From 00cd77be390286e8c77e97dd7eaa77332519ac81 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 26 Nov 2020 20:27:58 +0300 Subject: fix markdown errors and links --- general/environments/environments.md | 2 +- general/links/links.md | 92 ++++++++++++------------------------ general/references/references.md | 76 ++++++++++++++++------------- 3 files changed, 73 insertions(+), 97 deletions(-) diff --git a/general/environments/environments.md b/general/environments/environments.md index fd481fa..1cd536f 100644 --- a/general/environments/environments.md +++ b/general/environments/environments.md @@ -2,7 +2,7 @@ | Operating System | | | | |---|---|---|---| -| Ubuntu | 12.04.5 LTS 64-bit | (http://www.ubuntu.com) | Free software licenses (mainly GPL) | +| Ubuntu | ubuntu-latest | [ubuntu](http://www.ubuntu.com) | Free software licenses (mainly GPL) | | **Database** | | | | | MySQL | 5.5.40 | [http://www.mysql.com/](http://www.mysql.com/) | GPL (version 2) or proprietary | | **Python** | | | | diff --git a/general/links/links.md b/general/links/links.md index 2e60968..4fef6f2 100644 --- a/general/links/links.md +++ b/general/links/links.md @@ -23,6 +23,7 @@ #### KEY RESOURCES CONNECTED WITH GENENETWORK * Wellcome Trust Oxford Mouse Resource Portal + * WTSI Mouse Resource Portal * Sanger Mouse Sequencing Portal (David Adams and colleagues) @@ -30,19 +31,32 @@ * StRAnGER Gene Ontology and KEGG pathway analyzer * PhenoGen Informatics + * The Allen Mouse Brain Atlas + * AmiGO -* Synapse DB + +* Synapse DB + * ABI Panther -* BioGPS and its predecessor SymAtlas -* Perlegen/NIEHS Mouse Sequence Data + +* BioGPS and its predecessor SymAtlas + +* Perlegen/NIEHS Mouse Sequence Data + * Ontological Discovery Environment + * Semantic Gene Organizer -* UCSC Genome Browser and mirror -* Ensembl -* NCBI -* Mouse Phenome Database and the MPP SNP Browser -* WebGestalt + +* UCSC Genome Browser and mirror + +* Ensembl +* NCBI + +* Mouse Phenome Database and the MPP SNP Browser + +* WebGestalt + * GrAPPA Clique-based clustering tool @@ -69,11 +83,9 @@ - [Added Jan 15, 2010; last site review Jan 15, 2010 by RWW.] * **SNPedia** is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. - - [Added Jan 15, 2010; last site review Jan 15, 2010 by RWW.] * **Genoglyphix Browser** includes extensive data on human copy number variants as well as maps of low copy number repeat regions. - - [Added Nov 5, 2009; last site review Nov 5, 2009 by RWW.] * **Human Protein Reference DB**: a manually curated resource with data on 20, 000 proteins. Very effective interface and rich data. @@ -85,11 +97,9 @@ - [Added April 18, 2008; last site review Sept 19, 2008 by RWW.] * iHOP retrieves PubMed sentences that report interactions between a reference gene and associate genes and proteins. It allows the assembly of complex graphs that plot the literature interactions of genes. Effective interface for humans and machines. - - [Added Dec 25, 2004; last site review Sept 19, 2008 by RWW.] * **Human Protein Atlas** displays expression and localization of proteins in a large variety of normal human tissues and cancer cells as high resolution images of immunohistochemically stained tissues and cell lines. - - [Added Sept 22, 2007; last site review Sept 22, 2007 by RWW.] * **GoPubMed** is a simple tool that searches PubMed and sorts the results by GO and MeSH terms. @@ -99,15 +109,12 @@ - [Added Jan 1, 2005; last site review Sept 19, 2008 by RWW.] * **MGI** and **RGD** are reference sites for mouse and rat genetics, respectively. - - [Added Dec 22, 2004; last site review Sept 19, 2008 by RWW.] * **GenAtlas** provides summary data for approximately 19300 human genes and has a useful link that will fetch 10 Kb of upstream sequence for promoter analysis. - - [Added Jan 9, 2005; last site review Sept 19, 2008 by RWW.] * **PromoLign** aligns homologous regions of mouse and human promoters and highlights SNPs and transcription factor binding sites. Check the quick tutorial to see how to extract key data. This site requires an SVG plugin that may not be supported by some browsers and operating systems. - - [Added May 10, 2005; FAILED: last site review Sept 19, 2008 by RWW.] * **CGAP SNP Viewer** allows users to view SNPs in the context of transcripts, ORFs and protein motifs for either human or mouse genes. Try the *Ahr* gene in mouse as an example. @@ -118,29 +125,25 @@ - [Added May 29, 2005; last site review Sept 19, 2008 by RWW.] * **Synapse Database** at University of Pennsylvania is a comprehensive database of roughly 200 genes and proteins associated with the synapse. - - [Added Nov 26, 2006; last site review Sept 19, 2008 by RWW.] * **Singapore** Bio Databases and Tool. - - [Added Dec 22, 2004; Dragon Genome Explorer site FAILED last site review, changed link; Sept 19, 2008 by RWW.] - **MutDB** and **SNPs3D** provide great data on functional SNPs in human genes. To analyze the functional impact of non-synonymous SNPs you will also find **SNP Analyzer** useful because it evaluates SNP impact in terms of the whole protein structural context. - [Added Dec 22, 2004; last site review Sept 19, 2008 by RWW.] * **Alternative Splicing** Project provides great summaries and output graphs on splice variants in human, mouse, and Drosophila. - - [Added Nov 8, 2005; last site review Sept 19, 2008 by RWW.] > ### **Resources on Imprinting and Parental Origin Effects** * **Geneimprint** is a portal into the burgeoning field of genomic imprinting, collecting relevant articles and reviews, press reports, video and audio lectures, and genetic information - + [Added June 23, 2010 by RWW; last site review June 23, 2010 by RWW.] + - [Added June 23, 2010 by RWW; last