Skip to content

GN News

Jump to bottom
zsloan edited this page Mar 26, 2019 · 1 revision
2018-12-19: BXD Genotypes file status (December 2018)

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.

Update The new genotypes are now available in GeneNetwork as the 2019 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.

This file provides consensus genotypes for 198 BXD strains and for the two progenitor strains and the reciprocal F1s. Of the 198 BXD strains, 191 are independent, whereas 7 are substrains (e.g., BXD48 and BXD48a). This file provides approximate locations of 10300 recombinations, an average of 52 per strain. Genotypes were generated using Affymetrix, MUGA, MegaMUGA, and GigaMUGA Illumina platforms. Microsatellites and eQTL genotypes were generated by the Williams/Lu laboratory. Unknown genotypes were imputed as B or D, or were called as H (heterozygous) if the genotype was uncertain. Genotypes were manually curated by RW Williams. Genotypes were smoothed to remove unlikely recombination events. Almost all recombinations are supported by multiple markers, although only one or two representative markers may be provided in this file. The original parent file (BXD_El_Grande_Master_Used_to_Proof_Final_Genotypes_2016.xlxs) contains data for approximately 37000 markers. A subset of the most informative 7300 markers are included here. Genotypes for Chr Y and Chr M are provisional.

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

As of December 2018 GeneNetwork uses mm10 coordinates for mapping functions.

(Updated Dec 19, 2018 by RW Williams)

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 [email protected].

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.

See More News

2014-10-21: HZI Lung Flu Infected BXD (Nov16) 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.
2014-10-10: BXD Elicited Peritoneal Neutrophils Gene Expression profiling by array entered into GeneNetwork. 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 Brooke Miller, Arthur Centeno and Rob Williams).
2014-08-10: RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) Log2 profiling by array entered into GeneNetwork.

The goal of this project is to study expression of a large set of defined and undefined metabolites in fecal samples from a genetically diverse set of BXD mouse strains (females) raised either on a high fat diet or low fat diet. Samples were taken from animals at sacrifices directly from the large intestine.

Aim: Effect of genetics and diet on fecal metabolomics
Use UPLC-MS Broad Spectrum Metabolomics to study:Mice fecal samples To capture the most signal, all samples were analyzed under positive and negative ion mode using a reversed-phase separation. Please contact Robert Clark RTI International 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),
Clone this wiki locally