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2018-09-12: GeneNetwork 1 will be supported in 2018 but GeneNetwork 2 will become the main production server

GeneNetwork 2 is ready for testing and research projects. GeneNetwork 1 (GN1) and GeneNetwork 2 (GN2) share the a single database, but they use different code and algorithms for mapping and data analysis. There are some benefits of using GN2, including more powerful linear mixed model mapping methods that account for kinship structure.

The interface of GN2 is still a work in progress. Please send any suggestion, requests, or bug reports to rwilliams@uthsc.edu.

2018-09-12: 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).
2018-09-08: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2 and raw data. profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-23: HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-14: EPFL/LISP BXD HFD+CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-10: NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2 profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-07: NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-06: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-27: JAX Retina (Apr18) RNA-Seq log2-Z profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-11: UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-11: UCSD AIL Striatum (Apr18) RNA-Seq profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-11: UCSD AIL Hippocampus (Apr18) RNA-Seq profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-01-04: UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-29: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-12: EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-12: EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-12: EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow Diet Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, Chow Diet Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-04-27: INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-05-05: INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-05-05: INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-05-05: INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel (Mar18) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-04-28: INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-25: UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-26: UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-27: UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-28: UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-29: UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-24: UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA CXB Liver Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA BXD Liver Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-02-04: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 Z-score profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-02-04: UCSD CFW Striatum (Jan17) RNA-Seq Log2 Z-score profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-02-04: UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 Z-score profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-01-17: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-01-17: UCSD CFW Striatum (Jan17) RNA-Seq profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-01-17: UCSD CFW Hippocampus (Jan17) RNA-Seq profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-11-28: EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-11-28: EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-11-04: UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-10-02: BXD Genotypes file status (October 2016)

In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, and Danny Arends released new genotype files for many of the original BXD strains (BXD1 through BXD102), and for all of the new strains (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de Villena (University of North Carolina) and Gary Churchill (The Jackson Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with financial support from the University of Tennessee Center for Integrative and Translational Genomics.

The new genotypes are now available in GeneNetwork as the 2017 Genotype file. All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 GigaMUGA and many other markers we have typed, only about 6800 are useful (informative) in defining recombination events in the current set of BXDs. These informative markers either define unique recombination patterns across the 198 BXD strains (including extinct strains) or they define the proximal and distal ends of regions that do not contain any known recombinations in the BXD family.

The file does not include any markers for Chr Y or the mitochondrion.

As of October 2016 GeneNetwork still uses mm9 coordinates for mapping functions.

(Updated Oct 2, 2016 by RW Williams)

2016-09-29: TIGEM Human Retina RNA-Seq (Sep16) RPKM log2 profiling by array entered into GeneNetwork. This dataset is public available, please contact Michele Pinelli at Telethon Institute of Genetics and Medicine (TIGEM) for further information. (Implemented by Michele Pinelli, Arthur Centeno and Rob Williams).
2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA ** profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-07-26: Raw and processed data from our Hippocampus studies based on publication "Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource" can be accessed now through GEO series GSE84767.
2016-07-16: Gene expression data for 39 inbred mice strains for CD4+ T cells profiling by array entered into GeneNetwork. GEO Series: GSE60337. To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database.
2016-05-16: FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Michal Pravenec Czech Academy of Sciences for further information. (Implemented by Michal Pravenec, Arthur Centeno and Rob Williams).
2016-04-16: EPFL/ETHZ BXD Brown Adipose Proteome (Apr16) profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Arthur Centeno and Rob Williams).
2016-04-16: DoD TATRC Retina Affy MoGene 2.0 ST profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Eldon Geisert Emory Eye Center for further information. (Implemented by Eldon Geisert, Arthur Centeno and Rob Williams).
2016-04-16: VCU BXD NAc EtOH vs CIE Air M430 2.0 profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Michael Miles Virginia Commonwealth University for further information. (Implemented by Michael Miles, Arthur Centeno and Rob Williams).
2016-02-16: UCAMC LXS Whole Brain Saline and Ethanol RNA Sequence FPKM profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Richard Radcliffe University of Colorado at Denver for further information. (Implemented by Richard Radcliffe, Arthur Centeno and Rob Williams).
2016-02-16: UTHSC Hippocampus Illumina v6.1 NOS, NOE, RSS, and RSE data sets profiling by array entered into GeneNetwork.

This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = 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.

For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.

Please contact Rob Williams University of Tennessee Health Science Center for further information. (Implemented by Lu Lu, Arthur Centeno and Rob Williams).
2016-02-16: EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 GeneLevel Main (Feb16) RMA profiling by array entered into GeneNetwork.

The BXD genetic reference population is a recombinant inbred panel descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains of mice, which segregate for about 5 million sequence variants. Recently, some these variants have been established with effects on general metabolic phenotypes such as glucose response and bone strength. In this study, we examined both genetic variants across 40 strains of BXD and the two founder lines, in addition to a major environmental influence—long term feeding with chow diet (CD) or high fat diet (HFD)—to see how metabolic gene expression varies by genotype and environment, and gene-by-environment interactions. The basic heart phenotypes quantified in these cohorts were not affected by HFD feeding (e.g. blood pressure and heart rate).

Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Arthur Centeno and Rob Williams).
2015-12-09: INIA LCM (11 Regions) RNA-seq Transcript Level (Dec15) profiling by array entered into GeneNetwork. This dataset is now public, please contact Megan Mulligan University of Tennessee Health Science Center for further information. (Implemented by Megan Mulligan, Arthur Centeno and Rob Williams).
2015-12-07: UTHSC Affy MoGene 1.0 ST Spleen profiling by array entered into GeneNetwork. This is a preliminary release with known errors of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. Animals were generated at UTHSC by Lu Lu and colleagues. The spleen 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 dataset is now public, please contact Robert Williams University of Tennessee Health Science Center for further information. (Implemented by Lu Lu, Arthur Centeno and Rob Williams).
2015-11-10: Hippocampus Mouse Transcriptome Assay 1.0 GeneLevel Main (Nov15) RMA profiling by array entered into GeneNetwork. Please contact Megan Mulligan University of Tennessee Health Science Center for further information. (Implemented by Megan Mulligan, Arthur Centeno and Rob Williams).
2015-10-13: UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) RankInv profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-10-14: UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) RankInv profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-10-15: UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) RankInv profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-10-16: UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) RankInv profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-09-14: The Genotype-Tissue Expression (GTEx) is providing a comprehensive atlas of gene expression and regulation across 53 human tissues. The latest GTEx data release (dbGaP release phs000424.v5.p1) is now available on GeneNetwork.

Note: Please disregard confusing legend provided in Study tab of the study page which claims that study contains 552 subjects with genotypes - those totals are counts of subjects with all molecular data types, not just molecular genotypes.

More detailed representation of subject counts in molecular datasets (including genotypes) may be found in 'Molecular Data' tab at Common Fund (CF) Genotype-Tissue Expression Project (GTEx) dbGaP Study Accession: phs000424.v5.p1.

2015-05-30: UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) Exon Level RMA profiling by array entered into GeneNetwork.This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.

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