroenterologie 46:in press Full Text PDF Version
Han B, Altman NS, Mong JA, Klein LC, Pfaff DW, Vandenbergh DJ (2008) Comparing quantitative trait loci and gene expression data. Advances in Bioinformatics, doi:10.1155/2008/719818. Full Text PDF Version and Full Text HTML Version
Hayat Y, Yang J, Xu HM, Zhu J (2008) Influence of outliers on QTL mapping for complex traits. J Zhejiang Univ Sci B. 9:931-7
Heimel JA, Hermans JM, Sommeijer JP; Neuro-Bsik Mouse Phenomics consortium, Levelt CN (2008) Genetic control of experience-dependent plasticity in the visual cortex. Genes Brain Behav 7:915-23. Full Text PDF Version
Jan TA, Lu L, Li CX, Williams RW, Waters RS (2008) Genetic analysis of posterior medial barrel subfield (PMBSF) size in somatosensory cortex (SI) in recombinant inbred strains of mice. BMC Neuroscience 9:3 Full Text PDF Version
Johnson KR, Longo-Guessa C, Gagnona LH, Yub H, Zhengb QY (2008) A locus on distal chromosome 11 (ahl8) and its interaction with Cdh23 ahl underlie the early onset, age-related hearing loss of DBA/2J mice. Genomics 92:219-225
Jones LC, Beard JL, Jones BC (2008) Genetic analysis reveals polygenic influences on iron, copper, and zinc in mouse hippocampus with neurobiological implications. Hippocampus 18:398-410 Full Text PDF Version
Jones LC, Earley CJ, Allen RP, Jones BC (2008) Of mice and men, periodic limb movements and iron: how the human genome informs the mouse genome. Genes, Brain and Behavior 7:513-514. Full Text PDF Version
Kang HM, Ye C, Eskin E (2008) Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics doi:10.1534/genetics.108.094201 Full Text PDF Version. [An important method that can greatly improve the ability to resolve true genetic interactions in expression genetic studies.]
Kadarmideen HN (2008) Genetical systems biology in livestock: Application to gonadotrophin releasing hormone and reproduction. IET Systems Biology 2:423-441 Full Text PDF Version
Kerns RT, Miles MF (2008) Microarray analysis of ethanol-induced changes in gene expression. Alcohol: Methods and Protocols. In: Methods in Molecular Biology 447:395-410 Full Text PDF Version
Kotb M, Fathey N, Aziz R, Rowe S, Williams RW, Lu L (2008) Unbiased forward genetics and systems biology approaches to understanding how gene-environment interactions work to predict susceptibility and outcomes of infections. Novartis Found Symp 293:156-165; discussion pp 165-167, 181-183
Loos M (2008) The PhenoTyper automated home cage environment as a high throughput tool to detect behavioral abnormalities in mutant mice. Proceeding of Measuring Behavior (Maastricht, The Netherlands, Aug 26-29, 2008). Full Text PDF Version
Loudet O, Michael TP, Burger BT, Le Metté C, Mockler TC, Weigel D, Chory J (2008) A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana. Proc Natl Acad Sci USA 105:17193-8 Full Text HTML Version, and Full Text Supplement
Lu L, Wei L, Peirce JL, Wang X, Zhou J, Homayouni R, Williams RW, Airey DC (2008) Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight. BMC Genomics 9:444 Full Text HTML Version, and Full Text PDF Version
Macedo C, Magalhaes DA, Tonani M, Marques MC, Junta CM, Passos GA (2008) Genes that code for T cell signaling proteins establish transcriptional regulatory networks during thymus ontogeny. Mol Cell Biochem 318:63-71
Morahan G, Peeva V, Munish M, Williams R (2008) Systems genetics can provide new insights in to immune regulation and autoimmunity. Journal of Autoimmunity 31:233-236. Full Text PDF Version
Mozhui RT, Ciobanu DC, Schikorski T, Wang XS, Lu L, Williams RW (2008) Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genetics 4: e1000260. doi:10.1371/journal.pgen.1000260 Full Text HTML Version
New J, Kendall W, Huang J, Chesler E (2008) Dynamic visualization of coexpression in systems genetics data. IEEE Trans Visualization & Computer Graphics 14:1081-1095.
Pravenec M, Petretto E (2008) Insight into the genetics of hypertension, a core component of the metabolic syndrome. Genes and cell metabolism. Curr Opin Clin Nutr Metab Care 11:393-397 Full Text HTML Version
Pritchard M, Reeves RH, Dierssen M, Patterson D, Gardiner KJ (2008) Down syndrome and the genes of human chromosome 21: current knowledge and future potentials. Cytogenetics and Genome Research 121:67-77
Reiner DJ, Jan TA, Boughter JD Jr, Li CX, Lu L, Williams RW, Waters RS (2008) Genetic analysis of tongue size and taste papillae number and size in recombinant inbred strains of mice. Chemical Senses 33:693-707
Swertz MA, Tesson BM, Scheltema RA, Vera G, Jansen RC (2008) MOLGENIS for genetical genomics. Chapter 5. MGG: a customizable software infrastructure for genetical genomics. Full Text PDF Version
Williams RW, Lu L (2008) Integrative genetic analysis of alcohol dependence using the GeneNetwork web resources. In Pathways to Alcohol Dependence: Alcohol Research & Health 31:275-277 Full Text PDF Version
Woo JH, Zheng T, Kim JH (2008) DACE: Differential Allelic Co-Expression test for estimating regulatory associations of SNP and biological pathway. International Journal of Functional Informatics and Personalised Medicine 1:407-418
Yang RJ, Mozhui K, Karlsson RM, Cameron HA, Williams RW, Holmes A (2008) Variation in mouse basolateral amygdala volume is associated with differences in stress reactivity and fear learning. Neuropsychopharmacology. 33:2595-604 Full Text HTML Version, Full Text PDF Version
Zhang Y, Maksakova IA, Gagnier L , van de Lagemaat LN, Mager DL (2008) Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet 4(2): e1000007. doi:10.1371/journal.pgen.1000007 Full Text HTML Version

