Gene expression and pathway analysis of CTNNB1 in cancer and stem cells

Table 1 3D complex structures of β-catenin (CTNNB1) and interacting proteins

pdb_id	β-catenin (CTNNB1)			Proteins that interact with β-catenin
	ChainID	Length	UniProtID	Molecule	ChainID	Length	UniProtID	Contact protein name	Regulation of gene expression in GC cells compared to MSCs
1th1	B	513	CTNB1_HUMAN	APC	D	54	APC_HUMAN	Adenomatous polyposis coli protein	Not changed/-
1qz7	A	524	CTNB1_HUMAN	AXIN1	B	17	AXN_XENLA	Axin-1	-
3sl9	B	165	CTNB1_HUMAN	BCL9	D	23	BCL9_HUMAN	B-cell CLL/lymphoma 9 protein	-
1i7w	C	509	CTNB1_MOUSE	CDH1	D	60	CADH1_MOUSE	Cadherin-1	Up-regulated
1m1e	A	512	CTNB1_MOUSE	CTNNBIP1	B	65	CNBP1_HUMAN	Beta-catenin-interacting protein 1	-
3oux	A	503	CTNB1_MOUSE	LEF1	B	47	LEF1_MOUSE	Lymphoid enhancer-binding factor 1	Up-regulated
3tx7	A	504	CTNB1_HUMAN	NR5A2	B	218	NR5A2_HUMAN	Nuclear receptor subfamily 5 group A member 2	-
1g3j	A	439	CTNB1_HUMAN	TCF7L1	B	34	T7L1A_XENLA	Transcription factor 7-like 1-A	-
1jdh	A	508	CTNB1_HUMAN	TCF7L2	B	38	TF7L2_HUMAN	Transcription factor 7-like 2	Up-regulated
1dow	B	32	CTNB1_MOUSE	CTNNA1	A	205	CTNA1_MOUSE	Catenin alpha-1	Not changed/-
4ons	D	56	CTNB1_MOUSE	CTNNA2	C	230	CTNA2_MOUSE	Catenin alpha-2	-

Table 2 Genes mutated along with the CTNNB1 alteration

Gene symbol	Gene title	Cytoband	Mutation percentage		Log ratio	P-value	Ratio of GC cells to MSCs
			In altered group	In unaltered group
EPHA8	EPH receptor A8	1p36.12	29.17%	2.28%	3.68	1.45E-05	Signal intensity is low
SS18	Synovial sarcoma translocation Chromosome 18	18q11.2	16.67%	0.00%	> 10	3.84E-05	0.6
							1.4
ICE1	Interactor of little elongator complex ELL subunit 1	5p15.32	33.33%	4.56%	2.87	4.74E-05	1.5
PTCH1	Patched 1	9q22.3	29.17%	3.42%	3.09	8.16E-05	16.6
MSH3	MutS homolog 3	5q14.1	20.83%	1.14%	4.19	1.28E-04	Signal intensity is low
CARD11	Caspase recruitment domain family, member 11	7p22	29.17%	4.18%	2.8	2.03E-04	Signal intensity is low

Table 3 Gene ontology of mutated genes along with CTNNB1 alteration

Gene symbol	Gene ontology biological process
EPHA8	Protein 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
SS18	Microtubule 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
ICE1	Positive 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
PTCH1	Negative 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
MSH3	Meiotic 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
CARD11	Positive 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