Latest Updates and News from Genenetwork modify this page

2014-10-17: Notes on new BXD names.
  1. BXD73, BXD73a (original known as BXD80), and BXD73b (originally known as BXD103) are genetically very similar. BXD73 and BXD80 are genetically identical at 82264 of 100290 markers (82% identical by descent). BXD73 keeps its original name and JAX identifier number (JR#7117), whereas BXD80 is now referred to as BXD73a (JR#7124). BXD73 and BXD103 are genetically identical at 90917 of 100290 markers (90.6% identical by descent). BXD103 is now referred to as BXD73b (JR#7146).
  2. BXD48 and BXD48a (originally known as BXD96) are sister substrains, and are genetically identical at 93485 of 100290 markers (93.2% identical by descent). BXD48 retains its original name and JAX identifier number (JAX JR#7097) whereas BXD96 is now referred to as BXD48a (JR#7139).
  3. BXD65, BXD65a (originally known as BXD97), and BXD65b (originally known as BXD92) are sister substrains. BXD65 and BXD97 are genetically identical at 92225 of 100290 markers (92% identical by descent). BXD97 is now referred to as BXD65a (JR#7140). BXD65 and BXD92 are genetically identical at 6155 of 6459 markers (95.3% identical by descent). BXD65 retains its original name and JAX identifier (JR#7110) whereas BXD92 is now referred to as BXD65b (JR#9677).
2014-10-10: BXD Elicited Peritoneal Neutrophils Gene Expression profiling by array entered into GeneNetwork.
  • UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA **
  • UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) RMA Exon Level **
Currently this dataset is confidential, please contact Marko Radic University of Tennessee Health Science Center for further information. (Implemented by Marko Radic, Indira Neeli, Teruki Hagiwara, Arthur Centeno and Rob Williams).
2014-08-29: Mouse Diversity Panel Hippocampus Antidepressant profiling by array entered into GeneNetwork.
  • UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA **
Currently this dataset is confidential, please contact Brooke Miller University of Florida for further information. (Implemented by Robert Clark, Arthur Centeno and Rob Williams).
2014-08-08: BXD Fecal Metabolites LFD+HFD profiling by array entered into GeneNetwork.
  • RTI RCMRC BXD Fecal Metabolites LFD+HFD (Aug14) **
  • RTI RCMRC BXD Fecal Metabolites HFD (Aug14) **
  • RTI RCMRC BXD Fecal Metabolites LFD (Aug14) **
Currently this dataset is confidential, please contact Robert Clark for further information. (Implemented by Robert Clark, Arthur Centeno and Rob Williams).
2014-05-02: BXD Liver, Soluble Proteins CD and Hi-Fat Gene Expression profiling by array entered into GeneNetwork.
  • EPFL/ETHZ BXD Liver, Soluble Proteins CD (May14) SWATH **
  • EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH **
Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Evan Williams, Arthur Centeno and Rob Williams).
2014-04-03: UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level (Apr14) RMA profiling by array entered into GeneNetwork.
  • UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level (Apr14) RMA **

Currently this dataset is confidential, please contact Dennis D Black UT Le Bonheur Pediatric Specialists for further information. (Implemented by Dennis D Black, Arthur Centeno and Rob Williams).

2014-03-07: The Genotype-Tissue Expression (GTEx) is providing a comprehensive atlas of gene expression and regulation across multiple human tissues. The latest GTEx data release (dbGaP release phs000424.v4.p1) is now available on GeneNetwork.

