Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Abril, Josep F; Cebrià, Francesc; Rodríguez-Esteban, Gustavo; Horn, Thomas; Fraguas, Susanna; Calvo, Beatriz; Bartscherer, Kerstin; Saló, Emili

doi:10.1186/1471-2164-11-731

BMC Genomics

Table 2 Gene Ontology annotation for 90e set sequences.

From: Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

GO	Molecular Function	Count	Freq%	GO	Biological Process	Count	Freq%	GO	Cellular Component	Count	Freq%
GO:0000166	nucleotide binding	54,823	---	---	---	---	---	GO:0043229	intracellular organelle	60,817	---
---	unannotated	9,709	---	---	unannotated	62,834	---	---	unannotated	11,131	---
GO:0016787	hydrolase activity	5,197	35.669	GO:0043170	macromolecule metabolic process	5,793	35.610	GO:0043234	protein complex	2,918	40.788
GO:0016740	transferase activity	2,030	13.933	GO:0022607	cellular component assembly	2,182	13.413	GO:0044424	intracellular part	2,314	32.346
GO:0043167	ion binding	1,323	9.080	GO:0006810	transport	1,213	7.456	GO:0031982	vesicle	819	11.448
GO:0003735	structural constituent of ribosome	874	5.999	GO:0006950	response to stress	1,070	6.577	GO:0044425	membrane part	469	6.556
GO:0005488	binding	761	5.223	GO:0050789	regulation of biological process	1,012	6.221	GO:0016020	membrane	210	2.935
GO:0016491	oxidoreductase activity	703	4.825	GO:0006807	nitrogen compound metabolic process	722	4.438	GO:0005622	intracellular	111	1.552
GO:0022857	transmembrane transporter activity	678	4.653	GO:0048869	cellular developmental process	655	4.026	GO:0044446	intracellular organelle part	91	1.272
GO:0030235	nitric-oxide synthase regulator activity	597	4.097	GO:0065009	regulation of molecular function	622	3.823	GO:0005576	extracellular region	63	0.881
GO:0043176	amine binding	580	3.981	GO:0009056	catabolic process	507	3.117	GO:0045211	postsynaptic membrane	21	0.294
GO:0005515	protein binding	532	3.651	GO:0044419	interspecies interaction between organisms	280	1.721	GO:0044420	extracellular matrix part	19	0.266
GO:0003676	nucleic acid binding	401	2.752	GO:0055114	oxidation reduction	236	1.451	GO:0043233	organelle lumen	18	0.252
GO:0005215	transporter activity	387	2.656	GO:0065008	regulation of biological quality	206	1.266	GO:0031012	extracellular matrix	16	0.224
GO:0016829	lyase activity	71	0.487	GO:0048856	anatomical structure development	193	1.186	GO:0042597	periplasmic space	15	0.210
GO:0016853	isomerase activity	55	0.377	GO:0051649	establishment of localization in cell	183	1.125	GO:0000267	cell fraction	15	0.210
GO:0048037	cofactor binding	52	0.357	GO:0044237	cellular metabolic process	182	1.119	GO:0044462	external encapsulating structure part	11	0.154
GO:0016874	ligase activity	49	0.336	GO:0023060	signal transmission	150	0.922	GO:0031975	envelope	8	0.112
GO:0004871	signal transducer activity	45	0.309	GO:0048870	cell motility	141	0.867	GO:0005615	extracellular space	7	0.098
GO:0003824	catalytic activity	32	0.220	GO:0008152	metabolic process	139	0.854	GO:0009986	cell surface	6	0.084
GO:0060589	nucleoside-triphosphatase regulator activity	32	0.220	GO:0023033	signaling pathway	107	0.658	GO:0043204	perikaryon	5	0.070
GO:0042277	peptide binding	28	0.192	GO:0044238	primary metabolic process	83	0.510	GO:0030427	site of polarized growth	4	0.056
GO:0022892	substrate-specific transporter activity	22	0.151	GO:0042221	response to chemical stimulus	69	0.424	GO:0042995	cell projection	3	0.042
GO:0019208	phosphatase regulator activity	12	0.082	GO:0006996	organelle organization	47	0.289	GO:0030312	external encapsulating structure	2	0.028
GO:0003712	transcription cofactor activity	12	0.082	GO:0007017	microtubule-based process	42	0.258	GO:0031594	neuromuscular junction	2	0.028
GO:0019207	kinase regulator activity	11	0.075	GO:0044281	small molecule metabolic process	39	0.240	GO:0045177	apical part of cell	2	0.028
GO:0008289	lipid binding	9	0.062	GO:0051301	cell division	37	0.227	GO:0019028	viral capsid	1	0.014