site review June 23, 2010 by RWW.] * **Catalogue of Parent of Origin Effects** provides a list of imprinted and putatively imprinted genes with commentary by Ian Morison (University of Otago, New Zealand). Database was last updated in 2008. - - [Added June 23, 2010 by RWW; last site review June 23, 2010 by RWW.] > ### **Resources for the Spatial Analysis of Gene and Protein Expression** @@ -149,15 +152,12 @@ - [Added May 24, 2007 by RWW; last site review Sept 19, 2008 by RWW.] * The **mamep GeneExpression Links** image database of whole-mounted in situ hybridization of mid-gestation mouse embryos. Try entering the symbol *Ptch1*. - - [Added May 28, 2007 by RWW.] * The **Genes to Cognition** databases have a focus on proteins expressed in several key cellular compartments related to synpase function. - - [Added Aug 9, 2007 by RWW.] * **Cerebellar Development Transcriptome Database**. Expression data for the mouse cerebellum, both microarray and in situ. - - [Added Sept 1, 2010; last site review Sept 1, 2010 by RWW.] Several excellent resources can be used to explore patterns of gene expression primarily in C57BL/6J mice. This strain is one of the parents of the BXD, AXB/BXA, BXH, and CXB genetic reference populations that are key resources in the Gene Network and its companion site, the Mouse Brain Library. @@ -173,68 +173,55 @@ Several excellent resources can be used to explore patterns of gene expression p * **Mouse Atlas of Gene Expression** is a massive SAGE library. The Atlas has quantified the normal state for many tissues by determining the number and identity of genes expressed throughout development. The scope of the project encompasses multiple stages of development of C57BL/6J mouse, from the single cell zygote to the adult, and includes an extensive initial collection of 200 tissues. DiscoverySpace is a WebStart application for use with The Mouse Atlas of Gene Expression. * **Mahoney** Center maintains a rich image collection for ~1000 transcription factors expressed in brain (developmental stages, coronal plane). - - [Added Dec 22, 2004; sites reviewed last on Sept 26, 2005 by RWW.] ### Resources for the Analysis of Sets and Networks of Transcripts, Genes, Proteins, and SNPs * **GeneMANIA** helps you predict the function of your favourite genes and gene sets. Powerful and fast computational methods and a great use of Cytoscape Web. (2010 PDF). - - [Added July 1, 2010; last site review Aug 8, 2010 by RWW.] * **ToppGene Suite** A one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network - - [Added Jan 16, 2010; last site review Jan 16, 2010 by RWW.] * **WikiPathways** (WGCNA) is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. - - [Added Nov 12, 2009; last site review Nov 12, 2009 by RWW.] * **Pathway Commons** (WGCNA) is a search tool to find and visualize public biological pathway information. This site collates from several major sites. - - [Added Nov 12, 2009; last site review Nov 12, 2009 by RWW.] * **Sanger Mouse Genome Project SNP Finder** provides access to SNP and indels generated by sequencing 17 strains of mice (plus C57BL/6J). Marvelous. - - [Added Nov 18, 2009; last site review Nov 18, 2009 by RWW.] * **Weighted Gene Coexpression Network Analysis** (WGCNA) is a collection of R functions to perform weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. See the recent paper on WGCNA. - - [Added Aug 21, 2009; last site review Aug 21, 2009 by RWW.] * **GenomeNet** is a terrific site for the analysis of molecular networks. Download the very effective KegArray 0.2.6beta package (May 2005) for exploratory data analysis of microarray data set. This package is as good as most commerical software and includes with built-in linkage to the KEGG databases. Versions are available for Mac OS X and Windows. - [Added Jan 3, 2005; last site review Aug 5, 2005 by RWW.] * **Expression Profiler** at http://ep.ebi.ac.uk/ is a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Tools in the Expression Profiler allow you to perform cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, generate sequence logos, extract regulatory sequences, study protein interactions, as well as to link analysis results to external tools and databases. - - [Added May 20, 2008; last site review May 20, 2008 by RWW.] * **BioGRID**: the Biological General Repository for Interaction Datasets is a freely accessible database of protein and genetic interactions from Mt. Sinai, Toronto. - - [Added July 28, 2007; last site review July 28, 2007 by RWW.] * **CisMols Analyzer** at Cincinnati Children's Hospital (Aronow and colleagues) is a server and database for the analysis of cis element co-occurences in the promoters of a list of genes. The PolyDoms Analyzer is a tool for scanning through gene lists for those members of a pathway, ontolog, or disease that contain potentially harmful protein-coding SNPs. GenomeTraFaC is a comparative genomics-based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq Gene Orthologs. - - [Added Sept 23, 2006; last site review Sept 23, 2006 by RWW.] + - [Added Sept 23, 2006; last site review Sept 23, 2006 by RWW.] * **PolymiRTS** database that searches for microRNA (miRNA) targets in transcripts that overlap SNPs. This database will also search for genes with associated phenotype variants that may have variants in miRNA target sequence (Yan Cui, Lei Bao and colleagues). - [Added Sept 23, 2006; last site review Sept 23, 2006 by RWW.] * **MSigDB**: The Molecular Signature Database is part of the Broad Institute Gene Set Enrichment Analysis suite. MSigDB contains large numbers of static and partly annotated sets of genes/transcripts. Registration is not actually