The Genotype-Tissue Expression (GTEx) project is a collaborative effort that aims to identify correlations between genotype and tissue-specific gene expression levels that will help identify regions of the genome that influence whether and how much a gene is expressed. GTEx is funded through the Common Fund, and managed by the NIH Office of the Director in partnership with the National Human Genome Research Institute, National Institute of Mental Health, the National Cancer Institute, the National Center for Biotechnology Information at the National Library of Medicine, the National Heart, Lung and Blood Institute, the National Institute on Drug Abuse, and the National Institute of Neurological Diseases and Stroke, all part of NIH. This series of 837 samples represents multiple tissues collected from 102 GTEX donors and 1 control cell line. In total, 30 tissue sites are represented including Adipose, Artery, Heart, Lung, Whole Blood, Muscle, Skin, and 11 brain subregions. RNA-seq expression data, robust clinical data, pathological annotations, and genotypes are also available for these samples from dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v2.p1) and the GTEx portal (www.broadinstitute.org/gtex). While GTEx is no longer generating Affymetrix expression data, donor enrollment continues and is expected to reach 1,000 by the end of 2015. Updates to the GTEx data in dbGaP and the GTEx Portal will be made periodically. contributor: GTEx Laboratory, Data Analysis, and Coordinating Center (LDACC) contributor: The Broad Institute of MIT and Harvard (LDACC PIs: Kristin Ardlie and Gaddy Getz).