GeneNetwork (2007)

Aziz RK, Kansal R, Abdeltawab NF, Rowe SL, Su Y, Carrigan D, Nooh MM, Attia RR, Brannen C, Gardner LA, Lu L, Williams RW, Kotb M (2007) Susceptibility to severe Streptococcal sepsis: use of a large set of isogenic mouse lines to study genetic and environmental factors. Genes and Immunity 8:404-415
Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L, Cui Y (2007) An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Hum Mol Genet 16:1381-1390
Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y (2007) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res. 35(Database issue):D51-54 Full Text PDF Version, Full Text HTML Version
Benhamou JP, Rizzetto M, Reichen J, Rodés J (2007) Textbook of hepatology: from basic science to clinical practice. Blackwell Publishing, p. 379), ISBN 1405127414
Bennett B, Downing C, Carosone-Link P, Ponicsan H, Ruf C, Johnson TE (2007) Quantitative trait locus mapping for acute functional tolerance to ethanol in the L x S recombinant inbred panel. Alcohol Clin Exp Res. 31:200-208. [Phenotype data described in this paper are accessible in GeneNetwork in the LXS Phenotype database; ID numbers 10126, 10127, 10132, 10134, 10138, and 10139 (select Species=MOUSE, Group=LXS, Type=PHENOTYPES and search the ALL field with the term "functional" or just enter the ID numbers above.]
Cervino ACL, Darvasi A, Fallah Mi, Mader CC, Tsinoremas NF (2007) An integrated in silico gene mapping strategy in inbred mice. Genetics 175:321-333 Full Text PDF Version
Chesler EJ (2007) Bioinformatics of behavior. In Neurobehavioral Genetics, ed Jones BC, Mormede P CRC Press ISBN 084931903X InterScience 95-114), ISBN 1405127414
Chesler EJ (2007) Combining quantitative trait and gene-expression data. In Bioinformatics of Geneticists, ed Barnes MR, Wiley InterScience
Coppin H, Darnaud V, Kautz L, Meynard D, Aubry M, Mosser J, Martinez M, Roth MP (2007) Gene expression profiling of Hfe-/- liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers. Genome Biology 8:R221 Full Text PDF Version, Full Text HTML Version
Crawford NP, Qian X, Ziogas A, Papageorge AG, Boersma BJ, Walker RC, Lukes L, Rowe WL, Zhang J, Ambs S, Lowy DR, Anton-Culver H, Hunter KW (2007) Rrp1b, a new candidate susceptibility gene for breast cancer progression and metastasis. PLoS Genetics 3: e214 Full Text PDF Version, Full Text HTML Version
Dong H, Martin MV, Colvin J, Ali Z, Wang L, Lu L, Williams RW, Rosen GD, Csernansky JG, Cheverud JM (2007) Quantitative trait loci linked to thalamus and cortex gray matter volumes in BXD recombinant inbred mice. Heredity 99:62-69
Fox JG, Barthold SW, Davisson MT, Newcomer CE (2007) The mouse in biomedical research. (2nd ed). Academic Press, p. 530.
French L, Pavlidis P (2007) Informatics in neuroscience. Briefings in Bioinformatics 8:446-456
Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I (2007) Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology 46:548-557 Full Text PDF Version
Grice DE, Reenila I, Mannisto PT, Brooks Ai, Smith GG, Golden GT, Buxbaum JD, Berrettini WH (2007) Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine. BMC Genomics 8:76 Full Text PDF Version, Full Text HTML Version
Hancock JM, Mallon AM (2007) Phenobabelomics--mouse phenotype data resources. Brief Funct Genomic Proteomic 6:292-301
Hawes JJ, Tuskan RG, Reilly KM (2007) Nf1 expression is dependent on strain background: implications for tumor suppressor haploinsufficiency studies. Neurogenetics 8: 121-130. [Nf1 expression in whole brain (INIA data set) and in striatum (Rosen data set) was used to catalyze a detailed study of the degree of NPcis (Nf1 + Trp53) haploinsufficiency. Email: kreilly@ncifcrf.gov]
Hofstetter JR, Svihla-Jones DA, Mayeda AR (2007) A QTL on mouse chromosome 12 for the genetic variance in free-running circadian period between inbred strains of mice. J Circadian Rhythms 5:7 Full Text PDF Version, Full Text HTML Version
Hsu HC, Lu L, Yi N, Van Zant G, Williams RW, Mountz JD (2007) Quantitative trait locus mapping in aging systems. In: Methods in Molecular Biology (Vol 371). Biological Aging: Methods and Protocols, ed Tollefsbol TO, Humana Press, Inc., Netlibrary, Springer Google Book Search
Jawad M, Giotopoulos G, Fitch S, Cole C, Plumb M, Talbot CJ (2007) Mouse bone marrow and peripheral blood erythroid cell counts are regulated by different autosomal genetic loci. Blood Cells Mol Disease 38:69-77
Jessberger S, Gage FH (2007) ZOOMING IN: a new high-resolution gene expression atlas of the brain. Mol Syst Biol. 3:75
