Basic Study
Copyright ©The Author(s) 2015.
World J Stem Cells. Jan 26, 2015; 7(1): 208-222
Published online Jan 26, 2015. doi: 10.4252/wjsc.v7.i1.208
Table 1 Gene expression alterations of regulator of G-protein signaling family genes in mesenchymal stem cells and diffuse-type gastric cancer
Gene symbolDetailed descriptionP valueRatio of diffuse-type GC to MSCsProbe set ID
RGS1Immune response / signal transduction / adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway / negative regulation of signal transduction / termination of G-protein coupled receptor signaling pathway / positive regulation of GTPase activity0.0131004202988_s_at
0.00113808216834_at
RGS2Regulation of translation / cell cycle / spermatogenesis / regulation of G-protein coupled receptor protein signaling pathway / negative regulation of signal transduction / negative regulation of phospholipase activity / negative regulation of cardiac muscle hypertrophy / termination of G-protein coupled receptor signaling pathway / negative regulation of mitogen-activated protein (MAP) kinase activity / positive regulation of GTPase activity / negative regulation of G-protein coupled receptor protein signaling pathway / brown fat cell differentiation / relaxation of cardiac muscle / relaxation of vascular smooth muscle / positive regulation of cardiac muscle contraction / regulation of adrenergic receptor signaling pathway0.00714.51202388_at
RGS3Inactivation of mitogen-activated protein kinase (MAPK) activity / signal transduction / regulation of G-protein coupled receptor protein signaling pathway / negative regulation of signal transduction / termination of G-protein coupled receptor signaling pathway / positive regulation of GTPase activity1.00E-050.39203823_at
RGS4Inactivation of MAPK activity / regulation of G-protein coupled receptor protein signaling pathway / negative regulation of signal transduction / termination of G-protein coupled receptor signaling pathway / positive regulation of GTPase activity3.00E-040.17204337_at
0.0030.11204338_s_at
0.0040.14204339_s_at
RGS5Signal transduction / regulation of G-protein coupled receptor protein signaling pathway / negative regulation of signal transduction / termination of G-protein coupled receptor signaling pathway / positive regulation of GTPase activity0.0147.79209070_s_at
0.00881.82209071_s_at
0.00995.52218353_at
RGS10Negative regulation of signal transduction / termination of G-protein coupled receptor signaling pathway / positive regulation of GTPase activity0.0033.92204319_s_at
RGS19Autophagy / G-protein coupled receptor signaling pathway / small GTPase mediated signal transduction / negative regulation of signal transduction / termination of G-protein coupled receptor signaling pathway / positive regulation of GTPase activity9.00E-042.45204336_s_at
Table 2 Gene expression alterations of stem cell-related genes in mesenchymal stem cells and diffuse-type gastric cancer
Gene symbolGene nameP valueRatio of diffuse-type GC to MSCsProbe set ID
NANOGNanog homeobox0.003714.9220184_at
SUZ12SUZ12 polycomb repressive complex 2 subunit0.002235.41566191_at
TNFRSF8Tumor necrosis factor receptor superfamily, member 80.01261.98206729_at
CD9CD9 molecule0.00123.44201005_at
ICAM3Intercellular adhesion molecule-30.01432.69204949_at
CD200CD200 molecule0.00134.79209583_s_at
0.00024.35209582_s_at
THY1Thy-1 cell surface antigen0.00810.61208850_s_at
0.03010.79208851_s_at
0.00240.67213869_x_at
Table 3 Gene expression alterations of epithelial-mesenchymal transition-related genes in mesenchymal stem cells and diffuse-type gastric cancer
Gene symbolGene nameP valueRatio of diffuse-type GC to MSCsProbe set ID
TWIST1Twist family bHLH transcription factor 10.00040.2213943_at
PRRX1Paired related homeobox 11.00E-050.3226695_at
ZEB2Zinc finger E-box binding homeobox 20.0272.1203603_s_at
0.031.7228333_at
6.00E-053.9235593_at
TJP1Tight junction protein 10.1841.2202011_at
0.7951214168_s_at
CTNNB1Catenin (cadherin-associated protein), beta 1, 88 kDa0.0019.6223679_at
VIMVimentin0.0314.71555938_x_at
0.0160.7201426_s_at
FN1Fibronectin 10.2040.61558199_at
0.0150.7210495_x_at
0.0040.7211719_x_at
0.0010.6212464_s_at
4.00E-080.04214701_s_at
1.00E-100.02214702_at
0.0080.7216442_x_at
AKT1v-akt murine thymoma viral oncogene homolog 10.1871.2207163_s_at
AKT2v-akt murine thymoma viral oncogene homolog 28.00E-093.1225471_s_at
0.0024.4226156_at
0.00065.6236664_at
