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Beta Cell Gene Atlas Home

  About Beta Cell Gene Atlas

The Beta Cell Gene Atlas contains data on basal expression of genes in different beta cell sources – pancreatic beta cells, islets, whole pancreas, and beta cell lines -- from human, mouse, and rat.  The majority of the data is from microarray experiments; however, there is some data from Massively Parallel Signature Sequencing (MPSS) and Serial Analysis of Gene Expression (SAGE) experiments.

If you use the Atlas or any underlying expression datasets for your research, please cite the following reference: Kutlu, B. et al. (2009) Detailed transcriptome atlas of the pancreatic beta cell. BMC Medical Genomics. PubMed ID: 19146692. You can also find detailed information on how the Atlas was built in this paper.

Operating Instructions:

To operate the program, you specify one or more genes and click the "Submit Query" button. You can specify genes by entering identifiers in the text box, uploading a file of gene identifiers, or choosing an existing gene list from the drop-down menu.  The most reliable gene identifiers are Entrez Gene IDs (e.g., 3630).  See Entering Gene Identifiers for more information.

Results page:

The results page displays a gray-scale heatmap of the specified genes. A light blue cell indicates that we have no data for the gene in the given tissue. A red border around a cell indicates greater certainty in the data: specifically, the gene has >0.95 probability of being expressed in the tissue.

Controls above the heatmap let you adjust how the information is displayed. By default, columns are grouped by organism; click on "tissue" to group by tissue instead. Clicking on "gene rank" or "probability" displays numeric values in each cell instead of the gray-scale.

If a gene identifier matches multiple genes, a box will be displayed on the results page saying "There were ambiguous terms in your query. Click here to resolve them." You can click the link to correct the identifier. To pick the correct identifier(s), click on the box next to the appropriate identifier(s) and click on Submit Corrections. A new results page with the correct identifier(s) will be shown.

You can add a gene to the results by typing a gene identifier in the "Add a new gene box" and clicking Go.

You can save the displayed genes by clicking the "save list to My T1DBase" link at the top of the page. You can use the genes in another T1DBase program by clicking the "send list to tool" link at the top of the page. Clicking on one of the tools will cause a new page to be loaded with the gene list already included in the "Select a T1DBase List".

Scientific details:

The Beta Cell Gene Atlas is a collection of almost all available public microarray data generated with pancreatic beta cells and related cell lines and types. The expression data comes from 131 array analyses derived from 28 experiments (Table 1, refs 1-19). The basal (untreated cell) expression signal intensity values in each array were converted to ranks within the experiments; the highest value was used for genes represented by more than one probe. The rank values of genes in a given cell type were averaged with other calculated values from experiments performed with the same cell type.  The rank transformation of the expression values enable comparison of gene expression across different organisms and tissues.

Authors	GEO	RAD	Array Express	Cell/tissue type	Species	Reference
Akpinar et al.	gse3544			Islets	Rat	[1]
Cardozo et al.		2021	E-CBIL-8	β cells	Rat	[2]
Cardozo et al.		2020	E-CBIL-9	β cells	Rat	[3]
Casas et al.	gse2253			MIN6 Cell lines	Mouse
Dohi et al.			E_MEXP_536	Islets	Mouse	[4]
Ge et al.	gse2361			Islets	Human
Gomis et al.	gse2470			Islets	Rat
Gunton et al.		2160		Islets	Human	[5]
Habener et al.		870		Islets	Human
Ishikava et al.	gse1542			Ductal cells	Human	[6]
Kaestner et al.		1390		Islets	Mouse
Kaur et al.	gse769			Whole pancreas	Mouse	[7]
Kutlu et al.		2002	E-CBIL-10	INS-1 Cell lines	Rat	[8]
Logsdon et al.	gse3311			Whole pancreas	Rat	[9]
Maffei et al.		751		Islets Exocrine cells	Human	[10]
Mathis et al.	gse2254			Islets	Mouse	[11]
Parton et al.	gse2582			Islets	Rat	[12]
Rasschaert et al.		2001	E-CBIL-11	β cells	Rat	[13]
Shumeli et al.	gse803			Islets	Human	[14]
Su et al.	gse1133			Islets	Human	[15]
Thomas et al.	gse1591			INS-1 Cell lines	Rat	[16]
Vukkadapu et al.	gse1623			Islets	Mouse	[17]
Weir et al.		810		β cells	Human
Yliipaasto et al.				Islets	Human	[18]
Yoon et al.	gse2719			Islets	Human
Zhang et al.	gse2060			Islets, MIN6 cell lines	Human, mouse	[19]