WU-Minn HCP Consortium Open Access Data Use Terms

2014-01-31: BXD Heart Polar Metabolites Gene Expression profiling by array entered into GeneNetwork.
  • EPFL/LISP BXD CD Heart Affy Mouse Gene 2.0 ST Gene Level (Jan14) RMA **
  • EPFL/LISP BXD HFD Heart Affy Mouse Gene 2.0 ST Gene Level (Jan14) RMA **
  • EPFL/LISP BXD CD Heart Affy Mouse Gene 2.0 ST Exon Level (Jan14) RMA **
  • EPFL/LISP BXD HFD Heart Affy Mouse Gene 2.0 ST Exon Level (Jan14) RMA **
Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Evan Williams, Arthur Centeno and Rob Williams).
2014-01-30: GEO Series GSE15745 Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues.
  • GSE15745 NIH Human Brain Cerebellum ILM humanRef-8 v2.0 (May10) RankInv
  • GSE15745 NIH Human Brain Prefrontal Cortex ILM humanRef-8 v2.0 (May10) RankInv
  • GSE15745 NIH Human Brain Temporal Cerebral ILM humanRef-8 v2.0 (May10) RankInv
  • GSE15745 NIH Human Brain Pons ILM humanRef-8 v2.0 (May10) RankInv
Currently this dataset is in progress, please contact J Raphael Gibbs National Institutue on Aging, NIH for further information. Data originated from GTEx (Genotype-Tissue Expression) eQTL Browser (Implemented by J Raphael Gibbs, Arthur Centeno and Rob Williams).
2014-01-06: BXD Mouse Retina Blast Gene expression profiling by array entered into GeneNetwork.
  • DoD TATRC Retina Blast Affy MoGene 2.0 ST (Dec13) RMA Gene Level **
  • DoD TATRC Retina Blast Affy MoGene 2.0 ST (Dec13) RMA Exon Level **
Currently this dataset is confidential, please contact Eldon Geisert Emory Eye Center for further information. (Implemented by Eldon Geisert, Justin Templeton, Arthur Centeno and Rob Williams).
2013-12-16: BXD Liver Polar Metabolites and BXD Muscle Polar Metabolites Gene expression profiling by array entered into GeneNetwork.
  • EPFL/LISP BXD Liver Polar Metabolites CD+HFD (Dec13) **
  • EPFL/LISP BXD Liver Polar Metabolites HFD (Dec13) **
  • EPFL/LISP BXD Liver Polar Metabolites CD (Dec13) **
  • EPFL/LISP BXD Muscle Polar Metabolites CD+HFD (Dec13) **
  • EPFL/LISP BXD Muscle Polar Metabolites HFD (Dec13) **
  • EPFL/LISP BXD Muscle Polar Metabolites CD (Dec13) **
Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Evan Williams, Arthur Centeno and Rob Williams).
2013-12-02: BXD Mouse Retina Gene expression profiling by array entered into GeneNetwork.
  • DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA Gene Level **
  • DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA Exon Level **
Currently this dataset is confidential, please contact Eldon Geisert Hamilton Eye Institute Department of Ophthalmology for further information. (Implemented by Eldon Geisert, Justin Templeton, Arthur Centeno and Rob Williams).
2013-11-19: HZI PR8M-Infected Lungs Females RNAseq (Nov13) RPKM ** entered into GeneNetwork. Currently this dataset is confidential, please contact Klaus Schughart Department Experimental Mouse Genetics for further information. (Implemented by Klaus Schughart, Ashutosh Pandey, Arthur Centeno and Rob Williams).
2013-10-28: BXD CD Brown Adipose Gene expression profiling by array entered into GeneNetwork.
  • EPFL/LISP BXD CD Brown Adipose Affy Mouse Gene 2.0 ST Gene Level (Oct13) RMA **
  • EPFL/LISP BXD CD Brown Adipose Affy Mouse Gene 2.0 ST Exon Level (Oct13) RMA **
Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Evan Williams, Arthur Centeno and Rob Williams).
2013-09-23: Gene expression changes in the course of normal brain aging are sexually dimorphic. Expression profiling by array (Platform: GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) entered into GeneNetwork.
  • GSE11882 UCI Human Entorhinal Cortex Affy U133 Plus2 (Sep13) RMA
  • GSE11882 UCI Human Hippocampus Affy U133 Plus2 (Sep13) RMA
  • GSE11882 UCI Human Postcentral Gyrus Affy U133 Plus2 (Sep13) RMA
  • GSE11882 UCI Human Superior Frontal Gyrus Affy U133 Plus2 (Sep13) RMA
PMID: 18832152. GEO Series GSE11882. (Implemented by Nicole Claudia Berchtold, Arthur Centeno and Rob Williams).
2013-08-29: GeneNetwork 10-year anniversary. We now have a decade of expression data in GeneNetwork (first mRNA data is a BXD Whole Brain U74Av2 Aug03). Here are some current statistics:
  1. 437 expression data sets for all species. Many of these are "variants on a theme" such as Male, Female, Combined, or PDNN, RMA, MAS5 transformations.
  2. 240 expression data sets for the BXD family of mice The redundancy rate is probably about 3x (three versions of every primary data set).
  3. 13.7 million mRNA traits. Again, figure about 3x redundancy. That is ~4 million molecular assays across the family.
  4. 685 million mRNA strain-phenotype values for the BXD family. That means that we 50 strains on average per trait (685/13.7). For most of these we also have standard error terms, so we have over a billion data points for the BXD family.
2013-08-06: SEARCH FOR GENES BY AUTHOR. You can now search gene expression data sets using an author query. The search is not perfect yet, but try these queries in the search boxes:
  1. NAME=(Watson JD)
  2. NAME=(Snyder) will work but NAME=(Snyder M) does not yet work
  3. NAME=(Synder) is a typo, and will not work
  4. NAME=(Williams LU) is interpreted as two different authors (RW Williams and L Lu in this case).
We plan to refine this type of query and to add a query for Institutions (INST=Yale). (Implemented by Lei Yan).