Jones BC, Beard JL, Gibson JN, Unger EL, Allen RP, McCarthy KA, Earley CJ (2007) Systems genetic analysis of peripheral iron parameters in the mouse. American Journal of Physiology Regul Integr Comp Physiol 293: R116-124 Full Text HTML Version, and see full text of Jones et al., 1999.
Jones BC and Mormede JP (2007) Neurobehavioral genetics: methods and applications. (2007)" CRC Press, Taylor & Francis Group, Boca Raton, Florida, p. 102, ISBN 084931903X
Kadarmideen HN, Reverter A (2007) Combined genetic, genomic and transcriptomic methods in the analysis of animal traits. CABI Review: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2: No. 042 (16 pp) Full Text PDF Version
Korostynski M, Piechota M, Kaminska D, Solecki W. Przewlocki R (2007) Morphine effects on striatal transcriptome in mice. Genome Biology 8:R128
Lad HV, Liu L, Payá-Cano JL, Fernandes C, Schalkwyk LC (2007) Quantitative traits for the tail suspension test: automation, optimization, and BXD RI mapping. Mamm Genome. 2007 Jul;18(6-7):482-91 Full Text PubMed Central version
Liang Y, Jansen M, Aronow B, Geiger H, Van Zant G (2007) The quantitative trait gene latexin influences the size of the hematopoietic stem cell population in mice. Nature Genetics 39:141-142 (doi: 10.1038/ng1938). [Using the BXD mouse strains, Liang, Van Zant and colleagues, demonstrate that sequence variants in Lxn modulate cell cycling kinetics of bone marrow stem cells. High expression of Lxn mRNA and protein is associated with the C57BL/6J allele and with lower proliferative activity. The authors made good use of the BXD Hematopoietic Stem Cell data set and Lxn Affymetrix probe set 96065_at. Figures 1 and 5 were generated using GeneNetwork.]
Llamas B, Bélanger S, Picard S, Deschepper CF (2007) Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice. Physiol Genomics 31:176-82
Meng PH, Macquet A, Loudet O, Marion-Poll A, North HM (2007) Analysis of natural allelic variation controlling Arabidopsis thaliana seed germinability in response to cold and dark: identification of three major quantitative trait loci. Molecular Plant, doi:10.1093/mp/ssm014
Mouse Phenotype Database Integration Consortium (2007) Integration of mouse phenome data resources. Mammalian Genome, 18:157-163. PDF Preprint Version
Miyairi I, Tatireddigari VR, Mahdi OS, Rose LA, Belland RJ, Lu L, Williams RW, Byrne GI (2007) The p47 GTPases Iigp2 and Irgb10 regulate innate immunity and inflammation to murine Chlamydia psittaci. J Immunol 179:1814-1824
Mozhui K, Hamre KM, Holmes A, Lu L, Williams RW (2007) Genetic and structural analysis of the basolateral amygdala complex in BXD recombinant inbred mice. Behav Genet. 37:223-243 Full Text MS Word Version (authors' copy)
Peirce JL, Broman KW, Lu L, Williams RW (2007) A simple method for combining genetic mapping data from multiple crosses and experimental designs. PLoS ONE 2:e1036 Full Text PDF Version, Full Text HTML Version
Pérez-Enciso M, Quevedo JR, Bahamonde A (2007) Genetical genomics: use all data. BMC Genomics 8:69. Full Text PDF Version, Full Text HTML Version
Rosen GD, Bai J, Wang Y, Fiondella CG, Threlkeld SW, LoTurco JJ, Galaburda AM (2007) Disruption of neuronal migration by RNAi of Dyx1c1 results in neocortical and hippocampal malformations. Cereb Cortex 17:2562-72. Full Text PDF Version,
Rosen GD, Chesler EJ, Manly KF, Williams RW (2007) An informatics approach to systems neurogenetics. Methods Mol Biol 401:287-303
Sunkin SM, Hohmann JG (2007) Insights from spatially mapped gene expression in the mouse brain. Human Molecular Genetics 16: R209-219 Full Text PDF Version, Full Text HTML Version
Swertz MA, Jansen RC (2007) Beyond standardization: dynamic software infrastructure for systems biology. Nature Reviews Genetics:235-243
Taylor M, Valdar W, Kumar A, Flint J, Mott R (2007) Management, presentation and interpretation of genome scans using GSCANDB. Bioinformatics 23:1545-1549 Full Text PDF Version, Full Text HTML Version
Vazquez-Chona F, Lu L, Williams RW, Geisert EE (2007) Genetic influences on retinal gene expression and wound healing. Gene Regulation and Systems Biology 1:327-348 Full Text PDF Version
von Rohr P, Friberg M, Kadarmideen HN (2007) Prediction of transcription factor binding sites using results from genetical genomics investigations. Journal of Bioinformatics and Computational Biology 5:773-793 Full Text PDF Version
Wan X, Pavlidis P (2007) Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics 5:161-75. HTML example of using GEMMA and GeneNetwork.
Zou W, Aylor DL, Zeng ZB (2007) eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. BMC Bioinformatics 8:7. Full Text PDF Version, Full Text HTML Version.