[1]   Akpinar P, Kuwajima S, Krutzfeldt J, Stoffel M (2005) Tmem27: a cleaved and shed plasma membrane protein that stimulates pancreatic beta cell proliferation. Cell Metab 2: 385-397

[2]   Cardozo AK, Kruhoffer M, Leeman R, Orntoft T, Eizirik DL (2001) Identification of novel cytokine-induced genes in pancreatic beta-cells by high-density oligonucleotide arrays. Diabetes 50: 909-920

[3]   Cardozo AK, Heimberg H, Heremans Y, et al. (2001) A comprehensive analysis of cytokine-induced and nuclear factor-kappa B-dependent genes in primary rat pancreatic beta-cells. J Biol Chem 276: 48879-48886

[4]   Dohi T, Salz W, Costa M, Ariyan C, Basadonna GP, Altieri DC (2006) Inhibition of apoptosis by survivin improves transplantation of pancreatic islets for treatment of diabetes in mice. EMBO Rep 7: 438-443

[5]   Gunton JE, Kulkarni RN, Yim S, et al. (2005) Loss of ARNT/HIF1beta mediates altered gene expression and pancreatic-islet dysfunction in human type 2 diabetes. Cell 122: 337-349

[6]   Ishikawa M, Yoshida K, Yamashita Y, et al. (2005) Experimental trial for diagnosis of pancreatic ductal carcinoma based on gene expression profiles of pancreatic ductal cells. Cancer Sci 96: 387-393

[7]   Kaur S, Norkina O, Ziemer D, Samuelson LC, De Lisle RC (2004) Acidic duodenal pH alters gene expression in the cystic fibrosis mouse pancreas. Am J Physiol Gastrointest Liver Physiol 287: G480-490

[8]   Kutlu B, Cardozo AK, Darville MI, et al. (2003) Discovery of gene networks regulating cytokine-induced dysfunction and apoptosis in insulin-producing INS-1 cells. Diabetes 52: 2701-2719

[9]   Kubisch CH, Gukovsky I, Lugea A, et al. (2006) Long-term ethanol consumption alters pancreatic gene expression in rats: a possible connection to pancreatic injury. Pancreas 33: 68-76

[10]  Maffei A, Liu Z, Witkowski P, et al. (2004) Identification of tissue-restricted transcripts in human islets. Endocrinology 145: 4513-4521

[11]  Matos M, Park R, Mathis D, Benoist C (2004) Progression to islet destruction in a cyclophosphamide-induced transgenic model: a microarray overview. Diabetes 53: 2310-2321

[12]  Parton LE, Diraison F, Neill SE, et al. (2004) Impact of PPARgamma overexpression and activation on pancreatic islet gene expression profile analyzed with oligonucleotide microarrays. Am J Physiol Endocrinol Metab 287: E390-404

[13]  Rasschaert J, Liu D, Kutlu B, et al. (2003) Global profiling of double stranded RNA- and IFN-gamma-induced genes in rat pancreatic beta cells. Diabetologia 46: 1641-1657

[14]  Yanai I, Benjamin H, Shmoish M, et al. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21: 650-659

[15]  Su AI, Wiltshire T, Batalov S, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067

[16]  Thomas H, Senkel S, Erdmann S, et al. (2004) Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4alpha and HNF1beta in a pancreatic beta-cell line. Nucleic Acids Res 32: e150

[17]  Vukkadapu SS, Belli JM, Ishii K, et al. (2005) Dynamic interaction between T cell-mediated beta-cell damage and beta-cell repair in the run up to autoimmune diabetes of the NOD mouse. Physiol Genomics 21: 201-211

[18]  Ylipaasto P, Kutlu B, Rasilainen S, et al. (2005) Global profiling of coxsackievirus- and cytokine-induced gene expression in human pancreatic islets. Diabetologia 48: 1510-1522

[19]  Zhang X, Odom DT, Koo SH, et al. (2005) Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci U S A 102: 4459-4464

Open help in separate window

Examples:

• Dossier Example

  Create Query

Enter gene identifiers (one per line). Either type them into the box below or upload a file.

- OR -

Select a T1DBase List:   Dossier Example MHC Genes Prox1 activity controls pancreas morphogenesis Gene and protein kinase expression profiling of reactive oxygen Gene expression profiling:INS-1 cells overexpressing thioredoxin Cytokine Pathway from Beta Cell Gene Bank

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