BMC Bioinformatics

Table 1 Tabulates the total number of ontologies that were found for a given number of clusters for each dataset, as well as the number of significantly enriched ontologies.

From: Assessing and selecting gene expression signals based upon the quality of the measured dynamics

		Edge Only		LOOCV + EDGE
Gene Set	Clusters	Significant Ontologies	All Ontologies	Significant Ontologies	All Ontologies
GDS253	2	42	1696	136	1049
	3	133	1696	202	1049
	4	183	1696	288	1049
	5	222	1696	304	1049
	6	261	1696	352	1049
	7	330	1696	392	1049
	8	441	1696	438	1049
	9	455	1696	491	1049
	10	470	1696	499	1049
	11	497	1696	517	1049
	12	537	1696	540	1049
	13	584	1696	544	1049
	14	598	1696	558	1049
	15	620	1696	585	1049
	16	642	1696	593	1049
	17	673	1696	612	1049
	18	721	1696	619	1049
	19	733	1696	632	1049
GDS599	2	78	1292	96	140
	3	129	1292	109	140
	4	172	1292	117	140
	5	219	1292	121	140
	6	282	1292	121	140
	7	344	1292	122	140
	8	420	1292	128	140
	9	444	1292	128	140
	10	456	1292	131	140
	11	484	1292	131	140
	12	544	1292	131	140
	13	569	1292	131	140
	14	600	1292	132	140
	15	632	1292	133	140
	16	644	1292	133	140
	17	658	1292	133	140
	18	684	1292	133	140
	19	708	1292	134	140
GDS972	2	189	2372	98	1696
	3	211	2372	133	1696
	4	230	2372	183	1696
	5	265	2372	222	1696
	6	310	2372	261	1696
	7	330	2372	330	1696
	8	374	2372	411	1696
	9	413	2372	455	1696
	10	450	2372	470	1696
	11	471	2372	497	1696
	12	521	2372	537	1696
	13	558	2372	584	1696
	14	582	2372	598	1696
	15	609	2372	620	1696
	16	656	2372	642	1696
	17	707	2372	673	1696
	18	714	2372	721	1696
	19	773	2372	733	1696

In all of the cases, we see that after running the LOOCV filter as well as the selection via EDGE, the total number of ontologies that have been selected is lower, whereas the number of statistically significantly enriched ontologies remains relatively constant. Thus, the improvement in the total number of ontologies appears to be due primarily to the removal of genes that do not show significant co-functionality.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com