GeneNetwork (2006)

Aliesky HA, Pichurin PN, Chen CR, Williams RW, Rapoport B, McLachlan SM (2006) Probing the genetic basis for thyrotropin receptor antibodies and hyperthyroidism in immunized CXB recombinant inbred mice. Endocrinology 147:2789-800. Full Text PDF Version, Full Text HTML Version.
Bao L, Wei L, Peirce JL, Homayouni R, Li H, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D, Cui Y (2006) Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. Mammalian Genome 17:575-583 Full Text PDF Version, Full Text HTML Version.
Beatty J, Laughlin RE (2006) Genomic regulation of natural variation in cortical and noncortical brain volume. BMC Neuroscience 7:16 [This mapping study made use of both the Mouse Brain Libray online collection of sections of BXD brains and GeneNetwork/WebQTL.]
Bennett B, Carosone-Link P, Zahniser NR, Johnson TE (2006) Confirmation and fine mapping of ethanol sensitivity quantitative trait loci, and candidate gene testing in the LXS recombinant inbred mice. J Pharmacol Exp Ther 319:299-307 (doi: 10.1038/ng1938) Full Text PDF Version
Bennett B, Downing C, Parker C, Johnson TE (2006) Mouse genetic models in alcohol research. Trends Genet 22:367-74
Cervino ACL, Darvasi A, Fallahi M, Mader CC, Tsinoremas NF (2006) An integrated in silico gene mapping strategy in inbred mice (2006) Genetics 175:321-333
Chesler EJ, Langston MA (2006) Combinatorial genetic regulatory network analysis tools for high throughput transcriptomic data. In: Lecture Notes in Computer Science. Springer, Heidelberg, Vol. 4023: 150-165.
De Haro L, Panda S(2006) Systems biology of circadian rhythms: an outlook. Journal of Biological Rhythms 21:507 Full Text PDF Version
Jones LC, McCarthy KA, Beard JL, Keen CL, Jones BC (2006) Quantitative genetic analysis of brain copper and zinc in BXD recombinant inbred mice. Nutritional Neuroscience 9:81-92 [This paper includes a large data set consisting of 16 traits related to copper and zinc metabolism in the CNS that is part of the Mouse BXD Phenotype database in GeneNetwork. The entire data set can be found by entering the search term "Jones LC" in the ALL search field.]
Kadarmideen HN, Janss LLG (2006) Population and systems genetics analyses of cortisol in pigs divergently selected for stress. Physiological Genomics 29:57-65 Full Text PDF Version, Full Text HTML Version. [One of several great papers in a freely available (open) Special Issue of Mammalian Genome devoted to QTLs, Expression and Complex Trait Analysis. This study makes great use of the BXD INIA Brain mRNA M430 PDNN data set and GeneNetwork/WebQTL.]
Kadarmideen HN, von Rohr, P, Janss LLG (2006) From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mammalian Genome 17:548-564 Full Text PDF Version, Full Text HTML Version. [One of several great papers in a freely available (open) Special Issue of Mammalian Genome devoted to QTLs, Expression and Complex Trait Analysis. This study makes great use of the BXD INIA Brain mRNA M430 PDNN data set and GeneNetwork/WebQTL.]
Kamminga LM, Bystrykh LV, de Boer A, Houwer S, Douma J, Weersing E, Dontje B, de Haan G (2006) The Polycomb group gene Ezh2 prevents hematopoietic stem cell exhaustion. Blood 107:2170-2179 Full Text PDF Version
Keeley MB, Wood MA, Isiegas C, Stein J, Hellman K, Hannenhalli S, Abel T (2006) Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes. BMC Genomics 7: 146 (doi: 10.1186/1471-2164-7-146). Full Text HTML Version. [A combination of data sources including the Rosen HBP Striatum data set used to study opioid-related traits. Their Fig 3C and Fig 5 take good advantage of GeneNetwork and WebQTL output graphs.]
Lan H, Chen M, Flowers JB, Yandell BS, Stapleton DS, Mata CM, Mui ET, Flowers MT, Schueler KL, Manly KF, Williams RW, Kendziorski C, Attie A (2006) Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genetics 2:e6 [Please cite this work if you make use of the B6BTBRF2 liver transcriptome data.]
Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA (2006) An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Computional Biology 2:e159
Loney KD, Uddin RK, Singh SM (2006) Analysis of metallothionein brain gene expression in relation to ethanol preference in mice using cosegregation and gene knockouts. Alcohol Clin Exp Res 30:15-25
Martin MV, Dong H, Vallera D, Lee D, Lu L, Williams RW, Rosen GD, Cheverud JM, Csernansky JG (2006) Independent quantitative trait loci influence ventral and dorsal hippocampal volume in recombinant inbred strains of mice. Gene, Brain and Behavior 5:614-623.
