Other supporting information

Gene Model

Correlation Plot

Expression profile (Values are plotted in Log(2) values.)

Genes with related expresssion profiles.

Positively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT2P005470	0.926831	-	AT2G25840	OVA4 (ovule abortion 4)	-	-
OMAT1P004090	0.92647	-	AT1G11870	SRS (SERYL-TRNA SYNTHETASE)	-	-
OMAT3P012470	0.924808	-	AT3G48110	EDD1 (EMBRYO-DEFECTIVE-DEVELOPMENT 1)	-	-
OMAT5P007630	0.920348	-	AT5G22640	emb1211 (embryo defective 1211)	-	-
OMAT5P005845	0.918801	-	AT5G16715	EMB2247 (embryo defective 2247)	-	-
OMAT4P009530	0.916983	-	AT4G29060	emb2726 (embryo defective 2726)	-	-
OMAT1P014910	0.91373	-	AT1G53800	endonuclease	AT1G53801	other RNA
OMAT4P005200	0.903091	-	AT4G17560	ribosomal protein L19 family protein	-	-
OMAT1P013310	0.899784	-	AT1G48520	GATB (GLU-ADT SUBUNIT B)	-	-
OMAT4P013270	0.898433	-	AT4G38160	pde191 (pigment defective 191)	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT1P109920	-0.822718	-	AT1G31470	NFD4 (NUCLEAR FUSION DEFECTIVE 4)	-	-
OMAT5P012600	-0.766809	-	AT5G45130	RHA1 (RAB HOMOLOG 1)	-	-
OMAT5P020810	-0.755907	-	AT5G66930	unknown protein	-	-
OMAT1P107120	-0.752111	-	AT1G22180	SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein	-	-
OMAT4P110640	-0.745907	-	AT4G35860	ATGB2 (GTP-BINDING 2)	-	-
OMAT5P015580	-0.744131	-	AT5G53330	FUNCTIONS IN: molecular_function unknown	-	-
OMAT4P106750	-0.740056	-	AT4G24990	ATGP4	-	-
OMAT4P007880	-0.724441	-	AT4G25230	RIN2 (RPM1 INTERACTING PROTEIN 2)	-	-
OMAT5P007770	-0.72389	-	AT5G23090	NF-YB13 (NUCLEAR FACTOR Y, SUBUNIT B13)	-	-
OMAT5P013300	-0.720704	-	AT5G47120	ATBI1 (BAX INHIBITOR 1)	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 3.70e-54	:20 terms with high significance
3.70e-54 <	p-value	<= 8.76e-06	:With considering multiple testing correction; p <= 1.00e-02 / 1142
8.76e-06 <	p-value	<= 1.00e-02

