Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain

Table 1 Main functional categories from transcriptome analysis in NG 14 and RUT C30 strains

Functional category	FunCat number	Cluster 1	Cluster 2	Cluster 3	Cluster 4	Cluster 5	Cluster 6	Cluster 7	Cluster 8	Cluster 9	Total category
Ribosome biogenesis	12.01	52 (96%)			1 (2%)		1 (2%)				54
Metabolism	01.00	3 (7%)	4 (9%)	3 (7%)	22 (48%)	1 (2%)	7 (15%)	4 (9%)	2 (4%)		46
Extracellular metabolism (CAZymes)	01.25	1 (2%)	2 (4%)	3 (7%)	5 (11%)	5 (11%)	7 (15%)	2 (4%)	9 (20%)	12 (26%)	46
Transported compounds	20.01	4 (9%)	6 (14%)	(7%)	8 (19%)	4 (9%)	1 (2%)	10 (23%)	7 (16%)		43
Amino acid metabolism	01.01	10 (24%)	7 (17%)	6 (14%)	7 (17%)	7 (17%)	3 (7%)	1 (2%)	1 (2%)		42
Lipid, fatty acid and isoprenoid metabolism	01.06	8 (22%)	13 (36%)	2 (6%)	9 (25%)		1 (3%)	1 (3%)	2 (6%)		36
Transcriptional control	11.2.3.4	2 (10%)		1 (5%)	5 (25%)	7 (35%)		4 (20%)	1 (5%)		20
Extracellular protein degradation	01.25.03	1 (6%)	4 (24%)	2 (12%)	8 (47%)		2 (12%)				17
Energy metabolism	02.00	3 (19%)	4 (25%)	1 (6%)	7 (44%)				1 (6%)		16
Stress response	32.01	1 (7%)	1 (7%)		4 (29%)		3 (21%)	5 (36%)			14
Vesicular transport (secretion)	20.09.07	1 (8%)	1 (8%)		1 (8%)	7 (54%)			3 (23%)		13
Cellular communication, signal transduction	30.00	3 (23%)	2 (15%)		2 (15%)	4 (31%)	1 (8%)	1 (8%)			13
Secondary metabolism	01.20	2 (17%)	1 (8%)	2 (17%)	3 (25%)	1 (8%)	1 (8%)	2 (17%)			12
Detoxification	32.07	1 (9%)	3 (27%)	2 (18%)	4 (36%)		1 (9%)				11
Other categories		10 (26%)	4 (10%)	4 (10%)	7 (18%)	5 (13%)	3 (8%)	4 (10%)	2 (5%)		39
Unclassified		4 (13%)	1 (3%)	5 (16%)	13 (42%)	2 (6%)	5 (16%)		1 (3%)		31
Unknown protein		7 (9%)	14 (18%)	1 (1%)	18 (23%)	16 (20%)	14 (18%)	6 (8%)	3 (4%)		79
Total		113	67	35	124	59	50	40	32	12	532

Only the FunCat categories with more than ten genes in the whole dataset are considered main functional categories. The number of genes belonging to categories is provided for each cluster. Category-associated genes found more abundantly (at least a 2-gene of difference between clusters) are indicated in bold. Percentages in parentheses indicate the rounded percentage of genes from each category found in a cluster. Genes whose function could not be associated with a category were annotated as Unclassified. Genes without a predicted function were annotated as Unknown.

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