van Os R, Ausema A, Noach EJ, van Pelt K, Dontje BJ, Vellenga E, de Haan G (2006) Identification of quantitative trait loci regulating haematopoietic parameters in B6AKRF2 mice. British Journal of Haematolology 132:80-90.
Peirce JL, Li H, Wang J, Manly KF, Hitzemann RJ, Belknap JK, Rosen GD, Goodwin S, Sutter TR, Williams RW, Lu L (2006) How replicable are mRNA expression QTL? Mammalian Genome 17:643-656. Full Text PDF Version, Full Text HTML Version. [An important paper in which four matched expression data sets (whole brain and striatum) generated using both recombinant inbred and F2 intercrosses were directly compared.]
Ponomarev I, Maiya R, Harnett MT, Schafer GL, Ryabinin AE, Blednov YA, Morikawa H, Boehm SL 2nd, Homanics GE, Berman AE, Lodowski KH, Bergeson SE, Harris RA (2006) Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors. J Neurosci 26:5673-83 Full Text PDF Version, Full Text HTML Version
Radcliffe RA, Lee MJ, Williams RW (2006) Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Mammalian Genome 17:629-642 Full Text PDF Version, Full Text HTML Version
Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV (2006) Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Genes Brain Behav 5:257-273 [This study exploited the original GeneNetwork Affymetrix U74Av2 brain data set to validate a set of transcripts modulated by ethanol treatment.]
Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B (2006) Candidate genes and their regulatory elements: alcohol preference and tolerance. Mammalian Genome 17:669-688 Full Text PDF Version, Full Text HTML Version [A lovely paper describing results of a whole brain BXD study involving males from 30 strains (four individual arrays (not pooled) per strain). The data described in this study have been made accessible from GeneNetwork.]
Shifman S, Bell JT, Copley BR, Taylor M, Williams RW, Mott R, Flint J (2006) A high resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biology 4:2227-2237 Full Text PDF Version [A comprehensive analysis of recombination rates using several populations of mice, including most major genetic reference populations.]
van Os R, Ausema A, Noach EJ, van Pelt K, Dontje BJ, Vellenga E, de Haan G (2006) Identification of quantitative trait loci regulating haematopoietic parameters in B6AKRF2 mice. British Journal of Haematology 132:80-90
Veenstra-VanderWeele J, Qaadir A, Palmer AA, Cook EH Jr, de Wit H. (2006) Association between the casein kinase 1 epsilon gene region and subjective response to D-amphetamine. Neuropsychopharmacology 31:1056-1063 Full Text HTML Version [This mapping study made use of GeneNetwork/WebQTL to show that "the region that contains Csnk1e was also found to contain a QTL for MA sensitivity, and complementary data from WebQTL (Chesler et al, 2005) showed that this same region of mouse chromosome 15 influenced Csnk1e transcript abundance, indicating the presence of a cis-acting eQTL."]
Voy BH, Scharff JA, Perkins AD, Saxton AM, Borate B, Chesler EJ, Branstetter LK, Langston MA (2006) Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Computational Biology 2:e89. [A paper that introduces the use of cliques in analyzing microarray data sets. One of the GeneNetwork databases (BXD Hematopoietic Stem Cells) was used to follow up on a strong candidate gene, Tubby-like protein 4 Tulp4) that may have a role in immune function.
Williams RH, Cotsapas CJ, Cowley MJ, Chan E, Nott DJ, Little PF (2006) Normalization procedures and detection of linkage signal in genetical-genomics experiments. Nature Genetics 38:855-856. [A set of letters to the editor by Rohan Williams and colleagues, Chesler and colleagues, and Petretto and colleagues. All three letters highlight some of the technical challenges of analyzing expression data in a genetic context and point to the need for great care and attention to normalization methods. Well worth reviewing. Normalization is still very much an art, and it is quite likely that no one normalization procedure will be optimal for all different research questions. The old adage: "different horses for different courses" is likley to apply.]
Williams RW (2006) Expression genetics and the phenotype revolution. Mammalian Genome 17:496-502 Full Text PDF Version, Full Text HTML Version. [My take on where systems genetics may take us in the next few years.]