required to download data sets. - - [Added Jan 18, 2007; last site review Jan 18, 2007 by RWW.] * **C-INIA** MAGIC-B microarray knowledgebase from the Department of Pharmacology, University of Colorado, Denver, part of the NIAAA INIA project. Extensive public and privated brain array data sets in a powerful analytic web environment. - - [Added May 31, 2007 by RWW.] * GenMAPP 2.0 (2004), the Gene Map Annotation and Pathway Prolifer, is a free Windows application (simple registration required) with which you can visualize expression and other genomic data sets on maps of biological pathways. Very flexible suite of programs that you can also use to make custom gene annotation maps (and more). - + [Added Aug 5, 2005; last site review Aug 5, 2005 by RWW.] + - [Added Aug 5, 2005; last site review Aug 5, 2005 by RWW.] -**BIND** and **STRING** and IntAct are great sites that provide access to well curated data on protein-protein interactions. BIND and IntAct focus on experimentally verified interactions whereas STRING and preBIND incorporate inferred interaction based on other data types, including gene expression. Links to BIND and STRING have been added to the Trait Data and Analysis forms on the GeneNetwork BETA site. - - [Added Aug 21, 2005; last site reviews Aug 27, 2005 by RWW.] +**BIND** and **STRING** and IntAct are great sites that provide access to well curated data on protein-protein interactions. BIND and IntAct focus on experimentally verified interactions whereas STRING and preBIND incorporate inferred interaction based on other data types, including gene expression. Links to BIND and STRING have been added to the Trait Data and Analysis forms on the GeneNetwork BETA site.[Added Aug 21, 2005; last site reviews Aug 27, 2005 by RWW.] * **Microarray Module Maps** is a great site that databases a large number of coexpression modules defined using many cancer array studies. - - [Added Aug 26, 2005; last site review Aug 26, 2005 by RWW.] * **The Gene Ontology Consortium** maintains a well annotated list of open resources for the analysis of large expression data sets and gene ontologies. Note that there are several different lists, each with valuable links. @@ -246,42 +233,33 @@ Several excellent resources can be used to explore patterns of gene expression p - [Added January 7, 2006; last site review Jan 7, 2006 by RWW.] * **Clique-GO Analysis** is a novel tool for extracting cliques of coregulated transcripts. The current data requires Affymetrix U74Av2 probe set IDs as input. Try "103370_at" (the gene *Lin7c*) as an example. - - [Added Jan 4, 2005; last site review Jan 4, 2005 by RWW.] -* **Gemma and ErmineJ** are powerful resources for analysis and metaanalysis of gene expression data sets at UBC. Pavlidis and colleagues also provide updated GO data for common microarray platforms. - +* **Gemma and ErmineJ** are powerful resources for analysis and metaanalysis of gene expression data sets at UBC. Pavlidis and colleagues also provide updated GO data for common microarray platforms. - [Added Jan 4, 2005; last site review June 7, 2007 by RWW.] * **Cytoscape** is one of several SBML-compatible open source programs for visualizing molecular interaction networks and overlaying these networks with gene expression profiles and other data sets to generate and test specific hypotheses. - + [Added Jan 5, 2005; last site review Jan 5, 2005 by RWW.] + - [Added Jan 5, 2005; last site review Jan 5, 2005 by RWW.] * **Pathway Searcher** provides fast access to gene/protein interaction pathways. An intuitive interface. - - [Added Dec 30, 2004; last site review Dec 30, 2004 by RWW.] * **Gene Sorter** is a tool for generating and sorting sets of genes using a wide variety of information integrated into UCSC's Genome Brower. - - [Added Dec 31, 2004; last site review Dec 31, 2004 by RWW.] * **oPPOSUM** is a tool for finding over-represented transcription factor binding sites in lists of mouse and human genes. It handles about 100 out of greater than 600 TFBSs. - - [Added Jan 27, 2005; last site review Nov 21, 2005 by RWW.] * **MOTIF** and **PAINT** search for motifs in submitted sequences or lists of genes. Paint makes use of the TRANSFAC Pro database. - - [Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.] * **Arrowsmith** provides a fast way to evaluate known interactions or common mechanisms between two genes or proteins. It carries out a sophisticated comparison of the current PubMed database. - [Added Dec 22, 2004; last site review June 7, 2007 by RWW.] * **Chilibot** applies natural-language processing to the PubMed database to hunt for directed relationships among pairs or sets of genes, proteins, and keywords. - - [Added Dec 30, 2004; last site review Aug 13, 2009 by RWW.] -**Mouse Imprinting Resources**: +* **Mouse Imprinting Resources**: The Harwell Mouse Imprinting Resource, Duke University - Jirtle's Laboratory, RIKEN Candidate Imprinted Transcript Maps, and @@ -291,50 +269,41 @@ Several excellent resources can be used to explore patterns of gene expression p ### Resources for the Analysis of Phenotypes in Genetic Reference Populations * **MBL** is a extensive image database of brain sections from genetic reference populations of mice, including the BXD, AXB, CXB, BXH strains included in WebQTL. The MBL is a companion database of WebQTL. - - [Added Dec 22, 2004; last site review Aug 6, 2005 by RWW.] * **MPAD** Mouse Phenome Association Database v 1.0, by Eleazar Eskin and Hyun Min Kang. This resource performs genome-wide association mapping. Phenotype data sets are derived from the Mouse Phenome Project set of standard mouse strains. The permutation procedures account for the genetic