Bioinformatics Analysis Reveals Most Prominent Gene Candidates to Distinguish Colorectal Adenoma from Adenocarcinoma

Table 1

Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes in each comparison group.

Pathway ID	Pathway description	Number of observed genes	FDR	Number of genes up/down regulated
Carcinoma vs normal
Biological process
GO.0001932	Regulation of protein phosphorylation	29	7.58E-05	16↑/13↓
GO.0006730	One-carbon metabolic process	7	7.58E-05	1↑/6↓
GO.0006820	Anion transport	17	0.000315	4↑/13↓
GO.0009719	Response to endogenous stimulus	30	0.000315	8↑/22↓
GO.0015701	Bicarbonate transport	6	0.000315	0↑/6↓
Cellular component
GO.0005576	Extracellular region	63	9.38E-05	14↑/49↓
GO.0031982	Vesicle	53	0.000163	12↑/41↓
GO.0031988	Membrane-bounded vesicle	52	0.000163	12↑/40↓
GO.0044421	Extracellular region part	55	0.000163	13↑/42↓
GO.0070062	Extracellular exosome	42	0.00196	9↑/31↓
Molecular function
GO.0004089	Carbonate dehydratase activity	5	0.0001	0↑/5↓
GO.0003824	Catalytic activity	70	0.000147	15↑/55↓
GO.0005179	Hormone activity	7	0.00231	2↑/5↓
GO.0005488	Binding	106	0.00306	35↑/71↓
GO.0008237	Metallopeptidase activity	9	0.00509	3↑/6↓
KEGG
910	Nitrogen metabolism	5	5.28E-05	0↑/5↓
4964	Proximal tubule bicarbonate reclamation	4	0.00167	0↑/4↓
4976	Bile secretion	6	0.00167	0↑/6↓
5204	Chemical carcinogenesis	6	0.00167	0↑/6↓
4972	Pancreatic secretion	6	0.00513	0↑/6↓
Adenoma vs normal
Biological process
GO.0006820	Anion transport	15	5.23E-05	3↑/12↓
GO.0006730	One-carbon metabolic process	5	2.40E-03	0↑/5↓
GO.0015701	Bicarbonate transport	5	0.0024	0↑/5↓
GO.0015711	Organic anion transport	11	0.0024	3↑/8↓
GO.0006811	Ion transport	17	0.0359	3↑/14↓
Cellular component
GO.0005576	Extracellular region	47	4.53E-06	10↑/37↓
GO.0005615	Extracellular space	23	1.15E-05	6↑/17↓
GO.0044421	Extracellular region part	41	1.15E-05	8↑/33↓
GO.0031988	Membrane-bounded vesicle	37	0.000128	6↑/31↓
GO.0098589	Membrane region	19	0.000128	5↑/14↓
Molecular function
GO.0004089	Carbonate dehydratase activity	4	0.00115	0↑/4↓
KEGG
910	Nitrogen metabolism	4	1.89E-04	0↑/4↓
4976	Bile secretion	6	0.000189	1↑/5↓
4964	Proximal tubule bicarbonate reclamation	4	0.000204	0↑/4↓
Carcinoma vs adenoma
Biological process
GO.0022617	Extracellular matrix disassembly	6	3.11E-05	6↑/0↓
GO.0030198	Extracellular matrix organization	8	3.11E-05	8↑/0↓
GO.0009888	Tissue development	11	0.0017	8↑/3↓
GO.0060279	Positive regulation of ovulation	2	0.0128	2↑/0↓
GO.0018149	Peptide cross-linking	3	0.0138	3↑/0↓
Cellular component
GO.0005615	Extracellular space	14	4.03E-08	11↑/3↓
GO.0044420	Extracellular matrix component	6	5.01E-06	6↑/0↓
GO.0098644	Complex of collagen trimers	3	0.00151	3↑/0↓
GO.0005581	Collagen trimer	4	0.00166	4↑/0↓
GO.0044421	Extracellular region part	14	0.00637	10↑/4↓
Molecular function
GO.0050840	Extracellular matrix binding	3	0.0478	3↑/0↓
KEGG
4512	Extracellular-receptor interaction	4	0.00111	4↑/0↓
4510	Focal adhesion	4	0.0155	4↑/0↓
4974	Protein digestion and absorption	3	0.0155	3↑/0↓
5146	Amoebiasis	3	0.0219	3↑/0↓
4151	PI3K-Akt signaling pathway	4	0.0461	4↑/0↓