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
AT3G18600.1	0.991922	DEAD/DEAH box helicase, putative	OMAT3P106140	-	-	-
AT3G58660.1	0.991005	60S ribosomal protein-related	OMAT3P016460	-	-	-
AT3G13160.1	0.990282	pentatricopeptide (PPR) repeat-containing protein	OMAT3P104370	-	-	-
AT5G27120.1	0.989984	SAR DNA-binding protein, putative	OMAT5P009180	-	-	-
AT3G12270.1	0.988852	PRMT3 (PROTEIN ARGININE METHYLTRANSFERASE 3)	OMAT3P004290	-	-	-
AT3G23990.1	0.988777	HSP60 (HEAT SHOCK PROTEIN 60)	OMAT3P009110	-	-	-
AT4G04940.1	0.988765	transducin family protein / WD-40 repeat family protein	OMAT4P101390	-	-	-
AT5G14600.1	0.987956	tRNA (adenine-N1-)-methyltransferase	OMAT5P004980	-	-	-
AT3G44750.1	0.98779	HDA3 (HISTONE DEACETYLASE 3)	OMAT3P011580	-	-	-
AT1G18800.1	0.987705	NRP2 (NAP1-RELATED PROTEIN 2)	OMAT1P106010	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G17170.1	-0.760869	RABB1C (ARABIDOPSIS RAB GTPASE HOMOLOG B1C)	OMAT4P104230	-	-	-
AT3G03150.1	-0.734685	unknown protein	OMAT3P100900,OMAT3P100910	[OMAT3P100900]-, [OMAT3P100910]-	-	-
AT4G25650.2	-0.714465	ACD1-LIKE (ACD1-LIKE)	OMAT4P107010	-	-	-
AT5G36160.1	-0.707868	aminotransferase-related	OMAT5P108800	-	-	-
AT1G51402.1	-0.694352	unknown protein	OMAT1P014180	-	OMAT1P112450	-
AT2G36895.1	-0.69013	unknown protein	OMAT2P108545	-	-	-
AT1G20620.1	-0.68158	CAT3 (CATALASE 3)	OMAT1P007530,OMAT1P007540	[OMAT1P007530]-, [OMAT1P007540]-	OMAT1P106670	-
AT2G13920.1	-0.661717	pseudogene, CHP-rich zinc finger protein, putative, contains weak PHD zinc finger motifscontains weak PHD zinc finger motifsDC1 domain, a divergent protein kinase C domain of unknown function.	-	-	-	-
AT2G23810.1	-0.657389	TET8 (TETRASPANIN8)	OMAT2P104250	-	OMAT2P004810,OMAT2P004820	[OMAT2P004810]-, [OMAT2P004820]-
AT1G79040.1	-0.656969	PSBR (photosystem II subunit R)	OMAT1P023540	-	OMAT1P120810	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.01e-20	:20 terms with high significance
1.01e-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	4	GO:0042254	ribosome biogenesis	26/200	20.30	8.29e-28	-	no
B	3	GO:0022613	ribonucleoprotein complex biogenesis	26/200	19.65	2.03e-27	-	no
B	5	GO:0006364	rRNA processing	15/200	23.98	2.66e-18	-	no
B	5	GO:0009451	RNA modification	14/200	18.48	1.64e-15	-	no
B	5	GO:0006396	RNA processing	20/200	9.04	1.09e-14	-	yes
B	5	GO:0006412	translation	33/200	4.55	6.10e-14	-	no
B	4	GO:0010467	gene expression	56/200	2.75	3.32e-13	-	yes
B	4	GO:0044260	cellular macromolecule metabolic process	66/200	1.87	4.32e-08	-	yes
B	3	GO:0043170	macromolecule metabolic process	67/200	1.73	7.00e-07	-	yes
B	5	GO:0016070	RNA metabolic process	23/200	2.70	4.95e-06	-	yes
B	5	GO:0044267	cellular protein metabolic process	40/200	1.96	1.07e-05	-	no
B	3	GO:0006996	organelle organization	12/200	3.60	3.51e-05	-	no
B	3	GO:0044237	cellular metabolic process	71/200	1.50	5.31e-05	-	yes
B	4	GO:0019538	protein metabolic process	41/200	1.78	8.55e-05	-	no
B	5	GO:0034645	cellular macromolecule biosynthetic process	39/200	1.81	8.73e-05	-	no
B	4	GO:0009059	macromolecule biosynthetic process	39/200	1.80	9.33e-05	-	no
B	3	GO:0044238	primary metabolic process	71/200	1.43	2.58e-04	-	yes
B	5	GO:0090304	nucleic acid metabolic process	28/200	1.86	4.99e-04	-	yes
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	30/200	1.78	7.17e-04	-	yes
B	4	GO:0044249	cellular biosynthetic process	42/200	1.49	2.71e-03	-	no
B	3	GO:0009058	biosynthetic process	42/200	1.44	5.08e-03	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	30/200	1.54	6.35e-03	-	yes
B	3	GO:0006807	nitrogen compound metabolic process	30/200	1.51	8.35e-03	-	yes