GeneNetwork (2005)

Alberts R, Terpstra P, Bystrykh LV, de Haan G, Jansen RC (2005) A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays Genetics 171:1437-1439
Alberts R, Fu J, Swertz MA, Lubbers LA, Albers CJ, Jansen RC (2005) Combining microarrays and genetic analysis. Brief Bioinform. 6:135-145 Full text PDF version
Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke M, de Haan G (2005) Uncovering regulatory pathways affecting hematopoietic stem cell function using “genetical genomics." Nature Genetics, 37:225-232
Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin N, Langston MA, Threadgill DW, Manly KF, Williams RW (2005) Genetic dissection of gene expression reveals polygenic and pleiotropic networks modulating brain structure and function. Nature Genetics 37: 233-242
Flaherty L, Herron B, Symula D (2005) Genome Research 15:1741-1745 Full text PDF version
Garlow SJ, Boone E, Li W, Owens MJ, Nemeroff CB (2005) Genetic analysis of hypothalamic corticotropin-releasing factor system. Endocrinology 146: 2362-2368
Gammie SC, Hasen NS, Awad TA, Auger AP, Jessen HM, Panksepp JB, Bronikowski AM (2005) Gene array profiling of large hypothalamic CNS regions in lactating and randomly cycling virgin mice. Molecular Brain Research 139: 201-211
Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266 [www.brainchip.vcu.edu/kerns_apptable1.pdf for a complete table of modulated transcripts.]
Li HQ, Lu L, Manly KF, Wang J, Zhou M, Williams RW, Cui Y (2005) Inferring gene transcriptional modulatory relations: a genetical genomics approach. Human Molecular Genetics 14: 1119-1125
Li J, Burmeister M (2005) Genetical genomics: combining genetics with gene expression analysis. Human Molecular Genetics 14:163-169. [ Full text PDF version]
Lozier JN, Tayebi N, Zhang P (2005) Mapping of genes that control the antibody response to human factor IX in mice. Blood 105: 1029-1035
MacLaren EJ, Sikela JM (2005) Cerebellar gene expression profiling and eQTL analysis in inbred mouse strains selected for ethanol sensitivity. Alcoholism: Clinical and Experimental Research 29: 1568-1579. HTML and PDF reprints.
Matthews B, Bhave SV, Belknap JK, Brittingham C, Chesler EJ, Hitzemann RJ, Hoffman PL, Lu L, McWeeney S, Miles MR, Tabakoff B, Williams RW (2005) Complex genetics of interactions of alcohol and CNS function and behavior. Alcoholism: Clinical and Experimental Research 29:1706-1719
Mountz JD, Yang P, Wu Q, Zhou J, Tousson A, Fitzgerald A, Allen J, Wang X, Cartner S, Grizzle WE, Yi N, Lu L, Williams RW, Hsu HC (2005) Genetic segregation of spontaneous erosive arthritis and generalized autoimmune disease in BXD2 recombinant inbred strain of mice. Scadinavian Journal of Immunology 61:1-11 Full Text PDF Version
Li CX, Wei X, Lu L, Peirce JL, Wiliams RW, Waters RS (2005) Genetic analysis of barrel field size in the first somatosensory area (S1) in inbred and recombinant inbred strains of mice. Somatosensory and Motor Research 22:141-150
Palmer AA, Verbitsky M, Suresh R, Kamen HM, Reed CI, Li N, Burkhart-Kasch S, McKinnon CS, Belknap JK, Gilliam TC, Phillips TJ (2005) Gene expression differences in mice divergently selected for methamphetamine sensitivity. Mammalian Genome 16:291-305
Pravenec M, Kren V (2005) Genetic analysis of complex cardiovascular traits in the spontaneously hypertensive rat. Exp Physiol 90:273-276 Full Text PDF Version, Full Text HTML Version
Scott RE, White-Grindley E, Ruley HE, Chesler EJ, Williams RW (2005) P2P-R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P-R mRNA. Journal of Cellular Physiology 204:99-105 Full text HTML version
Vazquez-Chona FR, Khan AN, Chan CK, Moore AN, Dash PK, Rosario Hernandez R, Lu L, Chesler EJ, Manly KF, Williams RW, Geisert Jr EE (2005) Genetic networks controlling retinal injury. Molecular Vision 11:958-970
Yang H, Crawford N, Lukes L, Finney R, Lancaster M, Hunter KW (2005) Metastasis predictive signature profiles pre-exist in normal tissues. Clin Exp Metastasis 22:593-603 Full Text HTML Version