relations among these strains and provide much more appropriate genome-wide significance thresholds than previous mouse association mapping methods. - - [Added Nov 19, 2006; last site review Nov 19, 2006 by RWW. Link broken June 2007 probably due to move from UCSD to UCLA; check with EE.] * **GScan** at the Wellcome Trust, Oxford, is a sophisticated viewer and analysis tool with which to explore the genetic control of diverse phenotypes (including array data) generated using heterogeneous stock mice (Flint, Mott, and colleagues). - - [Added May 28, 2007 by RWW.] * **Phenome Project** provides access to a wide variety of phenotype data many common and wild inbred strains of mice. - - [Added Dec 22, 2004; last site review Dec 25, 2004 by RWW.] ### QTL Mapping Resources * **QSB**: QSB is a stand-alone JAVA program with a sophisticated GUI developed for genetical genomics or systems genetics, an emerging field that combines quantitative genetics and genomics. QSB stands for QTL mapping, Sequence polymorphism analysis (or SNP analysis) and Bayesian network analysis. QSB takes marker and array data from a segregating population as input and identifies significant QTLs and then evaluated networks of candidate genes associated with these QTLs. - - [Added July 29, 2005; last site review Jan 7, 2006 by RWW.] * **Positional Medline (PosMed)** is a knowledge-based ranking system of candidate genes within QTL intervals for human, mouse, rat, Arabidopsis, and rice. - + [Added Nov 4, 2009; last site review Nov 4, 2009 by RWW.] + - [Added Nov 4, 2009; last site review Nov 4, 2009 by RWW.] * **Genome - Phenome Superbrain Project** integrates various databases to build a comprehensive computerized encyclopedia of omic sciences in several species, including mouse, rat, human, and arabidopsis, etc. The goal is to evolve this intelligent system into a form of artificial intelligence that can solve a researcher's problems by exploiting a vast amount of information accumulated in documents and published data ranging from genomes to phenomes. - - [Added Sept 13, 2007; last site review Sept12, 2007 by RWW.] * **QTL Reaper** is software, written in C and compiled as a Python module, for rapidly scanning microarray expression data for QTLs. It is essentially the batch-oriented version of WebQTL. It requires, as input, expression data from members of a set of recombinant inbred lines and genotype information for the same lines. It searches for an association between each expression trait and all genotypes and evaluates that association by a permutation test. For the permutation test, it performs only as many permutations as are necessary to define the empirical P-value to a reasonable precision. It also performs bootstrap resampling to estimate the confidence region for the location of a putative QTL. - [Added Jan 27, 2005; last site review Jan 27, 2005 by KFM.] * **QTLNetwork 2.0** is a software package ofr mapping QTLs with epistatic and GXE interaction effects in experimental populations including double-haploid, recombinant inbred, backcross, F2, IF2 and BxFy populations. The program provides graphical presentations of QTL mapping results. The software is programmed by C++ programming language under Microsoft Visual C++ 6.0 environment. It works with Microsoft Windows operating systems, including Windows 95/98, NT, 2000, XP, 2003server. A new version of QTLNetwork is under developing, and its functions will be extended to include linkage group construction and marker-assisted virtual breeding. - - [Added June 21, 2007.] * **MouseHapMap** project genotypes from Mark Daly and colleagues. Approximately 140, 000 SNPs across 49 strains. Updated Feb 2006.used to explore the Oxford Wellcome Heterogeneous stock QTL mapping project population. It currently includes mapping data for 100+ phenotypes typed across 2000 animals and 13, 000 SNPs. - [Added May 10, 2006; last site review May 10, 2006 by RWW.] * A valuable list of **Software for QTL Data Analysis** and **Gene Expression Microarray Software** is managed by Brian Yandell at University of Wisconsin. - - [Added May 16, 2006; last site review May 16, 2006 by RWW.] * **GSCAN DB** is a browser used to explore the Oxford Wellcome Heterogeneous stock QTL mapping project population. It currently includes mapping data for 100+ phenotypes typed across 2000 animals and 13, 000 SNPs. - - [Added May 10, 2006; last site review May 10, 2006 by RWW.] @@ -348,7 +317,6 @@ Several excellent resources can be used to explore patterns of gene expression p ### Affymetrix Array Annotation Resources * Affy MOE430A and MOE430B Annotation files are explained more clearly that Affymetrix has ever done by Earl F Glynn at the Stowers Institute. (efg@stowers-insitute.org). - - [Added July 17, 2006; last site review June 7, 2007 by RWW. This Oct 7, 2005 file caused Grace Wheeler's Mac internet connection to break.] ### Information about this HTML page: diff --git a/general/references/references.md b/general/references/references.md index f9d05af..5ecbd0c 100644 --- a/general/references/references.md +++ b/general/references/references.md @@ -10,11 +10,13 @@ | [2020](#2020) | [2019](#2019) | [2018](#2018) | [2017](#2017) | [2016](#2016) | [2015](#2015) | [2014](#2014) | [2013](#2013) |[2012](#2012) | [2011](#2011) | [2010](#2010) |[2009](#2009) | [2008](#2008) |[2007](#2007) |[2006](#2006) | [2005](#2005) | [2004](#2004) | [2003](#2003) | Google Scholar search for _"genenetwork" OR "webqtl"_ generated: + 1. 1430 hits on 2016/09/08 2. 1730 hits on 2017/10/17 3. 2020 hits on 2019/05/13 [Google Scholar](https://scholar.google.com/scholar?as_q=&as_epq=&as_oq=genenetwork.org&as_eq=&as_occt=any&as_sauthors=&as_publication=&as_ylo=&as_yhi=&btnG=&hl=en&as_sdt=0%2C5)   search for *genenetwork.org*   generated: + 1. 1030 hits on 2019/05/13 2. 105 hits from 2018/01/01 to 2019/05/13 @@ -22,6 +24,7 @@ Google Scholar search for _"genenetwork" OR "webqtl"_ generated:
