A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Pinheiro, Daniel G; Galante, Pedro AF; de Souza, Sandro J; Zago, Marco A; Silva, Wilson A

doi:10.1186/1471-2105-10-170

BMC Bioinformatics

Table 2 Evaluation of Hierarchical Clustering Quality.

From: A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Id	Groups (Samples)	Unique tags * (%)	Overall F-measure
			cluster3 [32]/simcluster [21]
			M		A		S		C
				*		*		*		*
1	9(56)	29.21	0.65	0.69	0.62	0.57	0.55	0.54	0.52	0.52
			0.70	0.72	0.65	0.64	0.49	0.58
2	2(7)	29.11	0.84	1.00	0.90	0.90	0.90	0.90	0.90	0.90
			0.79	0.86	0.79	0.79	0.79	0.79
3	2(24)	30.88	0.88	0.88	0.88	0.88	0.88	0.90	0.88	0.88
			0.88	0.94	0.87	0.88	0.83	0.87
4	4(12)	33.35	0.94	1.00	0.94	1.00	0.94	0.94	0.94	0.94
			1.00	1.00	0.94	1.00	0.90	0.89
5	2(4)	28.80	0.83	0.83	0.83	0.83	0.83	0.83	0.83	0.83
			0.83	0.83	0.83	0.83	0.83	0.83
6	2(4)	42.70	1.00	1.00	1.00	1.00	1.00	1.00	1.00	1.00
			0.83	0.83	0.83	0.83	0.83	0.83
7	14(45)	34.72	0.72	0.74	0.69	0.64	0.64	0.64	0.61	0.61
			0.67	0.77	0.63	0.69	0.57	0.61
8	2(5)	27.57	0.88	1.00	0.88	1.00	0.88	1.00	0.88	0.88
			1.00	0.88	1.00	0.88	0.87	0.88
9	2(5)	41.48	0.88	0.88	0.88	0.88	0.75	0.75	0.75	0.75
			0.88	0.88	0.85	0.88	0.85	0.85
10	4(8)	45.00	0.83	0.83	0.83	0.83	0.83	0.83	0.83	0.83
			0.92	0.92	0.92	0.92	0.83	0.92
11	3(11)	40.70	0.90	0.90	0.90	0.90	0.90	0.90	0.90	0.90
			0.80	0.86	0.90	0.90	0.86	0.86
12	2(5)	28.30	0.77	0.80	0.77	0.77	0.77	0.77	0.77	0.77
			0.77	0.88	0.72	0.88	0.72	0.85
13	2(6)	37.71	0.90	1.00	0.90	0.90	0.90	0.90	0.90	0.90
			0.80	0.80	0.80	0.80	0.80	0.80
14	5(12)	33.63	0.83	0.83	0.83	0.83	0.83	0.83	0.76	0.76
			0.73	0.78	0.76	0.79	0.71	0.73

Groups of public SAGE libraries used in the hierarchical clustering analyses performed before and after (*) S3T filtering. Four clustering methods were applied: Pairwise complete-linkage (M), Pairwise single-linkage (S), Pairwise centroid-linkage (C), Pairwise average-linkage (A). The histological groups are: brain (1), cartilage (2), cerebellum (3), colon (4), liver (5), lung (6), mammary gland (7), other (8), ovary (9), pancreas (10), prostate (11), retina (12), stomach (13), white blood cells (14). For each group we have the Overall F-measure values for clusters generated with cluster3 and simcluster, respectively, in the first and second lines. The table cell pairs with values in bold represent cases where there was an improvement in the overall quality of clustering, according to F-measure, i.e. the F-measure was greater (21.43% – cluster3; 47.62% – simcluster) or the quality between clusters did not change (69.64% – cluster3; 42.86% – simcluster) after S3T filtering. The remaining table cell pairs, with values not in bold, represent cases where the F-measure was lower after S3T filtering (8.93% – cluster3; 9.52% – simcluster), i.e. where the resulting cluster was less concordant with their previously defined classes.

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ISSN: 1471-2105

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