Type of term (*1)	Depth of the term in ontology tree	ID/Term	Description	Number of genes	Over-Representative rate (*2)	p-value (*3)	PosMed p-value (*4) (Link to PosMed)	Found on gene annotation
B	3	GO:0009790	embryonic development	21/200	7.95	3.48e-14	-	no
B	5	GO:0006520	cellular amino acid metabolic process	19/200	9.03	4.69e-14	-	no
B	5	GO:0044106	cellular amine metabolic process	19/200	8.36	1.97e-13	-	no
B	4	GO:0009793	embryonic development ending in seed dormancy	19/200	8.29	2.28e-13	-	no
B	3	GO:0048316	seed development	20/200	7.34	6.13e-13	-	no
B	4	GO:0048608	reproductive structure development	26/200	5.33	6.79e-13	-	no
B	4	GO:0009308	amine metabolic process	19/200	7.59	1.15e-12	-	no
B	5	GO:0010154	fruit development	20/200	7.00	1.51e-12	-	no
B	3	GO:0003006	reproductive developmental process	26/200	4.72	1.12e-11	-	no
B	3	GO:0009791	post-embryonic development	26/200	4.39	5.59e-11	-	no
B	3	GO:0022414	reproductive process	26/200	4.31	8.37e-11	-	no
B	5	GO:0043436	oxoacid metabolic process	22/200	5.00	1.22e-10	-	yes
B	4	GO:0006082	organic acid metabolic process	22/200	4.98	1.29e-10	-	yes
B	4	GO:0042180	cellular ketone metabolic process	22/200	4.90	1.77e-10	-	yes
B	5	GO:0006412	translation	28/200	3.86	2.27e-10	-	no
B	4	GO:0006519	cellular amino acid and derivative metabolic process	19/200	5.47	4.06e-10	-	no
B	5	GO:0044271	cellular nitrogen compound biosynthetic process	16/200	6.05	1.72e-09	-	yes
B	3	GO:0044237	cellular metabolic process	84/200	1.78	2.67e-09	-	yes
B	3	GO:0048856	anatomical structure development	28/200	3.13	2.52e-08	-	no
B	4	GO:0044249	cellular biosynthetic process	56/200	1.99	8.20e-08	-	yes
B	3	GO:0044281	small molecule metabolic process	27/200	3.00	1.01e-07	-	yes
B	3	GO:0009058	biosynthetic process	57/200	1.96	1.09e-07	-	yes
B	4	GO:0034641	cellular nitrogen compound metabolic process	43/200	2.21	1.96e-07	-	yes
B	3	GO:0007275	multicellular organismal development	29/200	2.73	2.80e-07	-	no
B	3	GO:0006807	nitrogen compound metabolic process	43/200	2.17	3.39e-07	-	yes
B	5	GO:0044267	cellular protein metabolic process	42/200	2.06	1.83e-06	-	no
B	4	GO:0019538	protein metabolic process	45/200	1.95	3.39e-06	-	no
B	4	GO:0010467	gene expression	41/200	2.01	4.30e-06	1.77E-15	no
B	5	GO:0016070	RNA metabolic process	22/200	2.59	1.56e-05	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	57/200	1.62	4.91e-05	-	no
B	3	GO:0043170	macromolecule metabolic process	60/200	1.55	1.04e-04	-	no
B	3	GO:0044238	primary metabolic process	72/200	1.45	1.45e-04	-	yes
B	3	GO:0006996	organelle organization	11/200	3.30	1.49e-04	-	no
B	4	GO:0044283	small molecule biosynthetic process	13/200	2.86	2.09e-04	-	no
B	5	GO:0034645	cellular macromolecule biosynthetic process	36/200	1.67	7.60e-04	-	no
B	4	GO:0009059	macromolecule biosynthetic process	36/200	1.66	8.04e-04	-	no
B	5	GO:0090304	nucleic acid metabolic process	25/200	1.66	4.44e-03	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	27/200	1.60	5.58e-03	-	no
B	3	GO:0009628	response to abiotic stimulus	14/200	1.89	7.85e-03	-	no