## Highlighted References + #### **_Please send us citations to articles that we may have missed._** 1. Mulligan MK, Mozhui K, Prins P, Williams RW [2017](https://ncbi.nlm.nih.gov/pubmed/27933521) GeneNetwork: A Toolbox for Systems Genetics. In *Systems Genetics*, Methods in Molecular Biology 1488:75-120 @@ -57,7 +60,7 @@ Google Scholar search for _"genenetwork" OR "webqtl"_ generated: 8. Merkwirth C, Jovaisaite V, Durieux J, Matilainen O, Jordan SD, Quiros PM, Steffen KK, Williams EG, Mouchiroud L, Tronnes SU, Murillo V, Wolff SC, Shaw RJ, Auwerx J, Dillin A [2016](https://ncbi.nlm.nih.gov/pubmed/27133168) Two conserved histone demethylases regulate mitochondrial stress-induced longevity. Cell 165:1209-1223 -9. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW [2016]("https://ncbi.nlm.nih.gov/pubmed/26833085). Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications 7:10464 +9. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW [2016](https://ncbi.nlm.nih.gov/pubmed/26833085). Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications 7:10464 [Best reference on the BXD family of strains and the wide range of phenotypes that have been generated over the past 40 years.] - [PDF version](http://gn1.genenetwork.org/images/upload/Wang_PheWas_NatComm_2016.pdf) and the [Supplementary Tables in one Excel file](http://gn1.genenetwork.org/images/upload/Wang_SupplementalTables_NatComm_2016.xlsx) @@ -95,19 +98,18 @@ The first section lists key technical papers that are appropriate references whe 1. Mulligan MK, Mozhui K, Prins P, Williams RW [2016](https://ncbi.nlm.nih.gov/pubmed/26092713). GeneNetwork – A toolbox for systems genetics. In *Systems Genetics*, Methods in Molecular Biology; Schughart K, Williams RW eds.; Humana Press, in press [This is a currently the most comprehensive protocol and guide (20 Mb) for GeneNetwork.] - - [PDF Version](http://gn1.genenetwork.org/images/upload/Mulligan_How_To_Use_GeneNetwork_2016_v1.pdf) 2. Williams RW, Mulligan MK [2012](https://ncbi.nlm.nih.gov/pubmed/23195314). Genetic and molecular network analysis of behavior. Int Rev Neurobiol. 104:135-57. [Explains the use of GeneNetwork in behavioral neurogenetics] - PDF version -3. Williams EG, Auwerx J [2015](https://ncbi.nlm.nih.gov/pubmed/26140590). The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. [Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.] +3. Williams EG, Auwerx J [2015](https://ncbi.nlm.nih.gov/pubmed/26140590). The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. [Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.] - [PDF version](http://gn1.genenetwork.org/images/upload/WilliamsEG_Auwerx_Cell2015.pdf) -4. Wang J, Williams RW, Manly KF ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:299)) WebQTL: Web-based complex trait analysis. Neuroinformatics 1: 299-308 [*Full Text PDF Version*](http://www.genenetwork.org/pdf/webqtl.pdf). [A good technical reference to WebQTL and GeneNetwork] +4. Wang J, Williams RW, Manly KF ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:299)) WebQTL: Web-based complex trait analysis. Neuroinformatics 1: 299-308 [*Full Text PDF Version*](http://www.genenetwork.org/pdf/webqtl.pdf).[A good technical reference to WebQTL and GeneNetwork] -5. Williams RW, Gu J, Qi S, Lu L ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:299)) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2(11) [*Full Text Version*](http://genomebiology.com/content/2/11/RESEARCH0046). [A detailed analysis of the genetics of recombinant inbred strains] +5. Williams RW, Gu J, Qi S, Lu L ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:299)) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2(11)[*Full Text Version*](http://genomebiology.com/content/2/11/RESEARCH0046).[A detailed analysis of the genetics of recombinant inbred strains] 6. Chesler EJ, Wang J, Lu L, Qu Y, Manly KF, Williams RW ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:343)) 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*](http://www.nervenet.org/pdf/Genetic_Correlation_webQTL.pdf). [Best reference regarding interpretation of genetic correlations.] @@ -132,8 +134,11 @@ The first section lists key technical papers that are appropriate references whe - [Part 1](http://www.youtube.com/watch?v=5UniEc_pzs0) - [Part 2](http://www.youtube.com/watch?v=zjdOWC7zxt0) + - [Part 3](http://www.youtube.com/watch?v=caC0YGhDoo8) + - [Part 4](http://www.youtube.com/watch?v=eTzIcM3aspM) + - [Part 5](http://www.youtube.com/watch?v=Dnq7w4RIAXI) @@ -553,7 +558,7 @@ PMID: 25236450 7. Li D, Mulligan MK, Wang X, Miles MF, Lu L, Williams RW ([2010](http://www.ncbi.nlm.nih.gov/pubmed/20808911)) 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*](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012181) -8. Lionikas A, Carlborg O, Lu L; Peirce JL, Williams RW, Yu F, Vogler GP, McClearn GE, Blizard DA [2010](http://www.ncbi.nlm.nih.gov/pubmed/20233743) target="_blank" >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*](http://http://jhered.oxfordjournals.org/cgi/reprint/esq023?ijkey=BbuUGMafKrjFO5f&keytype=ref) +8. Lionikas A, Carlborg O, Lu L; Peirce JL, Williams RW, Yu F, Vogler GP, McClearn GE, Blizard DA [2010](http://www.ncbi.nlm.nih.gov/pubmed/20233743). 