2013-08-02: Experimental INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) PCA (principal component analysis) v080813 entered into GeneNetwork. Variance adjusted and denoised by Ashutosh Pandey (Implemented by Khyobeni Mozhui, Adrienne Adler, Jesse Ingels, Lu Lu, Ashutosh Pandey, Arthur Centeno and Rob Williams).
2013-07-11: Several features have been implemented or are currently being implemented for GeneNetwork 2:
  • A new interface for user registration is being developed for GeneNetwork 2, as well as an interface with which users can designate groups of data-sets and assign read/write privileges. (Implemented by Sam Ockman and Zach Sloan)
  • The correlation page has been mostly re-implemented. While the output is the same, all features re-implemented in GN2 have been almost entirely rewritten using much clearer business logic and a framework and templating language (Flask and Jinja2 respectively). (Implemented by Lei Yan and Zach Sloan)
  • The marker regression function has been re-implemented using the PyLMM code written by Nick Furlotte. This code is much more robust than the code currently used in the marker regression function of GN1 and accounts for kinship between samples/strains. (Implemented by Zach Sloan, Sam Ockman, and with code written by Nick Furlotte)
Future updates will continue to be posted in the news as they're completed.
2013-07-10: We added a link from GeneNetwork to BNW (Bayesian Network Web Server) at GeneNetwork collection page. (Implemented by Lei Yan).
2013-06-13: Whole-genome gene expression profiles of non-tumorous human lung tissues GEO Series GSE23546 entered into GeneNetwork. This SuperSeries is composed of the SubSeries: GSE23352 (Laval set: 499 samples), GSE23529 (UBC set: 405 samples), GSE23545 (GRNG set: 445 samples), please contact Yohan Bossé or Ke Hao for further information. Platform used: GPL10379 Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray. (Implemented by Yohan Bossé, Ke Hao and Arthur Centeno).
2013-06-04: When editing gene aliases, aliases can be split by comma, semicolon, vertical bar, space, line break. And then they all will be converted to semicolon (NCBI style). (Implemented by Lei Yan).
2013-04-13: DoD TATRC Retina Affy MoGene 2.0 ST Array (April 2013) RMA entered in GeneNetwork. This data set consists of 19 BXD strains, and DBA/2J parental strain. The data are now closed and not available for analysis. This is Robust Multi-array Average (RMA) expression data that has been normalized using what we call a 2z+8 scale, without special correction for batch effects. The data for each strain was computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.252 to 18.07 (11.83 units), a range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale. (Implemented by Eldon E. Geisert and Arthur Centeno).
2013-04-06: PLINK procedure upgraded: The PLINK calculation procedure was upgraded, so now the mapping time with PLINK is reduced to less than half. For Human CANDLE data, it took about 400+ seconds before, now it will take no more than 200 seconds. (Implemented by Lei Yan).
2013-03-21: New GeneNetwork UCSC Genome Browser mirror: We have installed a second GeneNetwork UCSC Genome Browser mirror site that supports mm10 and mm9. And we loaded DBA/2J Sequence and Structural Variants and C57BL6/NJ Sequence and Structural Variants for mm10. (Implemented by Lei Yan and Ashutosh Pandey).
2013-01-18: The Scripps Research Institute (TSRI) Dorsal Root Ganglia (DRG) Affy Mouse Genome 430 2.0 (Jan13) RMA Mouse Diversity Panel (MDP) entered into GeneNetwork. Currently this dataset is confidential, please contact Andrew Su for further information. (Implemented by Andrew Su and Arthur Centeno).
2013-01-08: Users can now chose the number of permutations that are used to estimate empirical P values for mapping results. We typically default to 2000 permutations, but if you need more precise estimates of P values it is possible to request up to 100,000 permutations. On a good day and without many other active users on GeneNetwork, the system can handle 1000 permutations per second. A histogram of the highest LRS scores for each of the many permutations is now displayed again in the Marker Regression output window. (Implemented by Zach Sloan and Lei Yan).
2012-11-08: First mappable RNA-seq data set in GeneNetwork for 29 genotypes of mice (BXD family) for whole brain RNA samples. We used a RiboMinus rather than polyA+ protocol. Approximately 15 million unique and aligned reads per sample were generated and used to compute the number of mRNAs (RPKM, normalized reads per per 1 kb of gene model per million tags). This data set summarizes values on a per GENE basis. We will be adding EXON level analysis in the next few weeks. To the best of our knowledge this is the first accessible and directly mappable RNA-seq data set available on the Internet. (Implemented by Khyobeni Mozhui, Arthur Centeno, David Li, Lu Lu, William Taylor, and Xusheng Wang).
2012-10-01: The core GeneNetwork code is now being rewritten in Python 2.7 using the Flask framework and Jinja2 HTML templating. Progress can be monitored on the GN GitHub site. Our goal is to produce an much more extensible and modular version of GeneNetwork (GN2.0). GN2.0 will initially not have nearly as many features as GN1.0 but it will be used as the base for all new coding. We expect to port GN2.0 to Python 3.3+ late in 2013 or early 2014. (Implemented by Lei Yan, Zach Sloan, Sam Ockman, with advice from Christian Fernandez).
