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
AT4G38270.1	0.950161	GAUT3 (Galacturonosyltransferase 3)	OMAT4P013330	-	-	-
AT3G51270.1	0.93854	ATP binding / catalytic/ protein serine/threonine kinase	OMAT3P013680	-	-	-
AT5G05540.1	0.929308	SDN2 (SMALL RNA DEGRADING NUCLEASE 2)	OMAT5P001810	-	-	-
AT3G52140.1	0.926318	tetratricopeptide repeat (TPR)-containing protein	OMAT3P014080,OMAT3P014085	[OMAT3P014080]-, [OMAT3P014085]-	-	-
AT5G26180.1	0.922018	NOL1/NOP2/sun family protein	OMAT5P008900	-	-	-
AT3G22330.1	0.921385	PMH2 (putative mitochondrial RNA helicase 2)	OMAT3P008410	-	-	-
AT1G01920.1	0.921335	SET domain-containing protein	-	-	-	-
AT5G50310.1	0.913992	kelch repeat-containing protein	OMAT5P014460	-	-	-
AT4G00660.2	0.910923	DEAD/DEAH box helicase, putative	OMAT4P000200	-	-	-
AT1G17470.1	0.909878	ATDRG1 (ARABIDOPSIS THALIANA DEVELOPMENTALLY REGULATED G-PROTEIN 1)	OMAT1P006470	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT3G54890.1	-0.759051	LHCA1	OMAT3P113280,OMAT3P113282	[OMAT3P113280]-, [OMAT3P113282]-	OMAT3P015090	-
AT5G36160.1	-0.755123	aminotransferase-related	OMAT5P108800	-	-	-
AT1G36756.1	-0.754652	unknown protein	-	-	-	-
AT5G54770.1	-0.75182	THI1	OMAT5P016150	-	OMAT5P114270	-
AT1G61520.1	-0.737396	LHCA3	OMAT1P016710	-	OMAT1P114900	-
AT1G37669.1	-0.734118	transposable element gene	-	-	-	-
AT4G05180.1	-0.730999	PSBQ-2	OMAT4P101480	-	-	-
AT2G07715.1	-0.729323	ribosomal protein L2, putative	-	-	-	-
AT4G10340.1	-0.729113	LHCB5 (LIGHT HARVESTING COMPLEX OF PHOTOSYSTEM II 5)	OMAT4P002520	-	-	-
AT1G18360.1	-0.725945	hydrolase, alpha/beta fold family protein	OMAT1P105920	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 7.84e-20	:20 terms with high significance
7.84e-20 <	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	13/200	5.87	5.95e-08	-	no
B	5	GO:0016070	RNA metabolic process	23/200	2.70	4.95e-06	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	58/200	1.65	2.46e-05	-	no
B	5	GO:0090304	nucleic acid metabolic process	31/200	2.06	4.00e-05	-	no
B	4	GO:0010467	gene expression	38/200	1.87	5.40e-05	-	no
B	3	GO:0043170	macromolecule metabolic process	61/200	1.58	5.43e-05	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	33/200	1.96	6.70e-05	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	35/200	1.80	2.19e-04	-	no
B	3	GO:0006807	nitrogen compound metabolic process	35/200	1.76	3.19e-04	-	no
B	3	GO:0044238	primary metabolic process	67/200	1.35	2.12e-03	-	no
B	5	GO:0006412	translation	15/200	2.07	2.70e-03	8.00E-05	no
B	3	GO:0044237	cellular metabolic process	63/200	1.33	4.17e-03	-	no

C	3	GO:0005622	intracellular	95/200	1.78	7.41e-11	-	no
C	5	GO:0005739	mitochondrion	25/200	3.91	1.52e-09	-	no
C	3	GO:0043229	intracellular organelle	80/200	1.73	2.86e-08	-	no
C	3	GO:0044424	intracellular part	85/200	1.67	4.91e-08	-	no
C	4	GO:0044428	nuclear part	16/200	4.81	4.95e-08	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	76/200	1.73	8.40e-08	-	no
C	3	GO:0043227	membrane-bounded organelle	76/200	1.73	8.45e-08	-	no
C	5	GO:0005634	nucleus	36/200	2.30	7.76e-07	3.64E-21	no
C	5	GO:0031981	nuclear lumen	12/200	4.96	1.12e-06	-	no
C	5	GO:0005730	nucleolus	10/200	5.83	1.40e-06	-	no
C	4	GO:0070013	intracellular organelle lumen	12/200	4.42	3.94e-06	-	no
C	3	GO:0043233	organelle lumen	12/200	4.41	4.04e-06	-	no
C	4	GO:0005737	cytoplasm	57/200	1.52	2.67e-04	-	no
C	3	GO:0043228	non-membrane-bounded organelle	15/200	2.52	3.52e-04	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	15/200	2.52	3.52e-04	-	no
C	3	GO:0044446	intracellular organelle part	24/200	1.67	4.76e-03	-	no
C	3	GO:0044422	organelle part	24/200	1.67	4.81e-03	-	no
C	4	GO:0044444	cytoplasmic part	48/200	1.38	6.50e-03	-	no

