生物信息学方法对人类和小鼠共同肝癌相关基因的筛选

表1 9套全基因组数据集的基本情况

类别	GSE14323	GSE6764	GSE9809	GSE9012	GSE19004	GSE2127	GSE23680	GSE15251	GSE8642
物种	homo sapiens	homo sapiens	mus musculus	mus musculus	mus musculus	mus musculus	mus musculus	mus musculus	mus musculus
文献	Mas等[9]	Wurmb-ach等[10]	Liao等[11]	Khetcho-umian等[12]	仅提供芯片信息	Sheth等[13]	Li等[14]	仅提供芯片信息	仅提供芯片信息
芯片	GPL96, GPL571	GPL570	GPL1261	GPL1261	GPL1261	GPL339	GPL6246	GPL8308	GPL339
实验设计	unpaired tissues	unpaired tissues	unpaired+paired, tissues	unpaired tissues	unpairedtissues	unpaired+paired tissues	paired, tissues	unpairedtissues	unpaired tissues
探针数	22k	55K	45k	45k	45k	22k	48k	49k	41k
HCC组织	47	35	3	5	5	9	4	2	6
对照	19	10	7	5	4	6	4	5	9

paired: 对HCC癌组织组的对照来自HCC患者本人或者同只、同窝小鼠; unpaired: 对HCC癌组织组的对照来自其他正常人群或者小鼠.

表2 人类与小鼠的共同差显基因

基因	基因名称	表达水平
itm2b	integral membrane protein 2B
abcc5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5
arf3	ADP-ribosylation factor 3
aspm	asp (abnormal spindle)-like, microcephaly associated (Drosophila)
cdc20	cell division cycle 20 homolog (S.cerevisiae)	上调
cttn	cortactin; predicted gene 8786
ddx39	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
dnm1l	dynamin 1-like
fabp4	fatty acid binding protein 4, adipocyte	上调
gnb1	guanine nucleotide binding protein (G protein), beta 1
golm1	golgi membrane protein 1	上调
gpr56	G protein-coupled receptor 56
ier5	immediate early response 5
itga3	integrin alpha 3
itgb1	integrin beta 1 (fibronectin receptor beta)
itm2c	integral membrane protein 2C
itpr3	inositol 1,4,5-triphosphate receptor 3
klf6	Kruppel-like factor 6
lmna	lamin A
lrrc59	leucine rich repeat containing 59
ly6d	lymphocyte antigen 6 complex, locus D	上调
map4k4	mitogen-activated protein kinase kinase kinase kinase 4
meox1	mesenchyme homeobox 1
nek2	NIMA (never in mitosis gene a)-related expressed kinase 2
rac1	RAS-related C3 botulinum substrate 1
scn8a	sodium channel, voltage-gated, type VIII, alpha
slc1a4	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4
tagln2	transgelin 2
tgfbr2	transforming growth factor, beta receptor II
tmc6	transmembrane channel-like gene family 6
tpm1	tropomyosin 1, alpha
trib3	tribbles homolog 3 (Drosophila)
tspan8	tetraspanin 8	上调
wsb2	WD repeat and SOCS box-containing 2
ywhaz	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide; predicted gene 4202
crbn	cereblon
abat	4-aminobutyrate aminotransferase
acsl1	acyl-CoA synthetase long-chain family member 1
akap1	A kinase (PRKA) anchor protein 1
cbs	cystathionine beta-synthase
cxcl12	chemokine (C-X-C motif) ligand 12	下调
gas1	growth arrest specific 1	下调
ghr	growth hormone receptor
gnmt	glycine N-methyltransferase	下调
igfals	insulin-like growth factor binding protein, acid labile subunit	下调
masp1	mannan-binding lectin serine peptidase 1
paics	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase; predicted gene 8445
pbld	phenazine biosynthesis-like protein domain containing
plxnc1	plexin C1; similar to plexin C1
sardh	sarcosine dehydrogenase
scnn1a	sodium channel, nonvoltage-gated 1 alpha
sirt3	sirtuin 3 (silent mating type information regulation 2, homolog) 3 (S. cerevisiae)

表3 人类与小鼠共同表达基因的通路分布

通路名称	基因	P值	与肝癌关系的文献报道
肥厚型心肌病	lmna, itga3, tpm1, itgb1	0.0088804	无
甘氨酸、丝氨酸、苏氨酸代谢通路	gnmt, sardh, cbs	0.0106734	有[15,16]
扩张型心肌病	lmna, itga3, tpm1, itgb1	0.0110271	无
轴突引导通路	plxnc1, rac1, itgb1, cxcl12	0.0270935	有[17-20]
味觉转导	gnb1, itpr3, scnn1a	0.0285055	无
致病性大肠杆菌感染	cttn, ywhaz, itgb1	0.0337804	无
致心律失常型右室心肌病	lmna, itga3, itgb1	0.0568722	无