0.00067.61560689_s_at
AKT3v-akt murine thymoma viral oncogene homolog 30.00066.2242876_at
0.0080.6212607_at
0.5491.2212609_s_at
0.3850.8219393_s_at
0.7721.1222880_at
0.00030.5242879_x_at
SFNStratifin0.0036633322_i_at
0.00811133323_r_at
EPCAMEpithelial cell adhesion molecule0.0009725201839_s_at
F11RF11 receptor0.000435221664_s_at
0.00221222354_at
0.0009201223000_s_at
0.01225224097_s_at
GJB2Gap junction protein, beta 2, 26 kDa0.02369223278_at
LEF1Lymphoid enhancer-binding factor 10.00226221558_s_at
JUNJun proto-oncogene0.0424.8201464_x_at
0.0225.1201466_s_at
0.0793.8201465_s_at
0.0194.1213281_at
TGFB1Transforming growth factor, beta 10.0022203085_s_at
TGFB2Transforming growth factor, beta 20.070.4209909_s_at
0.0550.6220407_s_at
0.5880.8228121_at
TGFB3Transforming growth factor, beta 30.0156.8209747_at
SP1Sp1 transcription factor0.00023.4224754_at
2.00E-052.7224760_at
HMGA2High mobility group AT-hook 20.0030.3208025_s_at
ITGA5Integrin, alpha 5 (fibronectin receptor, alpha polypeptide)0.0070.5201389_at
OCLNOccludin0.00088231022_at
0.0129.4235937_at
0.02711209925_at
0.004511227492_at
CXADRCoxsackie virus and adenovirus receptor0.013265203917_at
0.014297226374_at
0.02175239155_at
KRT8Keratin 80.012128209008_x_at
Table 4 Gene expression alterations of NOTCH signaling-related genes in mesenchymal stem cells and diffuse-type gastric cancer
Gene symbolGene nameP valueRatio of diffuse-type GC to MSCsProbe set ID
NOTCH1Notch 10.0046.9218902_at
NOTCH2Notch 20.0010.7202445_s_at
1.00E-050.5202443_x_at
1.00E-050.5212377_s_at
DLL1Delta-like 1 (Drosophila)0.00731224215_s_at
JAG2Jagged 20.0031132137_at
JAG1Jagged 10.0031.5209099_x_at
0.0221.4216268_s_at
0.491.1209098_s_at
WNT9AWingless-type MMTV integration site family, member 9A0.0275.4230643_at
WNT2BWingless-type MMTV integration site family, member 2B0.0264.4206458_s_at
WNT5AWingless-type MMTV integration site family, member 5A8.00E-050.3213425_at
3.00E-050.2205990_s_at
WNT5BWingless-type MMTV integration site family, member 5B0.00020.2221029_s_at
Table 5 Gene ontology of NOTCH family genes
Gene symbolGene ontology biological process
NOTCH10000122 // negative regulation of transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0001525 // angiogenesis // inferred from electronic annotation /// 0001701 // in utero embryonic development // inferred from electronic annotation /// 0001708 // cell fate specification // inferred from electronic annotation /// 0001837 // epithelial to mesenchymal transition // inferred from sequence or structural similarity /// 0001889 // liver development // inferred from electronic annotation /// 0001947 // heart looping // inferred from sequence or structural similarity /// 0002040 // sprouting angiogenesis // inferred from electronic annotation /// 0002052 // positive regulation of neuroblast proliferation // inferred from electronic annotation /// 0002437 // inflammatory response to antigenic stimulus // inferred from electronic annotation /// 0003157 // endocardium development // inferred from sequence or structural similarity /// 0003160 // endocardium morphogenesis // inferred from sequence or structural similarity /// 0003162 // atrioventricular node development // inferred from electronic annotation /// 0003169 // coronary vein morphogenesis // inferred from sequence or structural similarity /// 0003180 // aortic valve morphogenesis // inferred from mutant phenotype /// 0003181 // atrioventricular valve morphogenesis // inferred from sequence or structural similarity /// 0003184 // pulmonary valve morphogenesis // inferred from mutant phenotype /// 0003192 // mitral valve formation // inferred from mutant phenotype /// 0003198 // epithelial to mesenchymal transition involved in endocardial cushion formation // inferred from sequence or structural similarity /// 0003203 // endocardial cushion morphogenesis // inferred from sequence or structural similarity /// 0003207 // cardiac chamber formation // inferred from sequence or structural similarity /// 0003208 // cardiac ventricle morphogenesis // inferred from sequence or structural similarity /// 0003209 // cardiac atrium morphogenesis // inferred from sequence or structural similarity /// 0003213 // cardiac right atrium morphogenesis // inferred from sequence or structural similarity /// 0003214 // cardiac left ventricle morphogenesis // inferred from sequence or structural similarity /// 0003219 // cardiac right