C	5	GO:0009536	plastid	148/200	8.01	3.15e-110	3.64E-21	yes
C	4	GO:0044444	cytoplasmic part	159/200	4.58	4.40e-84	-	yes
C	4	GO:0005737	cytoplasm	162/200	4.33	7.27e-83	-	yes
C	4	GO:0043231	intracellular membrane-bounded organelle	161/200	3.66	7.20e-71	-	yes
C	3	GO:0043227	membrane-bounded organelle	161/200	3.66	7.35e-71	-	yes
C	4	GO:0044435	plastid part	79/200	13.89	5.30e-70	-	yes
C	3	GO:0043229	intracellular organelle	163/200	3.53	6.72e-70	-	yes
C	3	GO:0044424	intracellular part	167/200	3.28	6.17e-68	-	yes
C	3	GO:0005622	intracellular	169/200	3.18	2.61e-67	-	yes
C	5	GO:0044434	chloroplast part	73/200	13.18	1.17e-62	-	yes
C	5	GO:0009532	plastid stroma	56/200	22.66	3.48e-61	-	yes
C	3	GO:0044446	intracellular organelle part	84/200	5.86	3.42e-44	-	yes
C	3	GO:0044422	organelle part	84/200	5.85	3.65e-44	-	yes
C	3	GO:0044464	cell part	176/200	1.92	3.77e-37	-	yes
C	4	GO:0009579	thylakoid	29/200	11.65	1.49e-23	-	no
C	5	GO:0009526	plastid envelope	30/200	10.92	1.85e-23	-	no
C	4	GO:0031967	organelle envelope	33/200	7.92	3.63e-21	-	no
C	3	GO:0031975	envelope	33/200	7.92	3.63e-21	-	no
C	5	GO:0031976	plastid thylakoid	20/200	10.05	1.33e-15	-	no
C	4	GO:0031984	organelle subcompartment	20/200	9.99	1.50e-15	-	no
C	4	GO:0044436	thylakoid part	20/200	9.70	2.70e-15	-	no
C	5	GO:0042651	thylakoid membrane	19/200	10.50	2.70e-15	-	no
C	4	GO:0034357	photosynthetic membrane	19/200	10.36	3.48e-15	-	no
C	5	GO:0055035	plastid thylakoid membrane	18/200	10.39	1.57e-14	-	no
C	3	GO:0043228	non-membrane-bounded organelle	27/200	4.53	1.20e-11	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	27/200	4.53	1.20e-11	-	no
C	4	GO:0005840	ribosome	16/200	6.25	1.06e-09	-	no
C	3	GO:0030529	ribonucleoprotein complex	17/200	4.87	1.70e-08	-	no
C	5	GO:0005739	mitochondrion	20/200	3.13	2.04e-06	-	no
C	3	GO:0048046	apoplast	10/200	5.07	5.39e-06	-	no
C	3	GO:0016020	membrane	48/200	1.75	2.87e-05	-	no
C	3	GO:0031090	organelle membrane	10/200	3.43	1.86e-04	-	no

M	3	GO:0003735	structural constituent of ribosome	14/200	6.47	5.89e-09	-	no
M	3	GO:0016874	ligase activity	13/200	4.76	7.53e-07	-	no
M	4	GO:0003723	RNA binding	21/200	3.03	2.02e-06	0	yes
M	3	GO:0000166	nucleotide binding	28/200	2.12	5.60e-05	-	no
M	5	GO:0032555	purine ribonucleotide binding	22/200	2.24	1.38e-04	-	no
M	4	GO:0032553	ribonucleotide binding	22/200	2.24	1.38e-04	-	no
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	13/200	2.92	1.70e-04	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	13/200	2.89	1.88e-04	-	no
M	4	GO:0017076	purine nucleotide binding	22/200	2.12	3.08e-04	-	no
M	3	GO:0003676	nucleic acid binding	35/200	1.48	7.01e-03	0	yes
M	5	GO:0030554	adenyl nucleotide binding	16/200	1.77	9.66e-03	-	no
M	4	GO:0001883	purine nucleoside binding	16/200	1.77	9.66e-03	-	no
M	3	GO:0001882	nucleoside binding	16/200	1.76	9.90e-03	-	no