M	3	GO:0003676	nucleic acid binding	56/200	2.36	1.55e-10	2.00E-12	yes
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	15/200	3.37	1.18e-05	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	15/200	3.34	1.32e-05	-	no
M	5	GO:0032555	purine ribonucleotide binding	21/200	2.14	3.58e-04	-	no
M	4	GO:0032553	ribonucleotide binding	21/200	2.14	3.58e-04	-	no
M	3	GO:0000166	nucleotide binding	25/200	1.89	7.44e-04	1.00E-05	yes
M	4	GO:0017076	purine nucleotide binding	21/200	2.02	7.54e-04	-	no
M	3	GO:0016787	hydrolase activity	28/200	1.79	9.16e-04	-	no
M	4	GO:0003723	RNA binding	15/200	2.16	1.74e-03	3.00E-121	yes
M	5	GO:0030554	adenyl nucleotide binding	18/200	1.99	1.92e-03	-	no
M	4	GO:0001883	purine nucleoside binding	18/200	1.99	1.92e-03	-	no
M	3	GO:0001882	nucleoside binding	18/200	1.98	1.98e-03	-	no
M	4	GO:0016788	hydrolase activity, acting on ester bonds	13/200	2.19	2.76e-03	-	no

PS	5	PO:0009052	pedicel	156/200	1.92	7.37e-28	-	yes
PS	4	PO:0000037	shoot apex	159/200	1.85	7.56e-27	-	yes
PS	5	PO:0000013	cauline leaf	144/200	1.86	2.04e-22	-	yes
PS	3	PO:0009005	root	156/200	1.73	2.65e-22	-	yes
PS	5	PO:0008037	seedling	153/200	1.73	2.16e-21	-	yes
PS	5	PO:0020038	petiole	141/200	1.85	2.88e-21	-	yes
PS	4	PO:0009047	stem	149/200	1.77	3.42e-21	-	yes
PS	4	PO:0009025	leaf	156/200	1.70	3.74e-21	-	yes
PS	5	PO:0020039	leaf lamina	147/200	1.78	4.14e-21	-	yes
PS	3	PO:0009031	sepal	156/200	1.69	6.46e-21	-	yes
PS	4	PO:0009009	embryo	159/200	1.65	2.03e-20	-	yes
PS	5	PO:0008034	leaf whorl	156/200	1.65	7.84e-20	-	yes
PS	4	PO:0008033	phyllome whorl	156/200	1.65	7.84e-20	-	yes
PS	3	PO:0009010	seed	159/200	1.63	9.42e-20	-	yes
PS	4	PO:0009001	fruit	159/200	1.62	1.79e-19	-	yes
PS	3	PO:0006342	infructescence	159/200	1.62	1.79e-19	-	yes
PS	3	PO:0009013	meristem	142/200	1.77	2.38e-19	-	yes
PS	5	PO:0009027	megasporophyll	145/200	1.73	4.92e-19	-	yes
PS	3	PO:0009032	petal	148/200	1.69	1.00e-18	-	yes
PS	4	PO:0000230	inflorescence meristem	138/200	1.78	1.36e-18	-	yes
PS	3	PO:0006001	phyllome	159/200	1.55	2.85e-17	-	yes
PS	4	PO:0009026	sporophyll	147/200	1.63	6.59e-17	-	yes
PS	5	PO:0009028	microsporophyll	141/200	1.68	7.26e-17	-	yes
PS	5	PO:0009046	flower	159/200	1.53	1.57e-16	-	yes
PS	4	PO:0009049	inflorescence	159/200	1.52	3.18e-16	-	yes
PS	4	PO:0020030	cotyledon	128/200	1.74	1.26e-15	-	yes
PS	3	PO:0009006	shoot	161/200	1.48	1.81e-15	-	yes
PS	3	PO:0000084	sperm cell	72/200	2.22	2.77e-12	-	yes
PS	3	PO:0020097	generative cell	72/200	2.22	2.77e-12	-	yes
PS	3	PO:0020091	male gametophyte	123/200	1.48	3.59e-09	-	yes
PS	4	PO:0005679	epidermis	23/200	1.86	1.48e-03	-	no
PS	3	PO:0009014	dermal tissue	23/200	1.86	1.49e-03	-	no
PS	3	PO:0004013	epidermal cell	22/200	1.84	1.98e-03	-	no
PS	4	PO:0000293	guard cell	20/200	1.86	2.70e-03	-	no
PS	4	PO:0000351	guard mother cell	20/200	1.85	2.84e-03	-	no
PS	3	PO:0000070	meristemoid	20/200	1.85	2.90e-03	-	no
PS	5	PO:0006016	leaf epidermis	20/200	1.80	3.95e-03	-	no
PS	5	PO:0006035	shoot epidermis	20/200	1.79	4.28e-03	-	no
PS	5	PO:0000349	epidermal initial	20/200	1.77	4.63e-03	-	no
PS	4	PO:0004011	initial cell	20/200	1.76	4.98e-03	-	no
PS	3	PO:0004010	meristematic cell	20/200	1.76	5.06e-03	-	no