ventricle formation // inferred from electronic annotation /// 0003222 // ventricular trabecula myocardium morphogenesis // inferred from sequence or structural similarity /// 0003241 // growth involved in heart morphogenesis // inferred from sequence or structural similarity /// 0003256 // regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation // inferred from sequence or structural similarity /// 0003264 // regulation of cardioblast proliferation // inferred from electronic annotation /// 0003270 // Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation // inferred from electronic annotation /// 0003273 // cell migration involved in endocardial cushion formation // inferred from sequence or structural similarity /// 0003344 // pericardium morphogenesis // inferred from sequence or structural similarity /// 0006351 // transcription, DNA-dependent // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // traceable author statement /// 0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation /// 0006367 // transcription initiation from RNA polymerase II promoter // traceable author statement /// 0006955 // immune response // non-traceable author statement /// 0006959 // humoral immune response // inferred from electronic annotation /// 0007219 // Notch signaling pathway // inferred from mutant phenotype /// 0007219 // Notch signaling pathway // traceable author statement /// 0007220 // Notch receptor processing // traceable author statement /// 0007221 // positive regulation of transcription of Notch receptor target // inferred from sequence or structural similarity /// 0007275 // multicellular organismal development // inferred from electronic annotation /// 0007283 // spermatogenesis // inferred from electronic annotation /// 0007368 // determination of left/right symmetry // inferred from sequence or structural similarity /// 0007386 // compartment pattern specification // inferred from electronic annotation /// 0007409 // axonogenesis // inferred from electronic annotation /// 0007440 // foregut morphogenesis // inferred from electronic annotation /// 0007492 // endoderm development // inferred from electronic annotation /// 0007507 // heart development // inferred from mutant phenotype /// 0008284 // positive regulation of cell proliferation // inferred from direct assay /// 0008284 // positive regulation of cell proliferation // inferred from mutant phenotype /// 0008285 // negative regulation of cell proliferation // inferred from direct assay /// 0008544 // epidermis development // inferred from electronic annotation /// 0009790 // embryo development // inferred from electronic annotation /// 0009912 // auditory receptor cell fate commitment // inferred from electronic annotation /// 0010001 // glial cell differentiation // inferred from electronic annotation /// 0010467 // gene expression // traceable author statement /// 0010468 // regulation of gene expression // inferred from electronic annotation /// 0010718 // positive regulation of epithelial to mesenchymal transition // inferred from mutant phenotype /// 0010812 // negative regulation of cell-substrate adhesion // inferred from direct assay /// 0010832 // negative regulation of myotube differentiation // inferred from sequence or structural similarity /// 0014031 // mesenchymal cell development // inferred from sequence or structural similarity /// 0014807 // regulation of somitogenesis // inferred from electronic annotation /// 0021515 // cell differentiation in spinal cord // inferred from electronic annotation /// 0021915 // neural tube development // inferred from electronic annotation /// 0030154 // cell differentiation // inferred from electronic annotation /// 0030182 // neuron differentiation // inferred from electronic annotation /// 0030216 // keratinocyte differentiation // inferred from electronic annotation /// 0030279 // negative regulation of ossification // inferred from sequence or structural similarity /// 0030324 // lung development // inferred from electronic annotation /// 0030326 // embryonic limb morphogenesis // inferred from electronic annotation /// 0030334 // regulation of cell migration // inferred from electronic annotation /// 0030335 // positive regulation of cell migration // inferred from sequence or structural similarity /// 0030513 // positive regulation of BMP signaling pathway // inferred from sequence or structural