PS	5	PO:0020038	petiole	190/200	2.50	5.19e-68	-	yes
PS	5	PO:0020039	leaf lamina	191/200	2.32	4.72e-63	-	yes
PS	5	PO:0000013	cauline leaf	185/200	2.39	8.94e-60	-	yes
PS	4	PO:0020030	cotyledon	180/200	2.45	2.54e-57	4.99E-18	yes
PS	4	PO:0009025	leaf	191/200	2.08	3.70e-54	-	yes
PS	3	PO:0009013	meristem	182/200	2.27	5.41e-53	-	yes
PS	4	PO:0000037	shoot apex	185/200	2.15	1.92e-51	-	yes
PS	5	PO:0009028	microsporophyll	183/200	2.18	5.70e-51	-	yes
PS	5	PO:0009052	pedicel	180/200	2.21	9.09e-50	-	yes
PS	3	PO:0009032	petal	184/200	2.10	8.00e-49	-	yes
PS	5	PO:0008037	seedling	184/200	2.08	2.77e-48	1.16E-17	yes
PS	4	PO:0009047	stem	181/200	2.15	3.46e-48	-	yes
PS	5	PO:0009027	megasporophyll	180/200	2.14	2.06e-47	-	yes
PS	4	PO:0009026	sporophyll	183/200	2.03	1.19e-45	-	yes
PS	4	PO:0000230	inflorescence meristem	173/200	2.23	1.83e-45	-	yes
PS	3	PO:0006001	phyllome	191/200	1.86	2.30e-45	-	yes
PS	3	PO:0009031	sepal	184/200	1.99	7.46e-45	-	yes
PS	5	PO:0008034	leaf whorl	185/200	1.96	1.89e-44	-	yes
PS	4	PO:0008033	phyllome whorl	185/200	1.96	1.89e-44	-	yes
PS	4	PO:0009009	embryo	186/200	1.92	9.07e-44	-	yes
PS	3	PO:0009010	seed	186/200	1.90	8.08e-43	-	yes
PS	4	PO:0009001	fruit	186/200	1.89	2.02e-42	-	yes
PS	3	PO:0006342	infructescence	186/200	1.89	2.02e-42	-	yes
PS	3	PO:0009006	shoot	191/200	1.76	8.42e-41	-	yes
PS	5	PO:0009046	flower	186/200	1.79	3.81e-38	-	yes
PS	4	PO:0009049	inflorescence	186/200	1.78	1.08e-37	-	yes
PS	3	PO:0009005	root	164/200	1.82	5.90e-28	-	yes
PS	4	PO:0000293	guard cell	58/200	5.39	9.31e-28	-	yes
PS	4	PO:0000351	guard mother cell	58/200	5.37	1.17e-27	-	yes
PS	3	PO:0000070	meristemoid	58/200	5.36	1.28e-27	-	yes
PS	5	PO:0006016	leaf epidermis	58/200	5.22	5.17e-27	-	yes
PS	5	PO:0006035	shoot epidermis	58/200	5.18	7.43e-27	-	yes
PS	5	PO:0000349	epidermal initial	58/200	5.14	1.06e-26	-	yes
PS	4	PO:0004011	initial cell	58/200	5.11	1.48e-26	-	yes
PS	3	PO:0004010	meristematic cell	58/200	5.10	1.61e-26	-	yes
PS	3	PO:0004013	epidermal cell	58/200	4.86	1.89e-25	-	yes
PS	4	PO:0005679	epidermis	58/200	4.68	1.28e-24	-	yes
PS	3	PO:0009014	dermal tissue	58/200	4.68	1.31e-24	-	yes
PS	3	PO:0020091	male gametophyte	150/200	1.81	1.10e-22	-	yes

PG	4	PO:0001054	4 leaf senescence stage	184/200	2.39	8.27e-59	-	yes
PG	3	PO:0001050	leaf development stages	184/200	2.39	9.11e-59	-	yes
PG	5	PO:0001081	F mature embryo stage	183/200	2.30	5.75e-55	-	yes
PG	5	PO:0004507	D bilateral stage	184/200	2.23	1.51e-53	-	yes
PG	5	PO:0007133	leaf production	185/200	2.20	3.50e-53	-	yes
PG	4	PO:0007112	1 main shoot growth	185/200	2.20	3.64e-53	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	184/200	2.22	5.80e-53	-	yes
PG	3	PO:0007134	A vegetative growth	185/200	2.18	1.22e-52	-	yes
PG	5	PO:0001185	C globular stage	183/200	2.23	1.29e-52	-	yes
PG	4	PO:0007631	embryo development stages	185/200	2.05	5.90e-48	-	yes
PG	3	PO:0001170	seed development stages	185/200	2.05	1.26e-47	-	yes
PG	4	PO:0007616	4 anthesis	185/200	1.91	2.47e-42	-	yes
PG	5	PO:0007604	corolla developmental stages	185/200	1.87	5.52e-41	-	yes
PG	4	PO:0007600	3 floral organ development stages	187/200	1.84	7.01e-41	-	yes
PG	3	PO:0007615	flower development stages	187/200	1.79	9.19e-39	-	yes

