EPConDB News RSS Feed

New study available on "A Gene Expression Network Model of Type 2 Diabetes Links Cell Cycle."

21 Jul 2008 01:00:00 EDT

A microarray survey of gene expression in 6 tissues (including islets) was performed by the Attie lab (Keller et al., Genome Res. 2008) to look for coordinated changes that occur as diabetes develops in a mouse model of obesity. A summary of the study is available here. Details and data downloads are available here.

Change in differential expression query.

21 Jul 2008 01:00:00 EDT

EPConDB allows you to get a list of genes that are differentially expressed for certain studies (see example study with list). To make the lists comparable between studies, we use algorithms employing the same false discovery rates (FDR). As before, you can set the fold-change for filtering the list. What has changed is that you now can choose whether you want to impose a "80% confidence" filter which is equivalent to an FDR of 0.2 (20% of the list are expected to be false positives). Previously, the confidence level was a value you could set but it turns out that these were not always accurately matched to fold-changes due to the way both values were obtained for a transcript as a summarization of corresponding reporter values. Note that you can also look for studies where your gene of interest is differentially expressed here using the same approach.

T1DBase version 3.4 Released

16 Jun 2008 01:00:00 EDT

Version 3.4 is a major overhaul of T1DBase including new and updated datasets, a new front page and updated tools. Highlights include:

Full support for mouse build 37
Fully integrated human confirmed genetic regions and summary data from Wellcome Trust Case Control Consortium.
New DoTS - DoTS transcripts are consensus sequences generated by the clustering and assembly of ESTs from dbEST and
RNA sequences from GenBank, provided by University of Pennyslvania.
Updated tissue expression tool, visualise combined expression data to see a list of tissues that express a list of genes.
Updated gene dossier tool: upload a list of genes and see at a glance how they are associated with T1D specific data.
Updated T1DMart including new datasets: T1DGC MHC fine mapping genotyping call data now available to investigators with T1DGC approved access.

EPConDB 4.2 has been Released

16 May 2008 01:00:00 EDT

Version 4.2 of EPConDB has been released and includes new data sets and gene lists. The most exciting difference between 4.2 and previous versions is an update of the mouse and human gene transcripts. EPConDB 4.2 uses NCBI Build 36.1/hg18 and NCBI Build 37/mm9 for human and mouse genomes respectively.

Gene Transcripts are updated for Mouse and Human. Check here for your favorite gene.
Gene Expression Profiling of a Mouse Model of Pancreatic Islet Dysmorphogenesis investigates gene expression in late gestation and early postnatal total pancreas tissue from wild type and HNF6 transgenic animals. Knock out vs. wild type gene lists are available for both time points.

Other new studies are available and contain executive summaries. The data for these can be downloaded from the RAD repository but check back soon for gene lists!

Easily find EPConDB Studies

2 Apr 2008 01:00:00 EDT

A new set of search tools are available to help you find Studies.

Find all EPConDB studies that have a Gene List here.
To find a list of studies where your gene of interest is differentially expressed, use the "Differential Expression of a Specific Gene" Query.
A simple text search of all study annotation is provided here.
Narrow your search for studies further by using the "Query for Studies" section of our Query Page.

An Expression Study of FoxA2 in Mature beta Cells is Now Available

15 Feb 2008 01:00:00 EDT

Study "Foxa2 controls vesicle docking and insulin secretion in mature beta-cells" has been released. This study includes an executive summary and a list of differentially expressed genes (PaGE analysis).

Findings from this study:

Foxa2 inactivation in mature beta cells induces hyperinsulinemic hypoglycemia in Foxa2loxP/loxP,Pdx1-CreERT2 adult mice through alterations in intracellular second-messenger signaling that redistribute the insulin granules into the readily releasable pool.
Foxa2 is required for both fetal pancreas development and the function of mature beta cells.

Gao et al. Foxa2 Controls Vesicle Docking and Insulin Secretion in Mature beta Cells. Cell Metabolism. 2007. 6:267-279

EPConDB News Now Seen at BetaCell.org

17 Dec 2007 01:00:00 EDT

The BCBC website will be carrying the EPConDB RSS feed. This will enable users of the BCBC website to easily get updates on new features and data in EPConDB.

Release of EPConDB 4.1

1 Nov 2007 01:00:00 EDT

Version (4.1) of the EPConDB website is now available.