GO:0005201	extracellular matrix structural constituent	8	0.055	GO:0022613	ribonucleoprotein complex biogenesis	35	0.215	GO:0031252	cell leading edge	1	0.014
GO:0050840	extracellular matrix binding	6	0.041	GO:0019637	organophosphate metabolic process	34	0.209	GO:0044217	other organism part	1	0.014
GO:0061134	peptidase regulator activity	6	0.041	GO:0045184	establishment of protein localization	34	0.209	GO:0044297	cell body	1	0.014
GO:0030246	carbohydrate binding	6	0.041	GO:0009628	response to abiotic stimulus	23	0.141	GO:0044463	cell projection part	1	0.014
GO:0016248	channel inhibitor activity	5	0.034	GO:0019748	secondary metabolic process	21	0.129		TOTAL	7,154
GO:0003702	RNA polymerase II transcription factor activity	5	0.034	GO:0009058	biosynthetic process	21	0.129
GO:0005198	structural molecule activity	4	0.027	GO:0007155	cell adhesion	18	0.111
GO:0016986	transcription initiation factor activity	4	0.027	GO:0061024	membrane organization	16	0.098
GO:0042165	neurotransmitter binding	4	0.027	GO:0007275	multicellular organismal development	16	0.098
GO:0003682	chromatin binding	3	0.021	GO:0016192	vesicle-mediated transport	12	0.074
GO:0008430	selenium binding	3	0.021	GO:0043062	extracellular structure organization	10	0.061
GO:0030234	enzyme regulator activity	2	0.014	GO:0034330	cell junction organization	9	0.055
GO:0030528	transcription regulator activity	2	0.014	GO:0048609	reproductive process in a multicellular organism	9	0.055
GO:0009055	electron carrier activity	2	0.014	GO:0007154	cell communication	8	0.049
GO:0017056	structural constituent of nuclear pore	2	0.014	GO:0003008	system process	7	0.043
GO:0017080	sodium channel regulator activity	2	0.014	GO:0016049	cell growth	7	0.043
GO:0001871	pattern binding	2	0.014	GO:0016458	gene silencing	6	0.037
GO:0019239	deaminase activity	2	0.014	GO:0008219	cell death	5	0.031
GO:0043021	ribonucleoprotein binding	2	0.014	GO:0033036	macromolecule localization	4	0.025
GO:0008538	proteasome activator activity	2	0.014	GO:0048610	reproductive cellular process	4	0.025
GO:0030337	DNA polymerase processivity factor activity	1	0.007	GO:0051236	establishment of RNA localization	4	0.025
GO:0031406	carboxylic acid binding	1	0.007	GO:0071684	organism emergence from protective structure	4	0.025
GO:0042562	hormone binding	1	0.007	GO:0006955	immune response	4	0.025
GO:0046906	tetrapyrrole binding	1	0.007	GO:0007049	cell cycle	4	0.025
GO:0051540	metal cluster binding	1	0.007	GO:0009405	pathogenesis	4	0.025
	TOTAL	14,570		GO:0009607	response to biotic stimulus	4	0.025
				GO:0009791	post-embryonic development	4	0.025
				GO:0048646	anatomical structure formation involved in morphogenesis	4	0.025
				GO:0009790	embryonic development	3	0.018
				GO:0015976	carbon utilization	2	0.012
				GO:0032506	cytokinetic process	2	0.012
				GO:0045103	intermediate filament-based process	2	0.012
				GO:0070882	cellular cell wall organization or biogenesis	2	0.012
				GO:0006413	translational initiation	2	0.012
				GO:0009566	fertilization	2	0.012
				GO:0001906	cell killing	1	0.006
				GO:0043473	pigmentation	1	0.006
				GO:0009987	cellular process	1	0.006
				GO:0022402	cell cycle process	1	0.006
				GO:0022411	cellular component disassembly	1	0.006
				GO:0022415	viral reproductive process	1	0.006
				GO:0023061	signal release	1	0.006
				GO:0030030	cell projection organization	1	0.006
				GO:0051606	detection of stimulus	1	0.006
				GO:0000746	conjugation	1	0.006
				GO:0007163	establishment or maintenance of cell polarity	1	0.006
				GO:0009653	anatomical structure morphogenesis	1	0.006
					TOTAL	16,268

The most probable GO code in the three ontology categories--molecular function, biological process and cellular component-- for each sequence in the 90e data set was selected. For simplicity, only level one and two codes are shown here in order.

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ISSN: 1471-2164

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