similarity /// 0030514 // negative regulation of BMP signaling pathway // inferred from sequence or structural similarity /// 0030900 // forebrain development // inferred from electronic annotation /// 0031069 // hair follicle morphogenesis // inferred from electronic annotation /// 0031100 // organ regeneration // inferred from electronic annotation /// 0031960 // response to corticosteroid stimulus // inferred from electronic annotation /// 0032495 // response to muramyl dipeptide // inferred from electronic annotation /// 0032496 // response to lipopolysaccharide // inferred from electronic annotation /// 0035116 // embryonic hindlimb morphogenesis // inferred from electronic annotation /// 0035148 // tube formation // inferred from mutant phenotype /// 0035914 // skeletal muscle cell differentiation // inferred from electronic annotation /// 0035924 // cellular response to vascular endothelial growth factor stimulus // inferred from direct assay /// 0042127 // regulation of cell proliferation // inferred from electronic annotation /// 0042246 // tissue regeneration // inferred from electronic annotation /// 0042640 // anagen // inferred from electronic annotation /// 0043065 // positive regulation of apoptotic process // inferred from electronic annotation /// 0043066 // negative regulation of apoptotic process // inferred from electronic annotation /// 0043086 // negative regulation of catalytic activity // inferred from sequence or structural similarity /// 0045165 // cell fate commitment // inferred from electronic annotation /// 0045596 // negative regulation of cell differentiation // inferred from electronic annotation /// 0045603 // positive regulation of endothelial cell differentiation // inferred from electronic annotation /// 0045618 // positive regulation of keratinocyte differentiation // inferred from electronic annotation /// 0045662 // negative regulation of myoblast differentiation // inferred from mutant phenotype /// 0045665 // negative regulation of neuron differentiation // inferred from electronic annotation /// 0045668 // negative regulation of osteoblast differentiation // inferred from sequence or structural similarity /// 0045687 // positive regulation of glial cell differentiation // inferred from electronic annotation /// 0045892 // negative regulation of transcription, DNA-dependent // inferred from sequence or structural similarity /// 0045893 // positive regulation of transcription, DNA-dependent // inferred from sequence or structural similarity /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0045955 // negative regulation of calcium ion-dependent exocytosis // inferred from electronic annotation /// 0046427 // positive regulation of JAK-STAT cascade // inferred from sequence or structural similarity /// 0046533 // negative regulation of photoreceptor cell differentiation // inferred from electronic annotation /// 0048103 // somatic stem cell division // inferred from electronic annotation /// 0048663 // neuron fate commitment // inferred from electronic annotation /// 0048708 // astrocyte differentiation // inferred from electronic annotation /// 0048709 // oligodendrocyte differentiation // inferred from electronic annotation /// 0048711 // positive regulation of astrocyte differentiation // inferred from sequence or structural similarity /// 0048715 // negative regulation of oligodendrocyte differentiation // inferred from sequence or structural similarity /// 0048754 // branching morphogenesis of an epithelial tube // inferred from electronic annotation /// 0050678 // regulation of epithelial cell proliferation // inferred from electronic annotation /// 0050679 // positive regulation of epithelial cell proliferation // inferred from electronic annotation /// 0050767 // regulation of neurogenesis // inferred from electronic annotation /// 0050768 // negative regulation of neurogenesis // inferred from sequence or structural similarity /// 0050793 // regulation of developmental process // inferred from electronic annotation /// 0055008 // cardiac muscle tissue morphogenesis // inferred from sequence or structural similarity /// 0060038 // cardiac muscle cell proliferation // inferred from electronic annotation /// 0060045 // positive regulation of cardiac muscle cell proliferation // inferred from sequence or structural similarity /// 0060253 // negative regulation of glial cell proliferation // inferred from sequence or structural similarity /// 0060317 // cardiac epithelial to mesenchymal transition // inferred from sequence or structural similarity /// 0060411 // cardiac septum morphogenesis // inferred from sequence or structural similarity /// 0060412 // ventricular septum morphogenesis // inferred from mutant phenotype /// 0060528 // secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development // inferred from electronic annotation /// 0060548 // negative regulation of cell death // inferred from electronic annotation /// 0060740 // prostate gland epithelium morphogenesis // inferred from electronic annotation /// 0060768 // regulation of epithelial cell proliferation involved in prostate gland development // inferred from electronic annotation /// 0060842 // arterial endothelial cell differentiation // inferred from sequence or structural similarity /// 0060843 // venous endothelial cell differentiation // inferred from sequence or structural similarity /// 0060948 // cardiac vascular smooth muscle cell development // inferred from sequence or structural similarity /// 0060956 // endocardial cell differentiation // inferred from sequence or structural similarity /// 0060979 // vasculogenesis involved in coronary vascular morphogenesis // inferred from sequence or structural similarity /// 0060982 // coronary artery morphogenesis // inferred from sequence or structural similarity /// 0061314 // Notch signaling involved in heart development // inferred from mutant phenotype /// 0061384 // heart trabecula morphogenesis // inferred from sequence or structural similarity /// 0061419 // positive regulation of transcription from RNA polymerase II promoter in response to hypoxia // inferred from sequence or structural similarity /// 0070986 // left/right axis specification // inferred from electronic annotation /// 0071372 // cellular response to follicle-stimulating hormone stimulus // inferred from direct assay /// 0072017 // distal tubule development // inferred from electronic annotation /// 0072044 // collecting duct development // inferred from electronic annotation /// 0072144 // glomerular mesangial cell development // inferred from electronic annotation /// 0072602 // interleukin-4 secretion // inferred from electronic annotation /// 0090051 // negative regulation of cell migration involved in sprouting angiogenesis // inferred from direct assay /// 0090090 // negative regulation of canonical Wnt receptor signaling pathway // inferred from electronic annotation /// 0097150 // neuronal stem cell maintenance // inferred from expression pattern /// 1901201 // regulation of extracellular matrix assembly // inferred from sequence or structural similarity /// 2000737 // negative regulation of stem cell differentiation // inferred from mutant phenotype /// 2000811 // negative regulation of anoikis // inferred from mutant phenotype /// 2000974 // negative regulation of pro-B cell differentiation // inferred from sequence or structural similarity /// 2001027 // negative regulation of endothelial cell chemotaxis // inferred from direct assay
NOTCH20001701 // in utero embryonic development // inferred from electronic annotation /// 0001709 // cell fate determination // traceable author statement /// 0001890 // placenta development // inferred from electronic annotation /// 0002011 // morphogenesis of an epithelial sheet // inferred from electronic annotation /// 0002437 // inflammatory response to antigenic stimulus // inferred from electronic annotation /// 0003184 // pulmonary valve morphogenesis // inferred from mutant phenotype /// 0006351 // transcription, DNA-dependent // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // traceable author statement /// 0006367 // transcription initiation from RNA polymerase II promoter // traceable author statement /// 0006915 // apoptotic process // traceable author statement /// 0006917 // induction of apoptosis // traceable author statement /// 0006959 // humoral immune response // inferred from electronic annotation /// 0007050 // cell cycle arrest // inferred from direct assay /// 0007219 // Notch signaling pathway // traceable author statement /// 0007220 // Notch receptor processing // traceable author statement /// 0007275 // multicellular organismal development // non-traceable author statement /// 0007368 // determination of left/right symmetry // inferred from