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
AT5G64420.1	0.966275	DNA polymerase V family	OMAT5P019830	-	-	-
AT1G64185.1	0.961442	lactoylglutathione lyase family protein / glyoxalase I family protein	OMAT1P017625	-	-	-
AT1G52980.1	0.960096	GTP-binding family protein	OMAT1P014610	-	-	-
AT5G41970.1	0.959774	FUNCTIONS IN: molecular_function unknown	OMAT5P011550	-	-	-
AT5G20130.1	0.959683	unknown protein	OMAT5P006990	-	-	-
AT1G50920.1	0.950846	GTP-binding protein-related	OMAT1P014030	-	OMAT1P112405	-
AT3G11070.1	0.949179	outer membrane OMP85 family protein	OMAT3P003870	-	-	-
AT4G22670.1	0.946081	AtHip1 (Arabidopsis thaliana Hsp70-interacting protein 1)	OMAT4P006910	-	-	-
AT2G44065.1	0.944328	ribosomal protein L2 family protein	OMAT2P012150	-	-	-
AT3G13230.1	0.944052	RNA binding	OMAT3P004640	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G17170.1	-0.779007	RABB1C (ARABIDOPSIS RAB GTPASE HOMOLOG B1C)	OMAT4P104230	-	-	-
AT5G45350.1	-0.773006	proline-rich family protein	OMAT5P111240	-	-	-
AT5G02380.1	-0.766466	MT2B (METALLOTHIONEIN 2B)	OMAT5P100430	-	-	-
AT3G47540.1	-0.762722	chitinase, putative	OMAT3P012300	-	-	-
AT2G40880.1	-0.754	ATCYSA (CYSTATIN A)	OMAT2P010940	-	OMAT2P110180	-
AT1G07600.1	-0.748025	MT1A (METALLOTHIONEIN 1A)	OMAT1P102300	-	-	-
AT4G25650.2	-0.728163	ACD1-LIKE (ACD1-LIKE)	OMAT4P107010	-	-	-
AT3G53990.1	-0.727725	universal stress protein (USP) family protein	OMAT3P112910	-	-	-
AT2G23810.1	-0.719659	TET8 (TETRASPANIN8)	OMAT2P104250	-	OMAT2P004810,OMAT2P004820	[OMAT2P004810]-, [OMAT2P004820]-
AT2G06620.1	-0.719057	transposable element gene	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 4.67e-23	:20 terms with high significance
4.67e-23 <	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	18/200	8.13	1.25e-12	-	no
B	4	GO:0042254	ribosome biogenesis	12/200	9.37	6.53e-10	-	no
B	3	GO:0022613	ribonucleoprotein complex biogenesis	12/200	9.07	9.70e-10	-	no
B	4	GO:0010467	gene expression	48/200	2.36	4.32e-09	-	no
B	5	GO:0006412	translation	26/200	3.58	4.63e-09	-	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	3	GO:0043170	macromolecule metabolic process	59/200	1.52	1.94e-04	-	no
B	3	GO:0044237	cellular metabolic process	68/200	1.44	3.19e-04	-	no
B	3	GO:0044238	primary metabolic process	69/200	1.39	7.71e-04	-	no
B	5	GO:0044267	cellular protein metabolic process	34/200	1.67	1.07e-03	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	32/200	1.64	1.82e-03	-	no
B	5	GO:0090304	nucleic acid metabolic process	26/200	1.73	2.23e-03	-	no
B	3	GO:0006807	nitrogen compound metabolic process	32/200	1.61	2.50e-03	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	28/200	1.66	2.92e-03	-	no
B	4	GO:0019538	protein metabolic process	35/200	1.52	4.56e-03	-	no

