Latest Updates and News from Genenetwork modify this page

2011-7-20: GeneNetwork was moved to Amazon Cloud (EC2). (Implemented by Lei Yan)
2011-7-12: A SourceForge site for GeneNetwork was built: (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).
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 ( 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 and Julia Krushkal (jkrushka at 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 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 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 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).

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