Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Tintle, Nathan L; Sitarik, Alexandra; Boerema, Benjamin; Young, Kylie; Best, Aaron A; DeJongh, Matthew

doi:10.1186/1471-2105-13-193

BMC Bioinformatics

Table 1 Characteristics of the set of microarrays

From: Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Organism name	# of genes¹	# of arrays	Source²	Number of Gene sets
				Gene Ontology			KEGG maps³	MO: Predicted Operons³	SEED³			Total
				BP³	CC³	MF³	KEGG maps³	MO: Predicted Operons³	SS³	Scenario³	Path³	Total
Actinobacteria
Streptomyces coelicor A3(2)	7989	55	GEO	799	117	819	113	1626	200	139	158	3971
Bacteroidetes
Bacteroidesthetaiotaomicron VPI-5482	4778	41	GEO	695	84	615	79	1008	193	93	98	2865
Cyanobacteria
Synechococcuselongatus PCC 7942	1849	104	GEO	651	106	564	89	295	257	72	90	2124
Deinococcus-Thermus
Thermusthermophilus	2215	407	GEO	604	79	499	83	441	180	86	92	2064
Firmicutes
Staphylococcus aureus subsp. aureus Mu50	2750	852	PD	697	86	604	90	521	360	98	118	2574
Streptococcus agalactiae	1880	78	GEO	571	65	477	79	257	238	64	70	1830
Streptococcus pyogenes	1849	89	GEO	556	70	488	81	248	256	57	73	1829
Mollicutes
Mycoplasma pneumoniae M129	731	43	GEO	332	46	252	42	80	80	14	14	860
Proteobacteria
Alpha
Bradyrhizobiumjaponicum	8198	195	GEO	457	111	547	103	1672	421	138	156	3605
Rhodobactersphaeroides	4084	119	GEO	767	150	724	103	757	367	110	128	3106
Rickettsia rickettsii str.Iowa	1242	100	GEO	445	64	367	59	251	135	14	15	1350
Epsilon
Helicobacter pylori HPAG1	1521	56	GEO	572	76	426	77	248	174	42	42	1657
Gamma
Escherichia coli K12	4329	907	M3D	847	115	788	98	752	399	160	169	3328
Pasteurella multocida subsp. multocida str. Pm70	2001	72	GEO	653	77	673	81	365	328	88	91	2356
Pseudomonas aeruginosa PA01	5598	176	GEO	823	133	835	104	1042	389	136	154	3616
Shewanellaoneidensis MR-1	4050	245	M3D	746	112	641	95	705	328	109	125	2861
Vibrio parahaemolyticus RIMD 2210633	4515	42	GEO	719	109	602	93	920	418	144	165	3170
Total	--	3581	--	10934	1600	9921	1469	11188	4723	1564	1767	43166

¹ For which array data is available.
²M3D=Many Microbe Microarrays Database [18], PD=The Paul Dunman Laboratory, GEO=Gene Expression Omnibus [17].
³ Gene Ontology [13], BP=Biological Process, CC=Cellular Component, MF=Molecular Function, KEGG=Kyoto Encyclopedia of Genes and Genomes [14], MO= Microbes Online Predicted Operons using the method of Price et al. [16, 21], SEED [15, 22], SS=SEED subsystems, Scenario=SEED scenario, Path=SEED path.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com