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