Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens

Sinha, Rileen; Zimmer, Andreas D; Bolte, Kathrin; Lang, Daniel; Reski, Ralf; Platzer, Matthias; Rensing, Stefan A; Backofen, Rolf

doi:10.1186/1471-2229-10-76

BMC Plant Biology

Table 1 GO analyses of genes with alternative NAGNAG acceptor site

From: Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens

Organism/subset	Name	GO Term	FDR (q-value)	# in test group	# in reference group	# non annot. test	# non annot. reference group
P. patens alternative NAGNAG genes Sanger support	cytoplasmic part	GO:0044444	0.0133	78	5407	100	11894
	plastid	GO:0009536	0.04291	42	2607	136	14694
	membrane-bound organelle	GO:0043227	0.04291	89	6778	89	10523
	intracellular membrane-bound organelle	GO:0043231	0.04291	89	6778	89	10523
	intracellular part	GO:0044424	0.04963	105	8388	73	8913
*P. patens* alternative NAGNAG genes Sanger and/or 454 support	cytoplasmic part	GO:0044444	3.52E-04	168	5317	232	11762
	plastid	GO:0009536	8.35E-04	90	2559	310	14520
	membrane-bound organelle	GO:0043227	8.35E-04	196	6671	204	10408
	intracellular membrane-bound organelle	GO:0043231	8.35E-04	196	6671	204	10408
	intracellular part	GO:0044424	0.00379	229	8264	171	8815
	intracellular	GO:0005622	8.35E-04	251	9029	149	8050
	cytoplasm	GO:0005737	3.78E-04	191	6312	209	10767
	mitochondrion	GO:0005739	0.04193	53	1553	347	15526
	thylakoid	GO:0009579	0.02355	12	187	388	16892
	organelle	GO:0043226	0.00436	207	7373	193	9706
	intracellular organelle	GO:0043229	0.00436	207	7373	193	9706
*A. thaliana* alternative NAGNAG genes combined (Iida et al., 2008 and Schindler et al., 2008)	plastid	GO:0009536	0.0474	50	3021	192	17594
	membrane-bound organelle	GO:0043227	2.28E-04	113	6959	129	13656
	intracellular membrane-bound organelle	GO:0043231	2.28E-04	113	6959	129	13656
	intracellular	GO:0005622	5.17E-05	136	8421	106	12194
	organelle	GO:0043226	1.73E-04	119	7287	123	13328
	intracellular organelle	GO:0043229	1.73E-04	119	7287	123	13328
	nucleic acid binding	GO:0003676	5.98E-06	71	3230	171	17385
	nucleus	GO:0005634	2.02E-04	51	2342	191	18273
	DNA binding	GO:0003677	2.28E-04	49	2250	193	18365
	intracellular part	GO:0044424	2.82E-04	124	7881	118	12734
	cell part	GO:0044464	0.0027	159	11257	83	9358
	RNA binding	GO:0003723	0.01	15	506	227	20109
	binding	GO:0005488	0.01174	132	9231	110	11384
	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	GO:0006139	0.01314	47	2608	195	18007
	transcription factor activity	GO:0003700	0.01314	33	1646	209	18969
	transcription regulator activity	GO:0030528	0.04363	34	1852	208	18763

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ISSN: 1471-2229

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