2012-09-01: BXD Hypothalamic-Pituitary-Adrenal axis data sets have been completed and added to GeneNetwork. These data sets are accessible to all users without registration at two different levels of analysis--whole gene estimates of transcript expression, and single exon estimates of expression. The three primary data sets have now been error checked, and corrected. The hypothalamus data have been split by sex. PMID: 22593731. GEO Series GSE36674. (Implemented by Khyobeni Mozhui, Adrienne Adler, Jesse Ingels, Arthur Centeno, Lu Lu, and Rob Williams).
2012-07-20: BXD Pituitary gene expression data added to GeneNetwork. This is part of a systematic genetic analysis of the hypothalamic-pituitary-adrenal axis in the mouse (~5 strains). Data for hypothalamus and pituitary are complete and error checked. Data for the adrenals are still be error-checked. (Implemented by Khyobeni Mozhui, Adrienne Adler, Jesse Ingels, Arthur Centeno, Lu Lu, and Rob Williams).
2012-07-01: New beta SEARCH feature by NAME (testing stage) now allows searching for genes/transcripts by the name of authors and scientists who have worked set of genes. The search "name=rakic" or "name=(williams rw)" will find genes that have been linked to articles by "Rakic" of "RW Williams" in PubMed. We are still working on the interface for this new search type. Send any suggestions for improvements or problems that you encounter. (Implemented by Lei Yan and Ashutosh Pandey).
2012-06-04: GeneNetwork Development and Source Control now using GitHub . We have switched over from developing GeneNetwork using Apache Subversion (SVN) software versioning system to GitHub. GitHub (Implemented by Lei Yan with in collaboration with from Christian Fernandez and Sam Ockman).
2012-05-20: All GeneNetwork code is available on GitHub (Implemented by Lei Yan with in collaboration with from Christian Fernandez and Sam Ockman).
2012-05-04: Second Developmental Studies of the Genetics of Gene Expression in Brain have been entered into GeneNetwork (BIDMC/UTHSC Dev Neocortex P3 and P14 ILMv6.2 (Nov11) RankInv). Dr. Glenn Rosen and colleagues have contributed data on gene expression across sets of 32 BXD strains for the neocortex and striatum at two stages of development (postnatal days 3 and 14). They used the Illumina Mouse Genome 6 version 2 array. These data are matched by previous data sets for the adult neocortex and striatum. These data are now publicly available but users are requested to contact Glenn D. Rosen regarding the status of these new data. (Implemented by G Rosen, RW Williams and A Centeno).
2012-01-20: Mouse SNPs from dbSNP have been added to GeneNetwork. 10 million mouse SNPs from dbSNP (build 128) have been added to Variant Browser. They could be searched by name (e.g. rs31192936) (Implemented by Xiaodong Zhou and Ning Liu).
2012-01-20: Literature correlation has been update to 2011 version. Dr. Ramin Homayouni and Dr. Lijing Xu kindly provide the 2011 version of mouse gene-gene literature correlation matrix to GeneNetwork. (Implemented by Xiaodong Zhou).
2011-12-16: Expression data set for EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA ** has been entered in GeneNetwork. Laboratory of Integrative and Systems Physiology (LISP). This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please contact Johan Auwerx or Evan Williams at evan.williams@epfl.ch regarding use of these data. (Implemented by J Auwerx, E Williams, LA Rose, RW Williams and A Centeno).
2011-9-29: We have added liver gene expression data for many strains of mice from GEO series GSE16780. These data were generated by Dr. Jake Lusis and colleagues at UCLA and are currently listed as a BXD data set, although the study actually includes many other strains (see "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA". Since adding the data we have discovered errors in strain assignment that affect a majority of the conventional inbred strains and several RI strains. For this reason, these data should still be considered provisional. For complete information please refer to A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 2010 Feb;20(2):281-90. PMID: 20054062 (Implemented by Bennett BJ, Ghazalpour A. Data entered on 9-29-11 by A. Centeno under Accession number:GN373).
2011-9-17: The QTLminer feature was put into GeneNetwork production server.(Implemented by Rudi Alberts, Lei Yan, Ning Liu, Xiaodong Zhou)
2011-7-20: GeneNetwork was moved to Amazon Cloud (EC2). (Implemented by Lei Yan)
2011-7-12: A SourceForge site for GeneNetwork was built: https://sourceforge.net/projects/genenetwork/. (Implemented by Lei Yan, Robert Williams)
2011-7-11: A new account on our SVN server for GeneNetwork sharing was created. Anybody can get the latest version of GN source codes by checking out (this account cannot commit).
URL: http://tyche.uthsc.edu/repos/gn/
Username: gndownload
Password: gndownload
(Implemented by Lei Yan)
2011-7-5: Harvard Brain Tissue Resource Center/ Merck Research Laboratories. This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease and 170 controls matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC).

Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.

Acknowledgements. The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/). Investigators: Francine Benes/ Eric Schadt. (Implemented by Megan Mulligan, Rob Williams and Arthur Centeno).

2011-6-16: CANDLE Study expression data entered in GN. The primary goal of the CANDLE study is to study factors that affect brain development in young children. To this end, the current study will test specific hypotheses regarding factors that may negatively influence cognitive development in children. For information on genomic and genetic studies related to CANDLE, please contact: Drs. Ronald M. Adkins (radkins1 at uthsc.edu) and Julia Krushkal (jkrushka at uthsc.edu). This data set is currently confidential. (Implemented by Khyobeni Mozhui, Rob Williams and Arthur Centeno).
2011-6-6: Confidential Phenotype Trait Feature: We added one new feature of confidential phenotype trait to GeneNetwork. (Implemented by Xiaodong Zhou).
2011-6-6: SNP INDEL Variant Browser updated: We have greatly expanded and improved the SNP INDEL variant browser that is built into GeneNetwork. This resource enables users to rapidly review both known and confidently imputed sequence variants in the mouse genome. The data set includes over 65 million SNPs that are largely taken from sequencing efforts of David Adams and colleagues at the Sanger Institute and our own team at UT. The imputation of SNPs to other strains was carried out by Eleazar Eskin, Nick Furlotte, and colleagues at UCLA. (Implemented by Ning Liu and Xiaodong Zhou).
2011-6-6: Major Overhaul of Trait Data pages: The Trait Data and Analysis page has been redesigned to reduce complexity and visual clutter. Functions have not been changed, but may have been moved (Implemented by Zachary Sloan, Xiaodong Zhou, and Rob Williams).
2011-6-6: Upgraded GeneNetwork Hardware: We are converting GeneNetwork to MySQL master-slave replication with faster solid-state hard drives to improve performance. (Implemented by Lei Yan).
2011-3-21: Sample blocking: The user can now block individual samples/strains in the Trait Data and Analysis page by typing either an individual index number or a range (ex: 1,2,3,10-20). This feature was created to eliminate the need for a user to manually replace each sample's value with 'x'. (Implemented by Zachary Sloan).
2011-3-18: User login status: The user login status is shown in all dynamically generated pages by making use of session mechanism through entire GN system. (Implemented by Xiaodong Zhou).
2011-2-23: More space for your Trait Collections: We have greatly expanded the number of traits, transcripts, genes, and markers be added to your collections. The current limit is now 3,000; up from 100 in the previous version. This improvement was achieved by storing collection information using a different and more secure method (session control rather than cookies) (Implemented by Xiaodong Zhou).
2011-2-9: INIA Amygdala BLA Affy MoGene 1.0 ST (Nov10):

This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.

2011-2-9: INIA Hypothalamus Affy MoGene 1.0 ST (Nov10):

These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.
This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.