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*](http://http://jhered.oxfordjournals.org/cgi/reprint/esq023?ijkey=BbuUGMafKrjFO5f&keytype=ref) 9. Loguercio S, Overall RW, Michaelson JJ, Wiltshire T, Pletcher MT, Miller BH, Walker JR, Kempermann G, Su AI, Beyer A [2010]("http://www.ncbi.nlm.nih.gov/pubmed/21085707)Integrative analysis of low- and high-resolution eQTL. PLoS One 5(11):e13920 [*Full Text PDF Version*](http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=C93DEB44991B6401001E7585AC4C4393.ambra02?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0013920&representation=PDF) @@ -566,7 +571,8 @@ PMID: 25236450 13. Mulligan MK, Lu L, Overall RW, Kempermann G, Rogers GL, Langston MA, Williams RW ([2010](http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5510847)) 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*](http://gn1.genenetwork.org/images/upload/BDNF_Clique_Apr13.pdf) -14. Peidis P, Giannakouros T, Burow ME, Williams RW, Scott RE ([2010](http://www.ncbi.nlm.nih.gov/pubmed/20184719)) 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*]("http://www.biomedcentral.com/content/pdf/1752-0509-4-14.pdf) and +14. Peidis P, Giannakouros T, Burow ME, Williams RW, Scott RE ([2010](http://www.ncbi.nlm.nih.gov/pubmed/20184719)) 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*]("http://www.biomedcentral.com/content/pdf/1752-0509-4-14.pdf) and + 15. 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](http://www.ncbi.nlm.nih.gov/pubmed/19958391)) High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. Genes, Brain and Behavior 8:129-159 [*Full Text HTML Version*](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855868/) 16. Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E. ([2010](http://www.ncbi.nlm.nih.gov/pubmed/21047393)) 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*](http://www.biomedcentral.com/1471-2164/11/614) @@ -574,6 +580,7 @@ PMID: 25236450 17. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV ([2010](http://www.ncbi.nlm.nih.gov/pubmed/16594979)) 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*](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855868/) 18. Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ ([2010](http://gn1.genenetwork.org/images/upload/Suwanwela-1.JBMR.10.pdf)) Systems genetics analysis of mouse chondrocyte differentiation. JBMR, in press [*Full Text PDF version*](http://gn1.genenetwork.org/images/upload/Suwanwela-1.JBMR.10.pdf) + 19. Wang X, Chen Y, Wang X, Lu L. ([2010](http://www.ncbi.nlm.nih.gov/pubmed/20054728)) Genetic regulatory network analysis for *App* based on genetical genomics approach. Exp Aging Res 36:79-93 @@ -612,9 +619,9 @@ PMID: 25236450 11. Grisham W ([2009](http://www.funjournal.org/downloads/200981/grisham81.pdf)) 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*](http://www.funjournal.org/downloads/200981/grisham81.pdf) -
+
An excellent example of how resources such as GeneNetwork and the Mouse Brain Library can be used in class room labs. - + 12. Jellen LC, Beard JL, Jones BC ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19393285)) Systems genetics analysis of iron regulation. Biochemie in press. 19393285 @@ -640,14 +647,14 @@ An excellent example of how resources such as GeneNetwork and the Mouse Brain Li 19. Rosen GL, Pung C, Owens C, Caplow J, Kim H, Lu L, Williams RW ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19191878)) Genetic modulation of striatal volume in BXD recombinant inbred mice. Genes, Brain & Behavior 8:296-308 -20. 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](http://www.ncbi.nlm.nih.gov/pubmed/19381300)) Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. PLoS ONE 4:e5225. [*Full Text HTML Version*]("http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005225), +20. 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](http://www.ncbi.nlm.nih.gov/pubmed/19381300)) Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. PLoS ONE 4:e5225. [*Full Text HTML Version*](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005225), [*Full Text PDF Version*](http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0005225&representation=PDF). [Supplementary table 1 provides links to many transcripts and genes, some of which were mined from an analysis of GeneNetwork data sets.] 21. Silva GL, Junta CM, Sakamoto-Hojo ET, Donadi EA, Louzada-Junior P, Passos GA ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19758195)) Genetic susceptibility loci in rheumatoid arthritis establish transcriptional regulatory networks with other genes. Ann N Y Acad Sci 1173:521-37 22. Tapocik JD, Letwin N, Mayo CL, Frank B, Luu T, Achinike O, House C, Williams R, Elmer GI, Lee NH ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19386926)) Identification of candidate genes and gene networks specifically associated with analgesic tolerance to morphine. J Neurosci 2:5295-307 [*Full Text HTML*](http://www.jneurosci.org/cgi/content/full/29/16/5295) -23. 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]("http://www.ncbi.nlm.nih.gov/pubmed/19723493)) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167-77 +23. 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](http://www.ncbi.nlm.nih.gov/pubmed/19723493)) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167-77 [*Full Text PDF*](http://www.genenetwork.orghttp://gn1.genenetwork.org/images/upload/Thomas_Auwerx_2009.pdf) 24. Webb BT, McClay JL, Vargas-Irwin C, York TP, van den Oord EJCG ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19723493)) In silico whole genome association scan for murine prepulse inhibition. PLoS ONE 4: e5246. doi:10.1371/journal.pone.0005246 @@ -701,7 +708,7 @@ An excellent example of how resources such as GeneNetwork and the Mouse Brain Li 9. 