Supplementary information for HykGene

Supplementary information for the paper:

HykGene: A Hybrid Approach for Selecting Marker Genes for Phenotype Classification using Microarray Gene Expression Data

Yuhang Wang, Fillia Makedon, James Ford and Justin Pearlman.

1. Software available for download.

2. Data used in our paper for download.

3. Supplementary tables.

Table 2. Results on ALL/ALL data set using Relief-F

	Relief-F
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	98.61	94.44	8	100	7	0.014	98.61	93.06	7	100	6	0.014
SVM	98.61	94.44	7	100	10	0.025	98.61	95.83	3	98.61	12	0.025
C4.5	79.17	93.06	7	94.44	1	0.024	79.17	88.89	6	94.44	1	0.024
NB	97.22	94.44	8	98.61	4	0.027	98.61	95.83	10	100	5	0.014



Table 3. Results on ALL/ALL data set using Information Gain

	Information Gain
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	95.83	94.44	8	98.61	25	0.027	97.22	97.22	11	100	13	0.007
SVM	97.22	94.44	8	97.22	23	0.025	95.83	95.83	3	100	10	0.007
C4.5	83.33	94.44	8	94.44	1	0.021	80.56	93.06	4	94.44	1	0.008
NB	95.83	93.06	7	100	33	0.056	95.83	97.22	9	100	13	0.041



Table 4. Results on ALL/ALL data set using Chi Squared statistic

	Chi Squared statistic
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	95.83	95.83	11	98.61	18	0.088	95.83	94.44	5	98.61	5	0.008
SVM	97.22	94.44	10	97.22	4	0.007	97.22	95.83	14	98.61	5	0.003
C4.5	81.94	88.89	11	94.44	1	0.024	83.33	94.44	3	94.44	1	0.012
NB	95.83	95.83	4	98.61	8	0.012	95.83	97.22	11	98.61	4	0.022



Table 5. Results on Colon Tumor data set using Relief-F

	Relief-F
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	85.48	79.03	5	88.71	10	0.068	83.87	77.42	7	90.32	5	0.004
SVM	87.10	85.48	9	88.71	17	0.004	88.71	79.03	9	90.32	40	0.003
C4.5	82.26	80.65	11	87.10	32	0.000	82.26	72.58	6	87.10	38	0.000
NB	85.48	82.3	6	87.10	6	0.020	83.87	77.42	9	90.32	22	0.001



Table 6. Results on Colon Tumor data set using Information Gain

	Information Gain
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	87.10	85.48	6	90.32	28	0.018	83.87	85.48	8	88.71	54	0.025
SVM	87.10	80.65	5	90.32	17	0.014	87.10	82.26	14	88.71	47	0.001
C4.5	83.87	91.94	8	91.94	3	0.000	85.48	90.32	8	91.94	67	0.000
NB	85.48	74.19	7	87.1	12	0.023	79.03	70.97	5	85.48	13	0.007



Table 7. Results on Colon Tumor data set using Chi Squared statistic

	Chi Squared statistic
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	80.64	79.03	10	88.71	16	0.091	83.87	75.81	7	90.32	44	0.034
SVM	85.48	85.48	8	87.10	17	0.005	85.48	85.48	8	88.71	13	0.093
C4.5	83.87	67.74	7	87.10	9	0.017	90.32	87.10	8	90.32	16	0.009
NB	83.87	67.74	4	85.48	16	0.073	80.64	77.42	8	87.10	17	0.009



Table 8. Results on MLL data set using Relief-F

	Relief-F
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	95.83	90.28	7	97.22	36	0.062	95.83	72.22	3	98.61	15	0.013
SVM	97.22	91.67	7	97.22	30	0.019	98.61	70.83	3	100	39	0.054
C4.5	93.06	86.11	9	95.83	20	0.094	91.67	73.61	10	94.44	25	0.057
NB	97.22	91.67	8	97.22	16	0.261	97.22	73.61	3	98.61	38	0.061



Table 9. Results on MLL data set using Information Gain

	Information Gain
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	90.28	83.33	4	97.22	22	0.019	90.27	87.50	5	97.22	14	0.014
SVM	95.83	86.11	3	98.61	22	0.015	97.22	86.11	5	97.22	14	0.080
C4.5	94.44	84.72	10	94.44	31	0.083	91.67	83.33	4	91.67	15	0.121
NB	94.44	86.11	7	95.80	20	0.174	93.06	86.11	5	97.22	11	0.019



Table 10. Results on MLL data set using Chi Squared statistic

	Chi Squared statistic
	50 top-ranked genes						100 top-ranked genes
	All 50	SOM		HykGene			All 100	SOM		HykGene
	acc.	acc.	genes	acc.	genes	p-value	acc.	acc.	genes	acc.	genes	p-value
k-NN	95.83	81.94	6	97.22	38	0.086	94.44	87.50	4	100	26	0.012
SVM	95.83	86.11	4	98.61	25	0.276	97.22	91.67	6	98.61	11	0.030
C4.5	86.11	79.17	4	91.67	8	0.005	91.67	86.11	7	91.67	14	0.040
NB	94.44	83.33	5	95.83	18	0.242	94.44	88.89	11	97.22	15	0.357