2011-2-7: GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA **: Data set generated with support of NIAAA by Drs. Robert Rooney (Genome Explorations Inc.), Divyen Patel (Genome Explorations Inc.), and Kristin Hamre (UTHSC). All animals were on standard chow and water ad lib. Both the saline control group and the ethanol=treated group were given solutions via intragastric gavage with controls getting saline and the alcohol-treated group getting 6g/kg of ethanol. Ethanol-treated mice were generally comatose for 4-6 hrs but were responsive and moving by the next morning. Tissue was collected at 24 hours after the initial infusion.
This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
2011-2-3: OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv: The current study focused on the extent genetic diversity within a species (Mus musculus) affects gene co-expression network structure. To examine this issue, we have created a new mouse resource, a heterogeneous stock (HS) formed from the same eight inbred strains that have been used to create the collaborative cross (CC). The eight inbred strains capture > 90% of the genetic diversity available within the species. For contrast with the HS-CC, a C57BL/6J (B6) × DBA/2J (D2) F2 intercross and the HS4, derived from crossing the B6, D2, BALB/cJ and LP/J strains, were used. Brain (striatum) gene expression data were obtained using the Illumina Mouse WG 6.1 array, and the data sets were interrogated using a weighted gene co-expression network analysis (WGCNA).
Read full article: Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse.
2011-1-26: Auwerx Lab BXD Phenotype Data: We have entered the first large-scale metabolic, cardiovascular, and clinical chemistry data sets (n = 143 phenotypes) for the BXD strains of mice. Data are averages for males and females separately, for as many as 43 strains. Data were generated using animals born at UTHSC (Memphis) and phenotyped in Strasbourg, France in 2008 using EMPReSS Slim EUMORPHIA standard operating protocols. Blood pressure phenotypes were included in a PLoS Genetics paper in 2009, but we now provide the complete phenotypes from this cohort of animals. (Phenotyping by Hana Koutinkova, Johan Auwerx and colleagues; data processing by H Koutnikova, RW Williams, EG Williams, and Xiaodong Zhou).
2011-1-26: Expression data for the prefrontal cortex of the BXD strains have added into GN, mice from each genotype received 4 weekly cycles of chronic intermittent ethanol (CIE) vapor exposure (EtOH group) or air exposure (CTL group) in inhalation chambers. The general study design was generated by Dr. Michael Miles and colleagues. All data sets are currently being tested. Contact Dr. Miles at VCU Medical Center for access (Implemented by M Miles, RW Williams and A Centeno).
  1. VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **
  2. VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **
  3. VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **
2011-1-14: NCSU Expression data set for Drosophila melanogaster have been added to GeneNetwork. For more information about The Drosophila Genetic Reference Panel click here. (Julien F. Ayroles, Trudy F. C. Mackay).
  1. NCSU Drosophila Whole Body (Jan11) RMA
2011-1-11: Genome Explorations Expression data sets for Liver have been added to GeneNetwork. (Implemented by B Rooney, K Hamre, RW Williams and A Centeno).
  1. GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females **
  2. GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males **
  3. GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes **
  4. GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females **
  5. GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males **
  6. GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes **
2010-12-22: Phenotype traits can be searched by LRS. For instance, search by LRS=(23 46) or LRS=(9 99 Chr4 122 155). (Implemented by Xiaodong Zhou).
2010-12-20: The final quality controlled release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu) has been entered in GeneNetwork.
  1. UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA
2010-12-10: We built a new Cluster system. Four nodes were deployed. Every node is Dell PowerEdge R815, has 48 cores, 64G RAM, 1.3G RAM/core. CPU is AMD 1.86G Hz. The headmaster connects one Dell PowerVault MD1000 (15*2TB hard drives, RAID5). And Galaxy system was installed on the Cluster system. (Implemented by Lei Yan).
2010-10-29: First Developmental Studies of the Genetics of Gene Expression in Brain have been entered into GeneNetwork. Dr. Glenn Rosen and colleagues have contributed data on gene expression across sets of 32 BXD strains for the neocortex and striatum at two stages of development (postnatal days 3 and 14). They used the Illumina Mouse Genome 6 version 2 array. These data are matched by previous data sets for the adult neocortex and striatum. These data are open but users are requested to contact Glenn D. Rosen regarding the status of these new data. (Implemented by G Rosen, RW Williams and A Centeno).
2010-10-29: Large RNA-seq data for BXD Whole Brain is being added to our GeneNetwork version of the UCSC Genome Browser. We are still loading these data and eventually will display RNA-seq data for over 30 strains of mice. Gene level summary of these data will be entered into GeneNetwork for quantitative analysis later this year. Please contact RW Williams regarding the status of these new data. (Implemented by David Li, Lu Lu, Xusheng Wang, Lei Yan, and RW Williams).
2010-9-23: Genotype data for mouse strains BXD101, BXD102, and BXD103 have been added to GeneNetwork. These data were extracted from a large scale regenotyping of the BXD strains done using the Mouse Diversity array from Affymetrix that was designed by Pardo and Churchill. (Implemented by Ning Liu and Xiaodong Zhou).
2010-9-20: Five groups of gene expression data for the hippocampus of BXD strains of mice have been entered in GeneNetwork. NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection. (Implemented by Lu Lu, RW Williams and A Centeno).
2010-9-13: There is now a good Wikipedia entry for GeneNetwork. Please check, correct, and improve. (Implemented by RW Williams).
2010-9-13: GeneNetwork source code is now licenses using the Affero General Public License version 3. A SourceForge site will be set in the next few months. In the interim, please contact us directly for code. (Implemented by Xiaodong Zhou and RW Williams).
2010-08-02: We have installed a GeneNetwork UCSC Genome Browser mirror site that displays a set of 4.58 million SNPs that distinguish strain DBA/2J from the reference strain, C57BL/6J. Other DNA sequence and RNA-seq data sets will be added over the next several months. (Implemented by Lei Yan and Xusheng Wang).
2010-08-02: Tissue Correlation and Expression Level Services: We have added a new web interface that allows you to directly evaluate differences in gene expression across 30 different tissue types.