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](http://www.ncbi.nlm.nih.gov/pubmed/19017390)) Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genet 9:73 -[*Full Text HTML Version*]("http://www.biomedcentral.com/1471-2156/9/73) +[*Full Text HTML Version*](http://www.biomedcentral.com/1471-2156/9/73) 10. Dykstra B, de Haan G ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18008087)) Hematopoietic stem cell aging and self-renewal. Cell Tissue Res 331:91-101 @@ -732,7 +739,7 @@ An excellent example of how resources such as GeneNetwork and the Mouse Brain Li 19. Johnson KR, Longo-Guessa C, Gagnona LH, Yub H, Zhengb QY ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18662770)) 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 20. Jones LC, Beard JL, Jones BC ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18189309)) Genetic analysis reveals polygenic influences on iron, copper, and zinc in mouse hippocampus with neurobiological implications. Hippocampus 18:398-410 -[*Full Text PDF Version*](images/upload/Jones_2008_Hippocampus.pdf) +[*Full Text PDF Version*](http://gn1.genenetwork.org/images/upload/Jones_2008_Hippocampus.pdf) 21. Jones LC, Earley CJ, Allen RP, Jones BC ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18189309)) Of mice and men, periodic limb movements and iron: how the human genome informs the mouse genome. Genes, Brain and Behavior 7:513-514. @@ -811,9 +818,9 @@ Genes and cell metabolism. Curr Opin Clin Nutr Metab Care 11:393-397 3. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17099235)) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res. 35(Database issue):D51-54 [*Full Text PDF Version*](http://nar.oxfordjournals.org/cgi/reprint/35/suppl_1/D51), -[Full Text HTML Version*](http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D51) +[*Full Text HTML Version*](http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D51) -4. Benhamou JP, Rizzetto M, Reichen J, Rodés J ([2007](http://books.google.com/books?id=taE276KCyecC&dq=genenetwork+webqtl)) Textbook of hepatology: from basic science to clinical practice. Blackwell Publishing, p. [379]("http://books.google.com/books?id=taE276KCyecC&pg=PA379&lpg=PA379&dq=genenetwork+webqtl&source=web&ots=2CjGbbDh3B&sig=tXdbQ7KAGOyxOee9TECF40GXyywl)), ISBN 1405127414 +4. Benhamou JP, Rizzetto M, Reichen J, Rodés J ([2007](http://books.google.com/books?id=taE276KCyecC&dq=genenetwork+webqtl)) Textbook of hepatology: from basic science to clinical practice. Blackwell Publishing, p. [379](http://books.google.com/books?id=taE276KCyecC&pg=PA379&lpg=PA379&dq=genenetwork+webqtl&source=web&ots=2CjGbbDh3B&sig=tXdbQ7KAGOyxOee9TECF40GXyywl)), ISBN 1405127414 5. Bennett B, Downing C, Carosone-Link P, Ponicsan H, Ruf C, Johnson TE ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17250610)) 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.] @@ -837,7 +844,7 @@ CRC Press ISBN 084931903X InterScience [*Full Text HTML Version*](http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030214) -11. Dong H, Martin MV, Colvin J, Ali Z, Wang L, Lu L, Williams RW, Rosen GD, Csernansky JG, Cheverud JM ([2007]("http://www.ncbi.nlm.nih.gov/pubmed/17406662)) Quantitative trait loci linked to thalamus and cortex gray matter volumes in BXD recombinant inbred mice. Heredity 99:62-69 +11. Dong H, Martin MV, Colvin J, Ali Z, Wang L, Lu L, Williams RW, Rosen GD, Csernansky JG, Cheverud JM ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17406662)) Quantitative trait loci linked to thalamus and cortex gray matter volumes in BXD recombinant inbred mice. Heredity 99:62-69 12. Fox JG, Barthold SW, Davisson MT, Newcomer CE ([2007](http://books.google.com/books?id=vnRpW-gI9JMC)) The mouse in biomedical research. (2nd ed). Academic Press, p. 530. @@ -848,7 +855,7 @@ CRC Press ISBN 084931903X InterScience 15. 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*](http://www.biomedcentral.com/content/pdf/1471-2164-8-76.pdf), -[*Full Text HTML Version*]("http://www.biomedcentral.com/1471-2164/8/76) +[*Full Text HTML Version*](http://www.biomedcentral.com/1471-2164/8/76) 16. Hancock JM, Mallon AM ([2007](http://www.ncbi.nlm.nih.gov/pubmed/18192320)) Phenobabelomics--mouse phenotype data resources. Brief Funct Genomic Proteomic 6:292-301 @@ -886,7 +893,7 @@ CRC Press ISBN 084931903X InterScience 29. Meng PH, Macquet A, Loudet O, Marion-Poll A, North HM ([2007](http://mplant.oxfordjournals.org/cgi/content/full/ssm014v1)) 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 30. Mouse Phenotype Database Integration Consortium ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17436037)) Integration of mouse phenome data resources. Mammalian Genome, 18:157-163. -[*PDF Preprint Version*]("http://www.har.mrc.ac.uk/research/bioinformatics/publications/Preprint1.pdf) +[*PDF Preprint Version*](http://www.har.mrc.ac.uk/research/bioinformatics/publications/Preprint1.pdf) 31. Miyairi I, Tatireddigari VR, Mahdi OS, Rose LA, Belland RJ, Lu L, Williams RW, Byrne GI ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17641048)) The p47 GTPases Iigp2 and Irgb10 regulate innate immunity and inflammation to murine Chlamydia psittaci. J Immunol 179:1814-1824 @@ -896,13 +903,13 @@ CRC Press ISBN 084931903X InterScience 33. Peirce JL, Broman KW, Lu L, Williams RW ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17400728)) A simple method for combining genetic mapping data from multiple crosses and experimental designs. PLoS ONE 2:e1036 -[*Full Text PDF Version*]("http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=009B2741B48AC1CB94E68107E714A1B0?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0001036&representation=PDF), -[*Full Text HTML Version*]("http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0001036") +[*Full Text PDF Version*](http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=009B2741B48AC1CB94E68107E714A1B0?