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
OMAT5P100160	0.915928	-	AT5G01410	RSR4 (REDUCED SUGAR RESPONSE 4)	-	-
OMAT4P001150	0.892754	-	AT4G02990	mitochondrial transcription termination factor family protein / mTERF family protein	-	-
OMAT4P002320	0.892447	-	AT4G09730	DEAD/DEAH box helicase, putative	-	-
OMAT1P003430	0.879883	-	AT1G09900	pentatricopeptide (PPR) repeat-containing protein	-	-
OMAT5P016430	0.878981	-	AT5G55580	mitochondrial transcription termination factor family protein / mTERF family protein	-	-
OMAT1P114500	0.871963	-	AT1G59990	DEAD/DEAH box helicase, putative (RH22)	-	-
OMAT3P007980	0.863419	-	AT3G20930	RNA recognition motif (RRM)-containing protein	-	-
OMAT5P102490	0.852814	-	AT5G09320	VPS9B	-	-
OMAT4P013950	0.848462	-	AT4G39960	DNAJ heat shock family protein	-	-
OMAT4P000945	0.844665	-	AT4G02510	TOC159 (TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 159)	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT4P109980	-0.798452	-	AT4G34180	cyclase family protein	-	-
OMAT1P018280	-0.765957	-	AT1G65840	ATPAO4 (ARABIDOPSIS THALIANA POLYAMINE OXIDASE 4)	-	-
OMAT4P101420	-0.757168	-	AT4G05050	UBQ11 (UBIQUITIN 11)	-	-
OMAT1P109920	-0.755565	-	AT1G31470	NFD4 (NUCLEAR FUSION DEFECTIVE 4)	-	-
OMAT1P108430	-0.726764	-	AT1G26930	kelch repeat-containing F-box family protein	-	-
OMAT5P011130	-0.720888	-	AT5G40730	AGP24	-	-
OMAT4P011060	-0.717064	-	AT4G32870	unknown protein	-	-
OMAT1P119520	-0.712594	-	AT1G75620	glyoxal oxidase-related	-	-
OMAT2P011160	-0.711165	-	AT2G41380	embryo-abundant protein-related	-	-
OMAT2P107530	-0.708963	-	AT2G34140	Dof-type zinc finger domain-containing protein	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 6.47e-32	:20 terms with high significance
6.47e-32 <	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	5	GO:0006396	RNA processing	16/200	7.23	1.13e-10	3.82E-16	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	43/200	2.21	1.96e-07	-	no
B	3	GO:0006807	nitrogen compound metabolic process	43/200	2.17	3.39e-07	-	no
B	5	GO:0016070	RNA metabolic process	24/200	2.82	1.50e-06	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	35/200	2.07	1.17e-05	-	no
B	5	GO:0090304	nucleic acid metabolic process	32/200	2.13	1.61e-05	-	no
B	5	GO:0010154	fruit development	11/200	3.85	3.41e-05	-	yes
B	3	GO:0006996	organelle organization	12/200	3.60	3.51e-05	-	no
B	3	GO:0009790	embryonic development	10/200	3.79	7.81e-05	1.57E-16	yes
B	5	GO:0044271	cellular nitrogen compound biosynthetic process	10/200	3.78	7.97e-05	-	no
B	3	GO:0048316	seed development	10/200	3.67	1.03e-04	6.94E-18	yes
B	3	GO:0009791	post-embryonic development	16/200	2.70	1.03e-04	5.85E-19	yes
B	3	GO:0044237	cellular metabolic process	68/200	1.44	3.19e-04	-	no
B	4	GO:0048608	reproductive structure development	13/200	2.67	4.29e-04	-	yes
B	3	GO:0003006	reproductive developmental process	14/200	2.54	4.65e-04	-	yes
B	3	GO:0007275	multicellular organismal development	21/200	1.98	1.02e-03	-	yes
B	3	GO:0022414	reproductive process	14/200	2.32	1.15e-03	-	yes
B	5	GO:0043436	oxoacid metabolic process	11/200	2.50	1.69e-03	-	no
B	4	GO:0006082	organic acid metabolic process	11/200	2.49	1.73e-03	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	51/200	1.45	1.90e-03	-	no
B	4	GO:0042180	cellular ketone metabolic process	11/200	2.45	1.98e-03	-	no
B	4	GO:0044283	small molecule biosynthetic process	11/200	2.42	2.18e-03	-	no
B	3	GO:0043170	macromolecule metabolic process	54/200	1.40	3.16e-03	-	no
B	3	GO:0044238	primary metabolic process	66/200	1.33	3.41e-03	-	no
B	4	GO:0010467	gene expression	32/200	1.57	3.73e-03	1.77E-15	no
B	3	GO:0048856	anatomical structure development	17/200	1.90	3.97e-03	-	yes
B	3	GO:0044281	small molecule metabolic process	17/200	1.89	4.13e-03	-	no
B	3	GO:0009628	response to abiotic stimulus	14/200	1.89	7.85e-03	-	no