PG	5	PO:0001081	F mature embryo stage	157/200	1.97	7.66e-30	-	yes
PG	5	PO:0004507	D bilateral stage	158/200	1.92	1.34e-28	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	158/200	1.90	3.65e-28	-	yes
PG	4	PO:0007631	embryo development stages	158/200	1.75	1.35e-23	-	yes
PG	3	PO:0001170	seed development stages	158/200	1.75	2.34e-23	-	yes
PG	5	PO:0001185	C globular stage	150/200	1.83	3.13e-23	-	yes
PG	4	PO:0001054	4 leaf senescence stage	141/200	1.83	8.70e-21	-	yes
PG	3	PO:0001050	leaf development stages	141/200	1.83	9.22e-21	-	yes
PG	5	PO:0007133	leaf production	146/200	1.74	1.59e-19	-	yes
PG	4	PO:0007112	1 main shoot growth	146/200	1.74	1.63e-19	-	yes
PG	3	PO:0007134	A vegetative growth	146/200	1.72	3.45e-19	-	yes
PG	4	PO:0007616	4 anthesis	157/200	1.62	5.47e-19	-	yes
PG	4	PO:0007600	3 floral organ development stages	161/200	1.58	8.13e-19	-	yes
PG	5	PO:0007604	corolla developmental stages	158/200	1.60	1.17e-18	-	yes
PG	3	PO:0007615	flower development stages	161/200	1.54	2.42e-17	-	yes

KW	0	ipr002885	-	24/200	8.56	1.15e-16	-	no
KW	0	pentatricopeptide	-	24/200	8.26	2.64e-16	-	no
KW	0	nucleic	-	32/200	4.89	1.91e-14	2.00E-12	yes
KW	0	ipr014001	-	14/200	15.31	2.79e-14	-	no
KW	0	ipr014021	-	13/200	14.91	2.80e-13	-	no
KW	0	containing	-	50/200	3.00	3.10e-13	0	yes
KW	0	ipr001650	-	13/200	14.51	4.08e-13	-	no
KW	0	helicase	-	15/200	9.63	5.44e-12	-	no
KW	0	mitochondrion	-	24/200	4.38	3.13e-10	-	no
KW	0	ipr016024	-	13/200	7.04	6.16e-09	-	no
KW	0	armadillo	-	13/200	6.95	7.26e-09	-	no
KW	0	processing	-	11/200	7.75	2.33e-08	-	no
KW	0	repeat	-	34/200	2.62	7.66e-08	-	no
KW	0	translational	-	10/200	7.77	8.12e-08	-	no
KW	0	nucleolus	-	10/200	7.36	1.41e-07	-	no
KW	0	polymerase	-	10/200	6.79	3.17e-07	-	no
KW	0	motif	-	18/200	3.70	5.00e-07	0	yes
KW	0	terminal	-	40/200	2.08	2.70e-06	-	no
KW	0	superfamily	-	14/200	3.70	7.19e-06	-	no
KW	0	translation	-	15/200	3.03	4.30e-05	8.00E-05	no
KW	0	nuclear	-	10/200	3.25	2.91e-04	-	no
KW	0	cytoplasm	-	10/200	3.23	3.11e-04	-	no
KW	0	dependent	-	26/200	1.94	4.06e-04	-	no
KW	0	subunit	-	17/200	2.32	4.39e-04	1.00E-06	no
KW	0	nucleus	-	25/200	1.94	5.26e-04	3.64E-21	no
KW	0	embryo	-	16/200	2.30	6.56e-04	-	no
KW	0	putative	-	38/200	1.65	7.17e-04	-	no
KW	0	intracellular	-	13/200	2.52	7.43e-04	-	no
KW	0	cellular_component	-	65/200	1.33	3.56e-03	-	yes
KW	0	conserved	-	23/200	1.70	4.63e-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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