C	3	GO:0043228	non-membrane-bounded organelle	37/200	6.21	6.45e-20	-	yes
C	4	GO:0043232	intracellular non-membrane-bounded organelle	37/200	6.21	6.45e-20	-	yes
C	4	GO:0070013	intracellular organelle lumen	24/200	8.85	5.36e-17	-	yes
C	3	GO:0043233	organelle lumen	24/200	8.83	5.65e-17	-	yes
C	3	GO:0005622	intracellular	108/200	2.03	5.78e-17	-	yes
C	5	GO:0005730	nucleolus	20/200	11.67	6.55e-17	-	yes
C	3	GO:0044424	intracellular part	105/200	2.06	8.01e-17	-	yes
C	3	GO:0030529	ribonucleoprotein complex	25/200	7.17	1.99e-15	-	no
C	5	GO:0031981	nuclear lumen	21/200	8.69	5.78e-15	-	yes
C	4	GO:0005737	cytoplasm	83/200	2.22	2.24e-14	-	no
C	3	GO:0043229	intracellular organelle	94/200	2.04	3.07e-14	-	yes
C	4	GO:0044428	nuclear part	22/200	6.61	4.34e-13	-	yes
C	4	GO:0005840	ribosome	19/200	7.42	1.78e-12	-	no
C	5	GO:0005739	mitochondrion	29/200	4.53	2.16e-12	-	no
C	4	GO:0044444	cytoplasmic part	74/200	2.13	8.99e-12	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	84/200	1.91	6.04e-11	-	yes
C	3	GO:0043227	membrane-bounded organelle	84/200	1.91	6.08e-11	-	yes
C	3	GO:0044446	intracellular organelle part	38/200	2.65	9.30e-09	-	yes
C	3	GO:0044422	organelle part	38/200	2.65	9.51e-09	-	yes
C	4	GO:0033279	ribosomal subunit	10/200	6.16	8.27e-07	-	no
C	5	GO:0022626	cytosolic ribosome	10/200	5.43	2.78e-06	-	no
C	5	GO:0005634	nucleus	32/200	2.05	3.55e-05	3.64E-21	yes
C	3	GO:0044464	cell part	118/200	1.29	6.19e-05	-	yes
C	5	GO:0005829	cytosol	11/200	2.66	1.00e-03	-	no
C	3	GO:0043234	protein complex	14/200	2.14	2.55e-03	1.00E-06	no
C	5	GO:0009536	plastid	29/200	1.57	5.56e-03	-	no

M	3	GO:0003735	structural constituent of ribosome	17/200	7.85	8.51e-12	-	no
M	4	GO:0003723	RNA binding	28/200	4.03	8.12e-11	1.00E-11	no
M	3	GO:0003676	nucleic acid binding	49/200	2.07	2.03e-07	-	no
M	3	GO:0000166	nucleotide binding	31/200	2.35	2.99e-06	1.00E-11	yes
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	11/200	2.47	1.85e-03	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	11/200	2.45	2.00e-03	-	no
M	5	GO:0032555	purine ribonucleotide binding	19/200	1.94	2.09e-03	-	no
M	4	GO:0032553	ribonucleotide binding	19/200	1.94	2.09e-03	-	no
M	4	GO:0017076	purine nucleotide binding	19/200	1.83	3.93e-03	-	no

PS	4	PO:0000037	shoot apex	163/200	1.89	7.25e-30	-	yes
PS	5	PO:0020038	petiole	153/200	2.01	2.56e-29	-	yes
PS	5	PO:0009052	pedicel	156/200	1.92	7.37e-28	-	yes
PS	4	PO:0009025	leaf	163/200	1.77	6.25e-26	-	yes
PS	5	PO:0020039	leaf lamina	154/200	1.87	1.11e-25	-	yes
PS	4	PO:0009047	stem	154/200	1.83	1.98e-24	-	yes
PS	5	PO:0000013	cauline leaf	147/200	1.90	2.40e-24	-	yes
PS	3	PO:0009005	root	159/200	1.77	2.55e-24	-	yes
PS	3	PO:0009032	petal	155/200	1.77	4.67e-23	-	yes
PS	3	PO:0009031	sepal	159/200	1.72	7.16e-23	-	yes
PS	5	PO:0009028	microsporophyll	151/200	1.80	9.23e-23	-	yes
PS	5	PO:0008037	seedling	155/200	1.76	1.12e-22	-	yes
PS	4	PO:0009026	sporophyll	156/200	1.73	2.72e-22	-	yes
PS	3	PO:0009013	meristem	146/200	1.82	9.59e-22	-	yes
PS	5	PO:0008034	leaf whorl	159/200	1.69	9.76e-22	-	yes
PS	4	PO:0008033	phyllome whorl	159/200	1.69	9.76e-22	-	yes
PS	3	PO:0006001	phyllome	166/200	1.62	1.06e-21	-	yes
PS	4	PO:0000230	inflorescence meristem	142/200	1.83	6.49e-21	-	yes
PS	5	PO:0009027	megasporophyll	148/200	1.76	8.15e-21	-	yes
PS	3	PO:0009010	seed	160/200	1.64	2.20e-20	-	yes
PS	4	PO:0009001	fruit	160/200	1.63	4.22e-20	-	yes
PS	3	PO:0006342	infructescence	160/200	1.63	4.22e-20	-	yes
PS	4	PO:0009009	embryo	158/200	1.64	8.62e-20	-	yes
PS	4	PO:0020030	cotyledon	135/200	1.84	2.25e-19	-	yes
PS	3	PO:0009006	shoot	167/200	1.54	4.40e-19	-	yes
PS	5	PO:0009046	flower	162/200	1.56	2.65e-18	-	yes
PS	4	PO:0009049	inflorescence	162/200	1.55	5.56e-18	-	yes
PS	3	PO:0020091	male gametophyte	127/200	1.53	1.01e-10	-	yes
PS	3	PO:0000084	sperm cell	52/200	1.60	1.45e-04	-	yes
PS	3	PO:0020097	generative cell	52/200	1.60	1.45e-04	-	yes
PS	4	PO:0000351	guard mother cell	21/200	1.94	1.27e-03	-	yes
PS	3	PO:0000070	meristemoid	21/200	1.94	1.29e-03	-	yes
PS	5	PO:0006016	leaf epidermis	21/200	1.89	1.81e-03	-	yes
PS	5	PO:0006035	shoot epidermis	21/200	1.88	1.98e-03	-	yes
PS	3	PO:0004013	epidermal cell	22/200	1.84	1.98e-03	-	yes
PS	5	PO:0000349	epidermal initial	21/200	1.86	2.15e-03	-	yes
PS	4	PO:0004011	initial cell	21/200	1.85	2.33e-03	-	yes
PS	3	PO:0004010	meristematic cell	21/200	1.85	2.37e-03	-	yes
PS	4	PO:0005679	epidermis	22/200	1.78	3.17e-03	-	yes
PS	3	PO:0009014	dermal tissue	22/200	1.78	3.19e-03	-	yes