GeneNetwork (2004)

Baldwin NE, Chesler EJ, Kirov S, Langston MA, Snoddy JR, Williams RW, Zhang B (2004) Computational, integrative and comparative methods for the elucidation of genetic co-expression networks. Journal of Biomedicine and Biotechnology 2:172-180 HTML and PDF reprints.
Carlborg O, De Koning DJ, Chesler EJ, Manly KM, Williams RW, Haley CS (2004) Methological aspects of the genetic dissection of gene expression. Bioinformatics 10:1093
Chesler EJ, Williams RW (2004) Brain gene expression: genomics and genetics. International Review of Neurobiology 60:59-95
Fernandes K, Paya-Cano JL, Sluyter F, D'Souza U, Plomin R, Schalkwyk LC (2004) Hippocampal gene expression profiling across eight mouse inbred strains: towards understanding the molecular basis for behaviour. European Journal of Neuroscience 19:2576-2582 Full Text HTML Version
Henckaerts E, Langer JC, Hans-Willem Snoeck HW (2004) Quantitative genetic variation in the hematopoietic stem cell and progenitor cell compartment and in lifespan are closely linked at multiple loci in BXD recombinant inbred mice. Blood 104:374-379 Full Text HTML Version
Hitzemann R, Reed C, Malmanger B, Lawler M, Hitzemann B, Cunningham B, McWeeney S, Belknap J, Harrington C, Buck K, Phillips T, Crabbe J (2004) On the integration of alcohol-related quantitative trait loci and gene expression analyses. Alcoholism: Clinical and Experimental Research 28:1437-1448 [Please cite this paper is you plan to use the B6D2F2 OHSU data set.]
Maiya RP (2004) Regulation of dopamine transporter: a role for ethanol and protein interactions. Dissertation, University of Texas, Austin
Orth AP, Batalow S, Perrone M, Chanda SK (2004) The promise of genomics to identify novel therapeutic targets. Expert Opion of Therapeutic Targets 8:587-596
Pomp D, Allan MF, Wesolowski SR (2004) Quantitative genomics: Exploring the genetic architecture of complex trait predisposition. J Anim Sci 82:E300-E312 Full Text HTML Version
Ponomarev I, Schafer GL, Blednov YA, Williams RW, Iver VR, Harris A (2004) Convergent analysis of cDNA and short oligomer microarrays, mouse null mutant, and bioinformatics resources to study complex traits. Genes, Brain and Behavior 3:360-368
Simon P, Schott K, Williams RW, Schaeffel F (2004) Post-translational regulation of the immediate early gene EGR1 by light in the mouse retina. European Journal of Neuroscience 20:3371-3377
Zareparsi S, Hero A, Zack DJ, Williams RW, Swaroop A (2004) Seeing the unseen: microarray-based gene expression profiling in vision. Investigative Ophthalmology and Visual Science 45:2457-2462 Full text HTML version

