mRNA expression, functional profiling and multivariate classification of colon biopsy specimen by cDNA overall glass microarray

Table 1 The most differentially expressed genes between the 3 sample groups in the colon

Name	GenBank ID	DifferencesBetween sample groups	P	Number of valid cases/samplegroups	Ratio of means1in adenoma	Ratio of means1 in CRC	Ratio of means1 in IBD	Cell function
Adhesion
Bystin-like	L36720	1-3	0.0005	5, 2, 2	0.612 ± 0.62676	1.47 ± 0.789131	7.3375 ± 1.134906	Other cell adhesion
		2-3	0.0008					proteins
Apoptosis
Tumor necrosis factor	AF016267	1-2	0.0044	4, 4, 5	0.49075 ± 0.315247	2.7695 ± 1.308503	0.5032 ± 0.270649	Death domain
receptor superfamily,		2-3	0.0046					receptors
member10c, decoy
without an intracellular domain
Extracellular matrix, cytoskeleton
Matrix metalloproteinase	X75308	2-3	0.0395	10, 6, 6	0.8075 ± 0.406413	0.557 ± 0.324015	1.222333 ± 0.558757	Metallo
13 (collagenase 3)								proteinases
Metabolism, blood coagulation
Ubiquitin C	M26880	1-3	0.0325	10, 5, 5	0.9329 ± 0.687387	0.8456 ± 0.51739	2.3002 ± 1.110219	Protein turnover
		2-3	0.0227
Plasminogen activator, urokinase	M15476	1-3	0.0089	6, 5, 4	0.482167 ± 0.248489	1.0554 ± 0.524046	1.513 ± 0.417319	Serine proteases
Oncogenes and tumor suppression
AXL receptor	M76125	1-2	0.0209	7, 5, 4	0.258571 ± 0.237985	2.0162 ± 1.429626	1.3225 ± 0.780286	Oncogenes and
Tyrosine kinase								umor
								suppressors
Ras homolog gene family,	Z35227	1-2	0.0076	7, 5, 3	0.806429 ± 0.732179	2.736 ± 1.083434	1.115 ± 0.249638	Oncogenes and
member H								tumor suppressors
RAB5A, member	M28215	1-3	0.0151	8, 5, 5	0.5745 ± 0.438766	0.9958 ± 1.224974	2.263 ± 0.863959	General trafficking
RAS oncogene family
Receptors and ligands
Small inducible cytokine	M21121	1-2	0.0087	8, 4, 6	0.706125 ± 0.402215	1.94025 ± 0.799844	1.0615 ± 0.371365	Growth factors,
A5 (RANTES)								cytokines, and
								chemokines
Pleiotrophin (heparin	M57399	1-2	0.0373	5, 5, 2	0.3474 ± 0.242632	2.7236 ± 1.872401	0.477 ± 0.166877	Growth factors,
binding growth factor 8)								cytokines, and
								chemokines
Patched (Drosophila)	U43148	1-3	0.0043	9, 5, 5	0.653667 ± 0.463297	0.7752 ± 0.448416	3.8946 ± 2.578342	Growth factor and
homolog		2-3	0.0058					chemokine
								receptors
Stem cell growth factor;	D86586	1-2	0.01755	5, 5, 4	0.3264 ± 0.168316	1.6386 ± 0.957384	0.5585 ± 0.420226	Ggrowth factors,
lymphocyte secreted								cytokines, and
C-type lectin								chemokines
Interleukin 7 receptor	M29696	1-2	0.0096	8, 4, 4	0.40775 ± 0.12511	1.774 ± 1.113227	0.32975 ± 0.133809	Interleukin and
		2-3	0.0066					interferon
								receptors
Signal transduction
Myotonic dystrophy	Y12337	1-2	0.0253	10, 6, 6	0.7611 ± 0.296331	1.375167 ± 0.301345	1.4415 ± 0.521753	Intracellular
protein kinase like protein		1-3	0.0131					kinase
								network members
Transcription
Heat shock	M64673	1-2	0.0136	9, 6, 3	0.732444 ± 0.421368	1.7565 ± 0.747317	0.385333 ± 0.320644	Transcription
transcription factor 1								activators
								and repressors
Immediate early protein	M62831	2-3	0.0209	8, 5, 5	0.552875 ± 0.271426	0.4708 ± 0.276956	0.989 ± 0.255144	Basic transcription
								factors
High-mobility group	M23619	1-3	0.0003	9, 6, 5	0.734556 ± 0.324623	0.897667 ± 0.371581	1.7982 ± 0.238334	Chromatin
(nonhistone chromosomal)		2-3	0.0011					proteins
protein isoforms I and Y

¹Cy3/Cy5 (disease/normal).

Table 2 Results of the factor analysis

STAT. factor analysis	Factor loadings (Varimax raw) Extraction: Principal components (Marked loadings > 0.700000)		Cell function
	Factor 1	Factor 2
Stem cell growth factor	0.896313	-0.053631	Growth factors, cytokines,and chemokines
Pleiotrophin (heparin binding growth factor 8)	0.882657	0.006966	Growth factors, cytokines, and chemokines
Small inducible cytokine A5 (RANTES)	0.802949	0.169587	Growth factors, cytokines, and chemokines
Interleukin 7 receptor	0.835349	-0.151447	Interleukin and interferon receptors
Tumor necrosis factor receptor superfamily, member 10c	0.742897	-0.145755	Death domain receptors
Signal transducer and activator of transcription 2113 kDa	0.820315	0.066954	Transcription activators and repressors
Heat shock transcription factor 1	0.745691	0.032620	Transcription activators and repressors
Patched (Drosophila) homolog	-0.113082	0.768421	Growth factor and chemokine receptors
RAB5A, member RAS oncogene family	-0.044311	0.834146	General trafficking
Ubiquitin C	-0.045668	0.719247	Protein turnover
High-mobility group protein isoforms I and Y	-0.029882	0.943945	Chromatin proteins
Explorative variance	6.331196	4.710563