PG	5	PO:0001081	F mature embryo stage	156/200	1.96	4.33e-29	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	159/200	1.92	6.52e-29	-	yes
PG	5	PO:0004507	D bilateral stage	157/200	1.91	7.35e-28	-	yes
PG	5	PO:0001185	C globular stage	155/200	1.89	1.24e-26	-	yes
PG	4	PO:0007631	embryo development stages	159/200	1.77	2.80e-24	-	yes
PG	3	PO:0001170	seed development stages	159/200	1.76	4.88e-24	-	yes
PG	4	PO:0001054	4 leaf senescence stage	146/200	1.90	6.55e-24	-	yes
PG	3	PO:0001050	leaf development stages	146/200	1.90	6.98e-24	-	yes
PG	3	PO:0007134	A vegetative growth	153/200	1.81	1.54e-23	-	yes
PG	5	PO:0007133	leaf production	152/200	1.81	3.00e-23	-	yes
PG	4	PO:0007112	1 main shoot growth	152/200	1.81	3.08e-23	-	yes
PG	4	PO:0007600	3 floral organ development stages	165/200	1.62	2.14e-21	-	yes
PG	5	PO:0007604	corolla developmental stages	160/200	1.62	6.81e-20	-	yes
PG	3	PO:0007615	flower development stages	165/200	1.58	7.99e-20	-	yes
PG	4	PO:0007616	4 anthesis	158/200	1.63	1.34e-19	-	yes

KW	0	nucleolus	-	18/200	13.24	1.82e-16	-	yes
KW	0	ribosome	-	22/200	8.33	3.42e-15	-	no
KW	0	translation	-	28/200	5.65	2.17e-14	-	no
KW	0	ribosomal	-	22/200	7.29	5.82e-14	-	no
KW	0	mitochondrion	-	27/200	4.92	1.70e-12	-	no
KW	0	processing	-	14/200	9.86	1.71e-11	-	no
KW	0	transducin	-	10/200	13.63	2.22e-10	0	yes
KW	0	constituent	-	17/200	6.07	5.62e-10	-	no
KW	0	structural	-	18/200	5.13	3.03e-09	-	no
KW	0	ipr017986	-	11/200	8.20	1.24e-08	-	yes
KW	0	subunit	-	25/200	3.41	2.44e-08	3.00E-13	no
KW	0	complex	-	27/200	3.19	2.96e-08	1.00E-06	yes
KW	0	ipr001680	-	11/200	7.40	3.85e-08	-	yes
KW	0	ipr015943	-	11/200	7.32	4.39e-08	-	yes
KW	0	ipr011046	-	11/200	7.09	6.20e-08	-	yes
KW	0	eukaryotic	-	12/200	6.10	1.08e-07	-	no
KW	0	nucleotide	-	21/200	3.30	4.84e-07	1.00E-11	yes
KW	0	mitochondrial	-	11/200	4.88	3.25e-06	-	no
KW	0	motif	-	15/200	3.09	3.41e-05	4.00E-08	no
KW	0	intracellular	-	15/200	2.91	6.91e-05	-	no
KW	0	cytoplasm	-	11/200	3.55	7.39e-05	-	no
KW	0	ligase	-	12/200	3.07	1.68e-04	-	yes
KW	0	ubiquitin	-	13/200	2.89	1.88e-04	-	yes
KW	0	region	-	26/200	1.80	1.27e-03	-	yes
KW	0	repeat	-	22/200	1.69	5.61e-03	0	yes
KW	0	nucleic	-	13/200	1.99	6.32e-03	-	no
KW	0	terminal	-	29/200	1.50	9.96e-03	8.00E-07	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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