electronic annotation /// 0007399 // nervous system development // non-traceable author statement /// 0008285 // negative regulation of cell proliferation // inferred from direct assay /// 0009887 // organ morphogenesis // inferred from expression pattern /// 0010467 // gene expression // traceable author statement /// 0016049 // cell growth // inferred from direct assay /// 0019827 // stem cell maintenance // traceable author statement /// 0030097 // hemopoiesis // traceable author statement /// 0030154 // cell differentiation // inferred from electronic annotation /// 0030326 // embryonic limb morphogenesis // inferred from electronic annotation /// 0042246 // tissue regeneration // inferred from electronic annotation /// 0043065 // positive regulation of apoptotic process // inferred from electronic annotation /// 0043066 // negative regulation of apoptotic process // traceable author statement /// 0046579 // positive regulation of Ras protein signal transduction // inferred from direct assay /// 0046849 // bone remodeling // inferred from mutant phenotype /// 0050793 // regulation of developmental process // inferred from electronic annotation /// 0060413 // atrial septum morphogenesis // inferred from mutant phenotype /// 0060674 // placenta blood vessel development // inferred from electronic annotation /// 0061314 // Notch signaling involved in heart development // inferred by curator /// 0072602 // interleukin-4 secretion // inferred from electronic annotation
NOTCH30006351 // transcription, DNA-dependent // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0006367 // transcription initiation from RNA polymerase II promoter // traceable author statement /// 0007219 // Notch signaling pathway // traceable author statement /// 0007220 // Notch receptor processing // traceable author statement /// 0007275 // multicellular organismal development // inferred from electronic annotation /// 0010467 // gene expression // traceable author statement /// 0030154 // cell differentiation // inferred from electronic annotation /// 0030900 // forebrain development // inferred from electronic annotation /// 0045596 // negative regulation of cell differentiation // inferred from electronic annotation /// 0045665 // negative regulation of neuron differentiation // inferred from electronic annotation /// 0048661 // positive regulation of smooth muscle cell proliferation // inferred from electronic annotation /// 0048663 // neuron fate commitment // inferred from electronic annotation /// 0050793 // regulation of developmental process // inferred from electronic annotation /// 0072104 // glomerular capillary formation // inferred from electronic annotation
NOTCH40001569 // patterning of blood vessels // inferred from sequence or structural similarity /// 0001709 // cell fate determination // traceable author statement /// 0001763 // morphogenesis of a branching structure // inferred from sequence or structural similarity /// 0001886 // endothelial cell morphogenesis // inferred from electronic annotation /// 0006351 // transcription, DNA-dependent // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0006367 // transcription initiation from RNA polymerase II promoter // traceable author statement /// 0007219 // Notch signaling pathway // traceable author statement /// 0007220 // Notch receptor processing // traceable author statement /// 0007221 // positive regulation of transcription of Notch receptor target // traceable author statement /// 0007275 // multicellular organismal development // inferred from electronic annotation /// 0009790 // embryo development // inferred from sequence or structural similarity /// 0010467 // gene expression // traceable author statement /// 0030097 // hemopoiesis // traceable author statement /// 0030154 // cell differentiation // non-traceable author statement /// 0030879 // mammary gland development // inferred from direct assay /// 0045446 // endothelial cell differentiation // inferred from electronic annotation /// 0045596 // negative regulation of cell differentiation // non-traceable author statement /// 0045602 // negative regulation of endothelial cell differentiation // inferred from sequence or structural similarity /// 0045893 // positive regulation of transcription, DNA-dependent // traceable author statement /// 0050793 // regulation of developmental process // inferred from electronic annotation