The current version is mainly meant for testing. The interface still needs work.We have a long list of improvements in the works, but please send us your ideas. To test drive the tissue correlation feature you currently need to enter a set of mouse GeneID numbers. For example App is NCBI Enbrez Gene ID 11820. Bace is Gene ID 23821. If you enter these two numbers in the interface and then click your heels twice. You should get back a simple matrix of values that lists both Pearson and Spearman correlations based on a comparison of expression in 25 tissue types. Click on the correlation values and this will pop up two scatterplots (Pearson and Spearman types).

At the same time, this tool provides expression estimates for both genes, where a value of 8 in the Pearson plot represents the mean across all tissues and each unit represents a two-fold difference (log2 expression; Spearman rank values are just that--rank out of 25). To access this new feature select Search -> Tissue Correlation. All of the expression data are taken from on C57BL/6J litter mates studied using the Illumina Mouse 6 2.0 array (Implemented by Ning Liu, data from Lu Lu, RW Williams, and Xusheng Wang).

2010-08-02: The javascript that controls the sort menu on top of collection page has been improved. The old version doesn't work properly in IE browser. The new one works well in IE, Firefox, Safari. (Implemented by Ning Liu).
2010-07-02: Microarray annotations have been improved and will soon be more consistent across platforms. We now synchronize the gene level annotation of probes and probe sets. When gene level attributes such as gene symbols, alias, name, and other identifiers, are changed, the change is applied to all other probes and probe sets with the same Gene Id. (Implemented by Xiaodong Zhou).
2010-07-02: We have added Homologene identifiers to help in comparative analysis. (Implemented by Xiaodong Zhou)
2010-07-02: Improved Search Page that loads much more rapidly from even slow connections. We replaced the AJAX version of the Search Page with a javascript version. (Implemented by Ning Liu).
2010-07-02: Improved icons and GUI for selecting and analyzing GeneNetwork data sets. The use of icons enable fast recognition of functions and is also more compatible with touch screen interfaces. There are three types of icons:
  1. Selection tools with a grey background
  2. GeneNetwork analysis tools with blue background
  3. External resources analysis tools with a clear background
This GUI was implemented by Zach Sloan.
2010-07-02: We have improved interface for the partial correlations, Now both the zero order and higher order correlations use identical sample sizes for more direct comparisons. We have also added several checking procedures to help you avoid undesirable results. (Implemented by Xiaodong Zhou).

See More News