Basic Study
Copyright ©The Author(s) 2016.
World J Stem Cells. Nov 26, 2016; 8(11): 384-395
Published online Nov 26, 2016. doi: 10.4252/wjsc.v8.i11.384
Table 1 3D complex structures of β-catenin (CTNNB1) and interacting proteins
pdb_idβ-catenin (CTNNB1)
Proteins that interact with β-catenin
ChainIDLengthUniProtIDMoleculeChainIDLengthUniProtIDContact protein nameRegulation of gene expression in GC cells compared to MSCs
1th1B513CTNB1_HUMANAPCD54APC_HUMANAdenomatous polyposis coli proteinNot changed/-
3sl9B165CTNB1_HUMANBCL9D23BCL9_HUMANB-cell CLL/lymphoma 9 protein-
1m1eA512CTNB1_MOUSECTNNBIP1B65CNBP1_HUMANBeta-catenin-interacting protein 1-
3ouxA503CTNB1_MOUSELEF1B47LEF1_MOUSELymphoid enhancer-binding factor 1Up-regulated
3tx7A504CTNB1_HUMANNR5A2B218NR5A2_HUMANNuclear receptor subfamily 5 group A member 2-
1g3jA439CTNB1_HUMANTCF7L1B34T7L1A_XENLATranscription factor 7-like 1-A-
1jdhA508CTNB1_HUMANTCF7L2B38TF7L2_HUMANTranscription factor 7-like 2Up-regulated
1dowB32CTNB1_MOUSECTNNA1A205CTNA1_MOUSECatenin alpha-1Not changed/-
4onsD56CTNB1_MOUSECTNNA2C230CTNA2_MOUSECatenin alpha-2-
Table 2 Genes mutated along with the CTNNB1 alteration
Gene symbolGene titleCytobandMutation percentage
Log ratioP-valueRatio of GC cells to MSCs
In altered groupIn unaltered group
EPHA8EPH receptor A81p36.1229.17%2.28%3.681.45E-05Signal intensity is low
SS18Synovial sarcoma translocation Chromosome 1818q11.216.67%0.00%> 103.84E-050.6
ICE1Interactor of little elongator complex ELL subunit 15p15.3233.33%4.56%2.874.74E-051.5
PTCH1Patched 19q22.329.17%3.42%3.098.16E-0516.6
MSH3MutS homolog 35q14.120.83%1.14%4.191.28E-04Signal intensity is low
CARD11Caspase recruitment domain family, member 117p2229.17%4.18%2.82.03E-04Signal intensity is low
Table 3 Gene ontology of mutated genes along with CTNNB1 alteration
Gene symbolGene ontology biological process
EPHA8Protein phosphorylation // substrate-dependent cell migration // cell adhesion // transmembrane receptor protein tyrosine kinase signaling pathway // multicellular organismal development // nervous system development // axon guidance // phosphorylation // neuron remodeling // peptidyl-tyrosine phosphorylation // regulation of cell adhesion // neuron projection development // regulation of cell adhesion mediated by integrin // positive regulation of MAPK cascade // positive regulation of phosphatidylinositol 3-kinase activity // protein autophosphorylation // ephrin receptor signaling pathway
SS18Microtubule cytoskeleton organization // cell morphogenesis // transcription, DNA-templated // regulation of transcription, DNA-templated // cytoskeleton organization // response to drug // positive regulation of transcription from RNA polymerase II promoter // ephrin receptor signaling pathway
ICE1Positive regulation of intracellular protein transport // positive regulation of protein complex assembly // positive regulation of transcription from RNA polymerase III promoter // snRNA transcription from RNA polymerase II promoter // snRNA transcription from RNA polymerase III promoter
PTCH1Negative regulation of transcription from RNA polymerase II promoter // branching involved in ureteric bud morphogenesis // neural tube formation // neural tube closure // heart morphogenesis // signal transduction // smoothened signaling pathway // smoothened signaling pathway // regulation of mitotic cell cycle // pattern specification process // brain development // negative regulation of cell proliferation // epidermis development // regulation of smoothened signaling pathway // response to mechanical stimulus // organ morphogenesis // dorsal/ventral pattern formation // response to chlorate // positive regulation of cholesterol efflux // response to organic cyclic compound // protein processing // spinal cord motor neuron differentiation // neural tube patterning // dorsal/ventral neural tube patterning // neural plate axis specification // embryonic limb morphogenesis // mammary gland development // response to estradiol // response to retinoic acid // regulation of protein localization // limb morphogenesis // hindlimb morphogenesis // regulation of growth // negative regulation of multicellular organism growth // regulation of cell proliferation // response to drug // glucose homeostasis // negative regulation of sequence-specific DNA binding transcription factor activity // keratinocyte proliferation // negative regulation of osteoblast differentiation // negative regulation of smoothened signaling pathway // negative regulation of smoothened signaling pathway // negative regulation of epithelial cell proliferation // negative regulation of cell division // pharyngeal system development // mammary gland duct morphogenesis // mammary gland epithelial cell differentiation // smoothened signaling pathway involved in dorsal/ventral neural tube patterning // cell differentiation involved in kidney development // somite development // cellular response to cholesterol // cellular response to cholesterol // renal system development // cell proliferation involved in metanephros development // protein targeting to plasma membrane
MSH3Meiotic mismatch repair // ATP catabolic process // DNA repair // mismatch repair // cellular response to DNA damage stimulus // reciprocal meiotic recombination // somatic recombination of immunoglobulin gene segments // maintenance of DNA repeat elements // negative regulation of DNA recombination // positive regulation of helicase activity
CARD11Positive regulation of cytokine production // signal transduction // positive regulation of B cell proliferation // T cell costimulation // Fc-epsilon receptor signaling pathway // positive regulation of T cell proliferation // regulation of apoptotic process // positive regulation of I-kappaB kinase/NF-kappaB signaling // thymic T cell selection // positive regulation of interleukin-2 biosynthetic process // innate immune response // regulation of B cell differentiation // regulation of T cell differentiation // nucleotide phosphorylation // regulation of immune response // T cell receptor signaling pathway // positive regulation of T cell activation // positive regulation of NF-kappaB transcription factor activity