Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes

Table 1

Gene ontology categories of differentially expressed miRNA targets (pathway union).

Comparison	KEGG pathway	value	#genes	#miRNAs
Upregulated miRNAs in HLC d24 compared to HLC d20	Fatty acid biosynthesis	0	1	2
	ECM-receptor interaction	0	10	4
	Fatty acid metabolism	5.984709e – 10	2	2
	Proteoglycans in cancer	2.928118e − 09	31	3
	Hippo signaling pathway	0.0001180971	13	3
	Steroid biosynthesis	0.004048092	2	2
	Adherens junction	0.01782237	11	2
	Base excision repair	0.02708153	4	2
Upregulated miRNAs in HLC d20 compared to HLC d24	Lysine degradation	1.389225e − 08	9	2
	Chronic myeloid leukemia	0.0001602018	13	2
	Proteoglycans in cancer	0.0002270705	12	1
	Wnt signaling pathway	0.0006146658	12	1
	FoxO signaling pathway	0.003220974	18	2
	Cell cycle	0.003295535	9	1
	Pathways in cancer	0.004235095	17	1
	Progesterone-mediated oocyte maturation	0.03364343	8	1
	Oocyte meiosis	0.03398087	5	1
	Signaling pathways regulating pluripotency of stem cells	0.05899564	9	1
Upregulated miRNAs in HLC d20 compared to hepatocytes	Fatty acid biosynthesis	0	4	4
	ECM-receptor interaction	0	29	10
	Lysine degradation	0	26	17
	Proteoglycans in cancer	0	115	18
	MicroRNAs in cancer	2.065015e − 14	55	3
	Adherens junction	1.92849e − 10	56	14
	Fatty acid metabolism	2.435736e − 07	12	5
	Hippo signaling pathway	2.854731e − 07	76	15
	Prion diseases	3.567319e − 07	2	1
	Viral carcinogenesis	4.563306e − 07	90	10
	Pathways in cancer	7.078609e − 05	155	11
	Cell cycle	0.0002485214	62	9
	p53 signaling pathway	0.02762094	42	10
	Transcriptional misregulation in cancer	0.02815897	70	8
Upregulated miRNAs in hepatocytes compared to HLC d20	Fatty acid biosynthesis	0	4	7
	ECM-receptor interaction	0	39	15
	Lysine degradation	0	26	17
	Cell cycle	0	92	17
	Viral carcinogenesis	0	129	19
	Hippo signaling pathway	0	92	23
	Proteoglycans in cancer	0	140	23
	Pathways in cancer	1.110223e − 16	235	20
	Adherens junction	8.881784e – 16	59	20
	Hepatitis B	3.774758e − 15	83	13
	Chronic myeloid leukemia	3.940404e − 12	54	18
	Colorectal cancer	3.432521e − 11	43	17
	Glioma	9.944934e – 11	43	15
	Fatty acid metabolism	1.771966e – 06	14	8
	p53 signaling pathway	2.456315e – 06	47	16
	Small cell lung cancer	8.452771e – 06	57	14
	Oocyte meiosis	1.56543e − 05	65	12
	Thyroid hormone signaling pathway	2.996244e – 05	64	11
	Steroid biosynthesis	8.629469e – 05	7	12
	Prostate cancer	0.0004910115	65	13
	PI3K-Akt signaling pathway	0.001506451	118	10
	Focal adhesion	0.001709285	81	9
	TGF-beta signaling pathway	0.004683835	48	9
Upregulated miRNAs in HLC d24 compared to hepatocytes	Prion diseases	0	2	2
	Fatty acid biosynthesis	0	4	6
	Fatty acid metabolism	0	14	9
	Proteoglycans in cancer	0	107	15
	ECM-receptor interaction	0	34	18
	Adherens junction	2.136489e – 10	52	16
	Viral carcinogenesis	2.367215e – 07	84	11
	Hippo signaling pathway	8.686167e – 05	76	14
	Pathways in cancer	0.001098215	135	8
	Lysine degradation	0.001337938	24	10
	Transcriptional misregulation in cancer	0.003591186	53	7
	p53 signaling pathway	0.04591601	39	11
Upregulated miRNA hepatocytes compared to HLC d24	Fatty acid biosynthesis	0	4	7
	Hepatitis B	0	91	15
	ECM-receptor interaction	0	41	16
	Lysine degradation	0	27	18
	Cell cycle	0	93	18
	Viral carcinogenesis	0	132	18
	Pathways in cancer	0	247	21
	Hippo signaling pathway	0	91	22
	Proteoglycans in cancer	0	143	23
	Adherens junction	5.662137e – 15	58	19
	Chronic myeloid leukemia	1.465494e – 14	58	19
	Glioma	8.104628e – 14	46	16
	Colorectal cancer	8.277157e – 12	45	18
	p53 signaling pathway	2.698853e – 08	47	17
	Oocyte meiosis	1.888721e – 07	67	13
	Small cell lung cancer	5.78931e − 07	61	15
	Thyroid hormone signaling pathway	1.055741e – 05	64	11
	Prion diseases	2.777397e – 05	6	2
	Steroid biosynthesis	4.649816e – 05	10	11
	TGF-beta signaling pathway	6.111763e – 05	52	11
	Prostate cancer	0.0001105553	66	13
	Fatty acid metabolism	0.0001381028	13	7
	PI3K-Akt signaling pathway	0.0001991286	138	11
	FoxO signaling pathway	0.001107838	84	15
	Focal adhesion	0.001779401	90	9
	Bladder cancer	0.002833066	27	12
	Melanoma	0.01182136	41	10
	Protein processing in endoplasmic reticulum	0.01436954	105	12
	Endocytosis	0.01445943	97	12