GeneNetwork (2003)

Bolivar V, Flaherty L (2003) A region on chromosome 15 controls intersession habituation in mice. Journal of Neuroscience 23: 9435-9438 Full Text HTML and PDF Versions
Jones BC, Reed CL, Hitzemann R, Wiesinger JA, McCarthy KA, Buwen JP, Beard JL 2003) Quantitative genetic analysis of ventral midbrain and liver iron in BXD recombinant inbred mice. Nutr Neuroscience 6:369-77 Full Text PDF Version
Hitzemann R, Hitzemann B, Rivera S, Gatley J, Thanos P, Shou S, Lu L, Williams RW (2003) Dopamine D2 receptor binding, Drd2 expression and the number of dopamine neurons in the BXD recombinant inbred series: genetic relationships to alcohol and other drug associated phenotypes. Alcoholism: Clinical and Experimental Research 27:1-11
Hitzemann R, Malmanger B, Reed C, Lawler M, Hitzemann B, Coulombe S, Buck K, Rademacher B, Walter N, Polyakov Y, Sikela J, Williams RW, Flint J, Talbot C (2003) A strategy for integration of QTL, gene expression, and sequence analyses. Mammalian Genome 14:733-747
Lionikas A, Blizard DA, Vandenbergh DJ, Glover MG, Stout JT, Vogler GP, McClearn GE, Larsson L (2003) Genetic architecture of fast- and slow-twitch skeletal muscle weight in 200-day-old mice of the C57BL/6J and DBA/2J lineage. Physiological Genomics 16:141-152
Peirce J, Chesler EJ, Williams RW, Lu L (2003) Genetic architecture of the mouse hippocampus: identification of gene loci with regional effects. Genes, Brain and Behavior 2:238–252 Full Text PDF Version
Rosen GD, La Porte NT, Diechtiareff B, Pung, CJ, Nissanov J, Gustafson C, Bertrand L, Gefen S, Fan Y, Tretiak OJ, Manly KF, Parks MR, Williams AG, Connolly MT, Capra JA, Williams RW (2003) Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics 1:327–342 Full Text PDF Version

Background references on inbred strains and other key resources
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Williams RW, Gu J, Qi S, Lu L (2001) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2:46.1–46.18 Full Text HTML and PDF Version. [General background on recombinant inbred strains.]

Peirce JL, Lu L, Gu J, Silver LM, Williams RW (2004) A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genetics 5:7 Full Text PDF Version. [Background on the expanded set of BXD strains.]

Williams RW, Bennett B, Lu L, Gu J, DeFries JC, Carosone-Link PJ, Rikke BA, Belknap JK, Johnson TE (2004) Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mammalian Genome 15:637-647 [Background on origins and the genetic structure large panel of LXS strains. Please cite this paper is you have used LXS data sets.]

Grubb SC, Churchill GA, Bogue MA (2004) A collaborative database of inbred mouse strain characteristics. Bioinformatics 20:2857-2859 [One of two key papers on the Mouse Phenome Project and database at The Jackson Laboratory. The mouse diversity panel (MDP) is a superset of strains that are part of the Phenome Project. Full Text PDF Version.]

Bogue MA, Grubb SC (2004) The mouse phenome project. Genetica 122:71-74 [One of two key papers on the Mouse Phenome Project and database at The Jackson Laboratory. The mouse diversity panel (MDP) is a superset of strains that are part of the Phenome Project. Please contact Dr. Molly Bogue for information on the Phenome Project: mollyb@jax.org]

Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448, 1050-3

Loudet O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F (2002) Bay-0 x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics 104:1173-1184 Full Text PDF Version [Please cite this paper is you have used the BXS Arabidopsis data sets.]

Jirout M, Krenova D, Kren V, Breen L, Pravenec M, Schork NJ, Printz MP (2003) A new framework marker-based linkage map and SDPs for the rat HXB/BXH strain set. expression differences in mice diverently selected for methamphetamine sensitivity. Mammalian Genome 14: 537-546

Shifman S, Bell JT, Copley BR, Taylor M, Williams RW, Mott R, Flint J (2006) A high resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biology 4:2227-2237 Full Text PDF Version [A comprehensive analysis of recombination rates using several populations of mice, including most major GRPs.]

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This text originally generated by RWW, April 2003. Updated by RWW, Oct 15, Dec 17, 2004; RWW Jan 19, 2005; EJC Mar 9; RWW Mar 29, Apr 15; RWW Jan 7, 2006, Jan 21, July 26, Aug 26, 2006s; May 2007; Feb 2008; March 19 2008