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0001036&representation=PDF), +[*Full Text HTML Version*](http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0001036) 34. Pérez-Enciso M, Quevedo JR, Bahamonde A ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17352813)) Genetical genomics: use all data. BMC Genomics 8:69. [*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2164-8-69.pdf), -[*Full Text HTML Version*]("http://www.biomedcentral.com/1471-2164/8/69) +[*Full Text HTML Version*](http://www.biomedcentral.com/1471-2164/8/69) 35. Rosen GD, Bai J, Wang Y, Fiondella CG, Threlkeld SW, LoTurco JJ, Galaburda AM ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17218481)) Disruption of neuronal migration by RNAi of Dyx1c1 results in neocortical and hippocampal malformations. Cereb Cortex 17:2562-72. [*Full Text PDF Version*](http://cercor.oxfordjournals.org/cgi/reprint/bhl162v1.pdf) @@ -931,7 +938,7 @@ CRC Press ISBN 084931903X InterScience [*HTML example of using GEMMA and GeneNetwork*](http://www.bioinformatics.ubc.ca/pavlidis/lab/reuse/walkthrough.pdf) 43. Zou W, Aylor DL, Zeng ZB ([2007](http://www.biomedcentral.com/1471-2105/8/7)) eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. BMC Bioinformatics 8:7. -[*Full Text PDF Version*]("http://www.biomedcentral.com/content/pdf/1471-2105-8-7.pdf), +[*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2105-8-7.pdf), [*Full Text HTML Version*](http://www.biomedcentral.com/1471-2105/8/7) @@ -990,7 +997,7 @@ CRC Press ISBN 084931903X InterScience 21. Peirce JL, Li H, Wang J, Manly KF, Hitzemann RJ, Belknap JK, Rosen GD, Goodwin S, Sutter TR, Williams RW, Lu L [2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16783644&query_hl=1&itool=pubmed_docsum)) How replicable are mRNA expression QTL? Mammalian Genome 17:643-656. [*Full Text PDF Version*](http://www.springerlink.com/content/a23g75163p624324/fulltext.pdf), [*Full Text HTML Version*](http://www.springerlink.com/content/a23g75163p624324/fulltext.html). [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.] 22. 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](http://www.ncbi.nlm.nih.gov/pubmed/16783644) Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors. J Neurosci 26:5673-83 -[*Full Text PDF Version*](tp://www.jneurosci.org/cgi/reprint/26/21/5673.pdf), +[*Full Text PDF Version*](http://www.jneurosci.org/cgi/reprint/26/21/5673.pdf), [*Full Text HTML Version*](http://www.jneurosci.org/cgi/content/full/26/21/5673) 23. Radcliffe RA, Lee MJ, Williams RW ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16783639&query_hl=1&itool=pubmed_docsum)) 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*](http://www.springerlink.com/content/3u641hgk642221r6/fulltext.pdf), [*Full Text HTML Version*](http://www.springerlink.com/content/3u641hgk642221r6/fulltext.html) @@ -1016,7 +1023,8 @@ CRC Press ISBN 084931903X InterScience ### GeneNetwork (2005) -1. Alberts R, Terpstra P, Bystrykh LV, de Haan G, Jansen RC ([2005]("http://www.ncbi.nlm.nih.gov/pubmed&dopt=Abstract&list_uids=15711547&query_hl=10)) A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays Genetics 171:1437-1439 +1. Alberts R, Terpstra P, Bystrykh LV, de Haan G, Jansen RC ([2005](http://www.ncbi.nlm.nih.gov/pubmed&dopt=Abstract&list_uids=15711547&query_hl=10)) A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays Genetics 171:1437-1439 + 2. Alberts R, Fu J, Swertz MA, Lubbers LA, Albers CJ, Jansen RC ([2005](http://www.ncbi.nlm.nih.gov/pubmed/15975223)) Combining microarrays and genetic analysis. Brief Bioinform. 6:135-145 [*Full text PDF version*](http://bib.oxfordjournals.org/cgi/reprint/6/2/135.pdf) @@ -1047,23 +1055,23 @@ CRC Press ISBN 084931903X InterScience 13. 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](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16205371&query_hl=1&itool=pubmed_docsum)) Complex genetics of interactions of alcohol and CNS function and behavior. Alcoholism: Clinical and Experimental Research 29:1706-1719 -14. 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]("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15683449&query_hl=4)) Genetic segregation of spontaneous erosive arthritis and generalized autoimmune disease in BXD2 recombinant inbred strain of mice. Scadinavian Journal of Immunology 61:1-11 +14. 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](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15683449&query_hl=4)) 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*](http://gn1.genenetwork.org/images/upload/Mountz2005.pdf) -15. Li CX, Wei X, Lu L, Peirce JL, Wiliams RW, Waters RS ([2005]("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16338823&query_hl=12&itool=pubmed_docsum)) 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 +15. Li CX, Wei X, Lu L, Peirce JL, Wiliams RW, Waters RS ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16338823&query_hl=12&itool=pubmed_docsum)) 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 16. Palmer AA, Verbitsky M, Suresh R, Kamen HM, Reed CI, Li N, Burkhart-Kasch S, McKinnon CS, Belknap JK, Gilliam TC, Phillips TJ ([2005](http://www.ncbi.nlm.nih.gov/pubmed/16104378)) Gene expression differences in mice divergently selected for methamphetamine sensitivity. Mammalian Genome 16:291-305 -17. Pravenec M, Kren V ([2005](ttp://www.ncbi.nlm.nih.gov/pubmed/15728137)) Genetic analysis of complex cardiovascular traits in the spontaneously hypertensive rat. Exp Physiol 90:273-276 +17. 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