TXTGate: profiling gene groups with text-based information

Table 4 TXTGate profiling of cluster E from Eisen et al. [39]

Gene symbol		Cluster terms in Blaschke et al. [16]	Terms from TXTGate
Subcluster E1	TPT1 FBA1	glyceraldehyde-3-phosphate*	glyceraldehyd_3_phosphat_dehydrogenas
	GPM1 TKL1	glyceraldehyde-3-phosphate dehydrogenase*	glycolyt
	PGK1 CDC19	phosphoglycerate kinase*	glucos
	TDH3 HXK2	phosphoglycerate*	enzym
	TDH2 TYE7	mutase*	glycolysi
	ENO2 PFK1	dehydrogenase	carbon
	TDH1 ACS2	enolase	pyruv_kinas
		glycerol-3-phosphate dehydrogenase	ethanol
		osmotic stress	phosphoglycer_kinas
		phospoglycerate	growth
Subcluster E2	PDC5 PDC1	alcohol*	pyruv_decarboxylas
	PDC6	transketolase*	pyruv
		catabolite repression	glucos
		decarboxylase	enzym
		ethanol	alcohol
		glucose	decarboxyl
		glucose repression	ethanol
		hexokinases	ferment
		pyruvate	thiamin
		pyruvate decarboxylase	decarboxylas

Profiling is by subclustering (k = 2). High-scoring terms are shown for each subcluster E1 and E2. We also show the terms (excluding gene names) resulting from a similar analysis conducted by Blaschke et al. [16]. *Terms that were labeled specific to a subcluster by Blaschke et al. Although several of their settings are different from ours (because of the differences in MEDLINE corpus, textual analysis and the cluster algorithm used), a comparison of the term profiles in both analyses shows that TXTGate also identifies E1 as related to glycerol, whereas E2 is more related to pyruvate metabolism and ethanol fermentation. Complete data can be found in Additional data file 1.

ISSN: 1474-760X