The new features of this release include:

New studies
Comparison profiles
Better display of BCBC regents
Clickable network diagram of transcription factors involved in pancreas and islet cell development

The new studies are:

2440 - T Cell Mediated B-cell Damage and Repair in NOD Mice
2421 - Innocuous vs. Destructive Insulinitis
3021 - Neurogenin3 deficiency and Embryonic Pancreatic Gene Expression
2060 - Human Tissue Survey From Massively Parallel Signature Sequencing (MPSS)
18 non-pancreatic DGAP Studies

The study summaries are displayed at betacell.org as well as EPConDB.

Preview Release of EPConDB 4.1

21 Sep 2007 01:00:00 EDT

The next version (4.1) of the EPConDB website is now available for preview.

The new features of this release include:

New studies
Manually curated study summaries
Comparison profiles
Better display of BCBC regents
Clickable network diagram of transcription factors involved in pancreas and islet cell development

The new studies are:

2440 - T Cell Mediated B-cell Damage and Repair in NOD Mice
2421 - Innocuous vs. Destructive Insulinitis
3021 - Neurogenin3 deficiency and Embryonic Pancreatic Gene Expression
2060 - Human Tissue Survey From Massively Parallel Signature Sequencing (MPSS)
18 non-pancreatic DGAP Studies

The study summaries are displayed at betacell.org as well as EPConDB.

Release 4.0 of the EPConDB web site.

5 May 2007 01:00:00 EDT

EPConDB has been officially released using a new web site design. As part of this release, additional lists have been added to the improved query for Differentially Expressed Genes

A new web site design for EPConDB.

5 May 2006 01:00:00 EDT

A new release of EPConDB, using a new web site design, is now available for browsing. This is a pre-release of the site. Please let us know that you think and if you encounter any problems. New features of the site include: 1. An optional site login which saves your query history and site preferences. 2. The ability to sort, add and remove columns from your query results. 3. Downloading your search results and saving the file in your choice of formats, including Excel. 4. An RSS feed for news items.

EPConDB Version 3.44 released

28 Mar 2007 01:00:00 EDT

Version 3.44 of the EPConDB website has been released. EPConDB is a resource of the Beta Cell Biology Consortium and contains information on genes expressed in cells of the pancreas and their transcriptional regulation. EPConDB Version 3.44 includes: The following studies have been added to the Experiments page. GSIS study of rat INS1 cell lines Lipotoxicity study of rat INS1 cell lines FoxA1 and beta cell function HNF4alpha in beta cell function Inducible Ngn3 embryonic stem cells Sox4 null mice e12.5 pancreas Beta cell growth in Tcf-1 deficient mice Survivin transgenic mice pancreatic islet profile Genome-wide location analysis of HNF transcription factors in hepatocytes and pancreatic islets New lists of differentially expressed genes from the following studies have been added to the Experiments page (use the Analysis Result link) and the queries for Up and Down regulated gene expression. Type 2 diabetic individuals versus normal individuals Cyclophosphamide-induced beta cell destruction in NOD mice FoxA1 knockout versus wild type mice HNF4alpha knockout versus wild type mice Two lists of genes with HNF1alpha or HNF6 promoter binding sites, identified by ChIP-Chip assays are provided: Genome-wide location analysis of HNF1 alpha in islets Genome-wide location analysis of HNF6 in islets Gene expression profiles from six new studies were added to the profiles for individual genes. Please see the EPConDB website for more details. Genome-wide location analysis of HNF1 alpha in islets Genome-wide location analysis of HNF6 in islets Gene expression profiles from six new studies were added to the profiles for individual genes. Please see the EPConDB website for more details.. .

EPConDB version 3.43 released

20 Sep 2006 01:00:00 EDT

Version 3.43 of the EPConDB web site has been released.

The new EPConDB site release includes:

Five new lists of differentially expressed genes added to the Experiments page and the queries for Up and Down regulated gene expression.
The display of the differentially expressed gene lists has been updated. Users are able to sort the gene lists based upon confidence or fold change, and the genes are colored coded (up-regulated in red, down-regulated in green).
Ten new pancreatic transcription factors (e.g., Pax4) have been added to the Predicted Transcription Factor Target Gene Query.
The display of the gene result page from queries has been changed to include Entrez gene annotation and links to the gene page, expression profiles and the genome browser.
Two new expression studies have been added to the expression profiles for individual genes.

Analysis results from microarray studies have been provided as gene lists.

20 Feb 2006 01:00:00 EDT

Microarray studies submitted by the Beta Cell Biology Consortium have been analyzed, and the results have been provided as gene lists accessible from the Experiments page. The genes in these studies can also be queried for up regulated or down regulated expression based upon fold changes.

EPConDB RNA pages include links to BCBC protein antibodies.

5 May 2006 01:00:00 EDT

EPConDB RNA pages now include links to antibodies available through the Beta Cell Biology Consortium, BCBC web site.