Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes

Table 1.

Prediction of Smooth Muscle-Specific Genes

Expression
Correlation
Probability
UniGene ID
Annotation
105 1.00 0.99 Mm.3153 Myosin heavy chain 11, smooth muscle
174 0.86 0.94 Mm.16562 Actin gamma 2, smooth muscle, enteric
196 0.79 0.85 Mm.2006 Transgelin/SM-22 alpha
49 0.79 0.84 Mm.43921 RIKEN cDNA 4631426E05 gene
68 0.78 0.83 Mm.99349 Svs7
33 0.77 0.80 Mm.95705 Gamma-2 syntrophin
58 0.77 0.78 Mm.3089 ESTs
91 0.76 0.77 Mm.31259 SMAO
31 0.76 0.77 Mm.99224 ESTs
24 0.75 0.75 Mm.46214 Uroplakin 3
57 0.74 0.70 Mm.45481 RIKEN cDNA 1110032A04 gene
292 0.73 0.68 Mm.6712 Desmin
26 0.72 0.66 Mm.4351 Arginine vasopressin receptor 1A
26 0.70 0.58 Mm.100108 RIKEN cDNA 5730414M22 gene
31 0.68 0.50 Mm.152763 Svs3
32 0.66 0.43 Mm.3787 Svs6
344 0.66 0.42 Mm.16537 Actin, alpha 2, smooth muscle, aorta
31 0.65 0.40 Mm.57221 Homeobox B13
27 0.65 0.40 Mm.180124 Leiomodin 1 (smooth muscle)
41 0.64 0.34 Mm.86380 ESTs
29 0.63 0.33 Mm.34359 ESTs
26 0.63 0.32 Mm.89958 MRV integration site 1
54 0.63 0.30 Mm.25722 Purinergic receptor P2X
76 0.62 0.27 Mm.17807 ESTs
22 0.61 0.25 Mm.30933 ESTs
99 0.60 0.24 Mm.4356 Calponin 1
30 0.60 0.23 Mm.88548 ESTs
71 0.59 0.21 Mm.24684 ESTs
219 0.59 0.19 Mm.10661 Solute carrier family 2 member 4
222 0.58 0.19 Mm.34060 RIKEN cDNA 5830475I06 gene
55 0.58 0.17 Mm.45019 Cancer related gene-liver 1
286 0.58 0.17 Mm.28278 Caveolin, caveolae protein, 22 kD
50 0.57 0.17 Mm.27165 ESTs
134 0.57 0.16 Mm.28649 ESTs
189 0.57 0.16 Mm.38877 ESTs
60 0.57 0.15 Mm.23983 ESTs
81 0.57 0.15 Mm.34171 ESTs
43 0.57 0.15 Mm.83243 ESTs
49 0.57 0.15 Mm.12966 Plasma membrane associated protein, S3-12
284 0.57 0.15 Mm.205997 LPP
34 0.57 0.15 Mm.34461 ESTs
139 0.56 0.15 Mm.22941 RIKEN cDNA 4930435F02 gene
307 0.56 0.14 Mm.36850 Smoothelin
36 0.56 0.14 Mm.85304 Gob-5
147 0.56 0.14 Mm.7342 PDZ and LIM domain 3
51 0.56 0.13 Mm.314 ESTs
31 0.56 0.13 Mm.74658 ESTs
76 0.56 0.13 Mm.119265 ESTs
466 0.55 0.12 Mm.1987 Decorin
26 0.55 0.12 Mm.55337 ESTs
44 0.55 0.12 Mm.87506 ESTs
458 0.54 0.11 Mm.196484 Cysteine rich protein 1
94 0.54 0.11 Mm.1237 Peripheral myelin protein, 22 kD
51 0.54 0.11 Mm.35290 Expressed sequence AI552420
111 0.54 0.11 Mm.136207 Expressed sequence AA986860
66 0.54 0.10 Mm.183030 RIKEN cDNA 5430429D21 gene
52 0.54 0.10 Mm.44235 HNF-3/forkhead homolog 1 like
65 0.53 0.10 Mm.29953 RIKEN cDNA 5430437E11 gene
30 0.53 0.09 Mm.38127 Expressed sequence AI642000
118 0.53 0.09 Mm.27390 ESTs
22 0.52 0.08 Mm.112236 ESTs
253 0.52 0.08 Mm.36769 SLAP
58 0.52 0.08 Mm.31552 ESTs
49 0.52 0.08 Mm.23873 ESTs
... ... ... ...
[88 genes]
... ... ... ...
39 0.43 0.02 Mm.87553 Protocadherin beta 17
25 0.43 0.02 Mm.67539 RIKEN cDNA 4933406D09 gene
25 0.43 0.02 Mm.116986 Secreted and transmembrane 1
216
0.43
0.02
Mm.12842
Vinculin

  • Top-ranking genes based on profile similarity to SM-MHC. Smooth muscle cell markers underlined. Likely false positives (the Svs and decorin) in italics. Expression, Number of detections in UniGene; correlation, Pearson's correlation in the raw data set (see Methods); probability, logistic regression probability estimate for a gene to be an SMC marker. For brevity, genes with fewer than 20 detections have been excluded. The logistic regression estimate of the total number of SMC markers in the list shown is 20.4; standard error 3.06

This Article

  1. Published in Advance July 17, 2003, doi: 10.1101/gr.1197303 Genome Res. 13: 1838-1854

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