C	5	GO:0009536	plastid	87/200	4.71	1.82e-38	3.64E-21	yes
C	3	GO:0005622	intracellular	132/200	2.48	3.71e-32	6.67E-11	yes
C	3	GO:0044424	intracellular part	125/200	2.45	4.33e-29	6.67E-11	yes
C	4	GO:0005737	cytoplasm	107/200	2.86	4.91e-29	6.67E-11	yes
C	4	GO:0044444	cytoplasmic part	103/200	2.97	5.38e-29	-	yes
C	3	GO:0043229	intracellular organelle	118/200	2.56	2.02e-28	-	yes
C	4	GO:0043231	intracellular membrane-bounded organelle	115/200	2.62	2.20e-28	-	yes
C	3	GO:0043227	membrane-bounded organelle	115/200	2.62	2.22e-28	-	yes
C	4	GO:0044435	plastid part	31/200	5.45	2.55e-15	-	no
C	3	GO:0044464	cell part	141/200	1.54	3.78e-13	6.67E-11	yes
C	5	GO:0044434	chloroplast part	26/200	4.69	1.26e-11	6.67E-11	no
C	5	GO:0009532	plastid stroma	17/200	6.88	7.47e-11	6.67E-11	no
C	5	GO:0009526	plastid envelope	16/200	5.82	3.03e-09	6.67E-11	no
C	3	GO:0044446	intracellular organelle part	38/200	2.65	9.30e-09	-	no
C	3	GO:0044422	organelle part	38/200	2.65	9.51e-09	-	no
C	4	GO:0031967	organelle envelope	18/200	4.32	4.77e-08	6.67E-11	no
C	3	GO:0031975	envelope	18/200	4.32	4.77e-08	6.67E-11	no
C	5	GO:0005739	mitochondrion	18/200	2.81	2.57e-05	2.85E-12	no
C	3	GO:0043228	non-membrane-bounded organelle	17/200	2.85	3.39e-05	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	17/200	2.85	3.39e-05	-	no
C	4	GO:0009579	thylakoid	10/200	4.02	4.63e-05	6.67E-11	no

M	3	GO:0003676	nucleic acid binding	49/200	2.07	2.03e-07	-	no
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	16/200	3.60	2.80e-06	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	16/200	3.56	3.17e-06	-	no
M	5	GO:0032555	purine ribonucleotide binding	23/200	2.34	5.07e-05	-	no
M	4	GO:0032553	ribonucleotide binding	23/200	2.34	5.07e-05	-	no
M	3	GO:0016787	hydrolase activity	31/200	1.98	8.29e-05	-	no
M	4	GO:0017076	purine nucleotide binding	23/200	2.22	1.20e-04	-	no
M	3	GO:0000166	nucleotide binding	26/200	1.97	3.27e-04	-	no
M	4	GO:0003723	RNA binding	16/200	2.31	6.50e-04	0	no

PS	5	PO:0020038	petiole	166/200	2.18	4.80e-40	-	yes
PS	5	PO:0000013	cauline leaf	165/200	2.14	3.33e-38	9.45E-20	yes
PS	4	PO:0000037	shoot apex	172/200	2.00	1.52e-37	-	yes
PS	5	PO:0020039	leaf lamina	168/200	2.04	9.99e-37	-	yes
PS	5	PO:0009052	pedicel	164/200	2.02	3.97e-34	-	yes
PS	4	PO:0020030	cotyledon	155/200	2.11	7.06e-33	4.99E-18	yes
PS	5	PO:0008037	seedling	168/200	1.90	2.40e-32	6.67E-11	yes
PS	4	PO:0009025	leaf	170/200	1.85	2.01e-31	4.19E-17	yes
PS	4	PO:0009047	stem	163/200	1.93	4.69e-31	-	yes
PS	3	PO:0009032	petal	165/200	1.88	2.48e-30	-	yes
PS	3	PO:0009031	sepal	168/200	1.82	1.71e-29	-	yes
PS	4	PO:0009009	embryo	171/200	1.77	4.38e-29	0	yes
PS	5	PO:0008034	leaf whorl	169/200	1.79	5.29e-29	-	yes
PS	4	PO:0008033	phyllome whorl	169/200	1.79	5.29e-29	-	yes
PS	5	PO:0009028	microsporophyll	159/200	1.90	2.54e-28	-	yes
PS	3	PO:0009010	seed	171/200	1.75	2.71e-28	3.72E-17	yes
PS	5	PO:0009027	megasporophyll	159/200	1.89	2.98e-28	-	yes
PS	4	PO:0009001	fruit	171/200	1.74	5.81e-28	-	yes
PS	3	PO:0006342	infructescence	171/200	1.74	5.81e-28	-	yes
PS	4	PO:0009026	sporophyll	163/200	1.81	3.45e-27	-	yes
PS	3	PO:0006001	phyllome	172/200	1.68	4.25e-26	-	yes
PS	4	PO:0000230	inflorescence meristem	149/200	1.92	2.17e-25	-	yes
PS	5	PO:0009046	flower	172/200	1.65	3.44e-25	1.90E-12	yes
PS	3	PO:0009013	meristem	151/200	1.88	5.47e-25	-	yes
PS	4	PO:0009049	inflorescence	172/200	1.64	8.18e-25	-	yes
PS	3	PO:0009005	root	159/200	1.77	2.55e-24	2.85E-12	yes
PS	3	PO:0009006	shoot	173/200	1.59	2.85e-23	-	yes
PS	3	PO:0020091	male gametophyte	123/200	1.48	3.59e-09	-	yes
PS	4	PO:0000293	guard cell	26/200	2.42	1.04e-05	-	no
PS	4	PO:0000351	guard mother cell	26/200	2.41	1.13e-05	-	no
PS	3	PO:0000070	meristemoid	26/200	2.40	1.16e-05	-	no
PS	5	PO:0006016	leaf epidermis	26/200	2.34	1.87e-05	-	no
PS	5	PO:0006035	shoot epidermis	26/200	2.32	2.12e-05	-	no
PS	5	PO:0000349	epidermal initial	26/200	2.31	2.39e-05	-	no
PS	4	PO:0004011	initial cell	26/200	2.29	2.67e-05	-	no
PS	3	PO:0004010	meristematic cell	26/200	2.29	2.74e-05	-	no
PS	3	PO:0004013	epidermal cell	26/200	2.18	6.23e-05	-	no
PS	4	PO:0005679	epidermis	26/200	2.10	1.16e-04	-	no
PS	3	PO:0009014	dermal tissue	26/200	2.10	1.17e-04	-	no