KW	0	chloroplast	-	142/200	8.04	2.67e-104	1.97E-17	yes
KW	0	stroma	-	41/200	21.99	2.53e-44	-	yes
KW	0	thylakoid	-	25/200	11.74	1.15e-20	-	no
KW	0	defective	-	24/200	9.80	4.79e-18	-	no
KW	0	plastid	-	20/200	13.25	4.88e-18	3.64E-21	no
KW	0	envelope	-	22/200	9.63	1.53e-16	-	no
KW	0	embryonic	-	19/200	8.85	6.79e-14	-	no
KW	0	translation	-	27/200	5.45	1.49e-13	-	no
KW	0	ending	-	17/200	9.55	3.19e-13	-	no
KW	0	dormancy	-	17/200	8.97	9.14e-13	-	no
KW	0	ribosome	-	19/200	7.20	3.07e-12	-	no
KW	0	bacterial	-	14/200	9.27	4.09e-11	-	yes
KW	0	structural	-	19/200	5.42	4.71e-10	-	no
KW	0	components	-	13/200	8.01	1.19e-09	-	no
KW	0	ribosomal	-	16/200	5.30	1.22e-08	-	no
KW	0	synthetase	-	11/200	7.65	2.68e-08	-	no
KW	0	constituent	-	15/200	5.35	2.74e-08	-	no
KW	0	development	-	24/200	3.44	3.80e-08	2.18E-15	no
KW	0	biogenesis	-	10/200	7.36	1.41e-07	-	no
KW	0	alpha	-	23/200	3.15	3.45e-07	-	no
KW	0	nucleotide	-	21/200	3.30	4.84e-07	-	no
KW	0	embryo	-	22/200	3.17	5.52e-07	-	no
KW	0	recognition	-	11/200	5.00	2.53e-06	-	no
KW	0	biosynthetic	-	21/200	2.94	3.22e-06	-	yes
KW	0	phosphate	-	12/200	3.96	1.29e-05	5.94E-16	no
KW	0	terminal	-	38/200	1.97	1.60e-05	-	no
KW	0	conserved	-	29/200	2.14	3.47e-05	-	no
KW	0	biosynthesis	-	10/200	4.12	3.71e-05	3.75E-16	yes
KW	0	pentatricopeptide	-	11/200	3.79	4.01e-05	-	no
KW	0	motif	-	14/200	2.88	1.23e-04	-	no
KW	0	ipr002885	-	10/200	3.57	1.32e-04	-	no
KW	0	mitochondrion	-	15/200	2.73	1.39e-04	-	no
KW	0	synthase	-	13/200	2.96	1.48e-04	-	no
KW	0	ligase	-	12/200	3.07	1.68e-04	-	no
KW	0	membrane	-	44/200	1.65	2.49e-04	-	no
KW	0	class	-	14/200	2.34	1.08e-03	-	no
KW	0	process	-	34/200	1.66	1.15e-03	-	yes
KW	0	nucleic	-	14/200	2.14	2.52e-03	0	yes
KW	0	dependent	-	23/200	1.72	4.06e-03	2.39E-15	yes
KW	0	encodes	-	37/200	1.45	7.61e-03	-	no

(*1)	[B]:Biological process(Gene ontology), [C]:Cellular component(Gene ontology), [M]:Molecular function(Gene ontology), [PS]:Plant Structure(Plant ontology), [PG]:Growth and developmental stages(Plant ontology), [KW]:words found in gene description.
(*2)	([# of genes with the term] / [# of sampling (200)]) / ([# of genes with the term among whole genes] / [# of whole genes])
(*3)	P-values were calculated on hypergeometric distribution in which we found n genes with a annotation term during 200 highly correlated genes, while we had N genes with the term in the whole genes.
(*4)	PosMed is a system which serve a p-values showing a relationship between the gene and the annotation term based on literature information and Gene-Gene interaction suchas co-expression or protein-protein interactions.

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label http://www.w3.org/2000/01/rdf-schema#label