PG	5	PO:0001081	F mature embryo stage	169/200	2.12	5.87e-40	6.67E-11	yes
PG	5	PO:0001078	E expanded cotyledon stage	169/200	2.04	3.58e-37	-	yes
PG	5	PO:0004507	D bilateral stage	168/200	2.04	9.06e-37	1.57E-17	yes
PG	3	PO:0007134	A vegetative growth	170/200	2.01	9.67e-37	6.27E-18	yes
PG	4	PO:0001054	4 leaf senescence stage	163/200	2.12	1.01e-36	-	yes
PG	3	PO:0001050	leaf development stages	163/200	2.12	1.09e-36	7.56E-19	yes
PG	5	PO:0007133	leaf production	169/200	2.01	2.66e-36	4.07E-18	yes
PG	4	PO:0007112	1 main shoot growth	169/200	2.01	2.75e-36	-	yes
PG	5	PO:0001185	C globular stage	166/200	2.02	2.92e-35	6.67E-11	yes
PG	4	PO:0007631	embryo development stages	169/200	1.88	6.47e-32	1.98E-17	yes
PG	3	PO:0001170	seed development stages	169/200	1.87	1.22e-31	-	yes
PG	5	PO:0007604	corolla developmental stages	171/200	1.73	1.02e-27	-	yes
PG	4	PO:0007616	4 anthesis	168/200	1.73	1.74e-26	-	yes
PG	4	PO:0007600	3 floral organ development stages	171/200	1.68	9.90e-26	-	yes
PG	3	PO:0007615	flower development stages	171/200	1.63	5.21e-24	-	yes

KW	0	chloroplast	-	87/200	4.93	5.52e-40	1.97E-17	yes
KW	0	pentatricopeptide	-	21/200	7.23	2.38e-13	-	no
KW	0	ipr002885	-	20/200	7.14	1.05e-12	-	no
KW	0	plastid	-	13/200	8.61	4.60e-10	3.64E-21	no
KW	0	envelope	-	13/200	5.69	8.83e-08	6.67E-11	no
KW	0	nucleic	-	22/200	3.37	1.92e-07	-	no
KW	0	defective	-	13/200	5.31	2.04e-07	0	yes
KW	0	processing	-	10/200	7.05	2.18e-07	3.82E-16	no
KW	0	stroma	-	11/200	5.90	4.47e-07	6.67E-11	no
KW	0	mitochondrion	-	16/200	2.92	4.10e-05	2.85E-12	no
KW	0	development	-	18/200	2.58	8.12e-05	2.18E-15	no
KW	0	containing	-	32/200	1.92	1.22e-04	3.00E-23	no
KW	0	dependent	-	27/200	2.02	1.74e-04	6.67E-11	no
KW	0	embryo	-	17/200	2.45	2.31e-04	0	yes
KW	0	terminal	-	34/200	1.76	3.86e-04	6.67E-11	no
KW	0	biosynthetic	-	15/200	2.10	2.33e-03	-	no
KW	0	factor	-	29/200	1.66	2.57e-03	6.67E-11	no
KW	0	repeat	-	23/200	1.77	2.74e-03	3.00E-23	yes
KW	0	process	-	32/200	1.56	4.10e-03	6.67E-11	no
KW	0	translation	-	11/200	2.22	4.40e-03	6.67E-11	no
KW	0	intracellular	-	11/200	2.13	6.01e-03	6.67E-11	no
KW	0	putative	-	34/200	1.47	8.00e-03	6.67E-11	no
KW	0	conserved	-	22/200	1.63	9.07e-03	6.67E-11	no
KW	0	expression	-	10/200	2.07	9.78e-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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