C	3	GO:0030529	ribonucleoprotein complex	43/200	12.33	2.72e-35	-	no
C	3	GO:0043228	non-membrane-bounded organelle	50/200	8.39	8.59e-33	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	50/200	8.39	8.59e-33	-	no
C	3	GO:0005622	intracellular	124/200	2.33	1.65e-26	-	no
C	4	GO:0005840	ribosome	31/200	12.10	1.44e-25	-	no
C	3	GO:0044424	intracellular part	119/200	2.33	4.92e-25	-	no
C	3	GO:0044446	intracellular organelle part	57/200	3.98	1.06e-20	-	no
C	3	GO:0044422	organelle part	57/200	3.97	1.11e-20	-	no
C	3	GO:0043229	intracellular organelle	104/200	2.25	1.54e-19	-	no
C	4	GO:0070013	intracellular organelle lumen	26/200	9.59	3.92e-19	-	no
C	3	GO:0043233	organelle lumen	26/200	9.56	4.15e-19	-	no
C	4	GO:0033279	ribosomal subunit	21/200	12.93	1.34e-18	-	no
C	5	GO:0005730	nucleolus	21/200	12.25	4.27e-18	-	no
C	5	GO:0005739	mitochondrion	36/200	5.63	5.17e-18	-	no
C	5	GO:0022626	cytosolic ribosome	20/200	10.87	2.76e-16	-	no
C	5	GO:0031981	nuclear lumen	22/200	9.10	5.17e-16	-	no
C	4	GO:0005737	cytoplasm	86/200	2.30	6.19e-16	-	no
C	4	GO:0044444	cytoplasmic part	82/200	2.36	8.77e-16	-	no
C	5	GO:0015934	large ribosomal subunit	14/200	15.21	3.07e-14	-	no
C	4	GO:0044428	nuclear part	22/200	6.61	4.34e-13	-	no
C	3	GO:0044464	cell part	138/200	1.51	8.64e-12	-	no
C	4	GO:0044429	mitochondrial part	14/200	10.03	1.34e-11	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	85/200	1.93	2.23e-11	-	no
C	3	GO:0043227	membrane-bounded organelle	85/200	1.93	2.25e-11	-	no
C	5	GO:0044445	cytosolic part	13/200	8.68	4.14e-10	-	no
C	5	GO:0005829	cytosol	19/200	4.59	7.87e-09	-	no
C	4	GO:0031966	mitochondrial membrane	10/200	8.94	1.93e-08	-	no
C	5	GO:0005740	mitochondrial envelope	10/200	8.36	3.87e-08	-	no
C	3	GO:0031090	organelle membrane	10/200	3.43	1.86e-04	-	no
C	5	GO:0005634	nucleus	30/200	1.92	1.95e-04	-	no
C	4	GO:0031967	organelle envelope	11/200	2.64	1.07e-03	-	no
C	3	GO:0031975	envelope	11/200	2.64	1.07e-03	-	no
C	3	GO:0043234	protein complex	13/200	1.99	6.37e-03	-	no

M	3	GO:0003735	structural constituent of ribosome	28/200	12.93	4.34e-24	-	no
M	4	GO:0003723	RNA binding	20/200	2.88	7.12e-06	3.00E-43	yes
M	3	GO:0000166	nucleotide binding	29/200	2.20	2.19e-05	-	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	5	GO:0032555	purine ribonucleotide binding	20/200	2.04	8.85e-04	-	no
M	4	GO:0032553	ribonucleotide binding	20/200	2.04	8.85e-04	-	no
M	4	GO:0017076	purine nucleotide binding	20/200	1.93	1.76e-03	-	no
M	3	GO:0016787	hydrolase activity	27/200	1.73	1.90e-03	-	yes
M	3	GO:0003676	nucleic acid binding	37/200	1.56	2.22e-03	3.00E-43	yes

PS	4	PO:0000037	shoot apex	156/200	1.81	1.00e-24	-	yes
PS	5	PO:0009052	pedicel	149/200	1.83	4.75e-23	-	yes
PS	5	PO:0020038	petiole	142/200	1.87	7.06e-22	-	yes
PS	3	PO:0009005	root	153/200	1.70	2.12e-20	-	yes
PS	3	PO:0009032	petal	149/200	1.70	2.61e-19	-	yes
PS	3	PO:0009031	sepal	152/200	1.65	1.74e-18	-	yes
PS	5	PO:0020039	leaf lamina	142/200	1.72	3.50e-18	-	yes
PS	4	PO:0009009	embryo	154/200	1.59	2.08e-17	-	yes
PS	5	PO:0000013	cauline leaf	135/200	1.75	3.37e-17	-	no
PS	4	PO:0009025	leaf	149/200	1.62	5.30e-17	-	yes
PS	5	PO:0009028	microsporophyll	141/200	1.68	7.26e-17	-	yes
PS	3	PO:0009010	seed	154/200	1.57	8.56e-17	-	yes
PS	4	PO:0009001	fruit	154/200	1.57	1.54e-16	-	yes
PS	3	PO:0006342	infructescence	154/200	1.57	1.54e-16	-	yes
PS	5	PO:0008034	leaf whorl	150/200	1.59	2.33e-16	-	yes
PS	4	PO:0008033	phyllome whorl	150/200	1.59	2.33e-16	-	yes
PS	5	PO:0009027	megasporophyll	140/200	1.67	2.78e-16	-	no
PS	5	PO:0008037	seedling	144/200	1.63	3.49e-16	-	yes
PS	4	PO:0009026	sporophyll	144/200	1.60	2.56e-15	-	yes
PS	3	PO:0006001	phyllome	154/200	1.50	1.62e-14	-	yes
PS	5	PO:0009046	flower	155/200	1.49	2.37e-14	-	yes
PS	4	PO:0009049	inflorescence	155/200	1.48	4.56e-14	-	yes
PS	3	PO:0009006	shoot	158/200	1.46	7.44e-14	-	yes
PS	4	PO:0009047	stem	134/200	1.59	3.91e-13	-	yes
PS	3	PO:0009013	meristem	129/200	1.61	1.06e-12	-	no
PS	4	PO:0000230	inflorescence meristem	125/200	1.61	3.87e-12	-	no
PS	4	PO:0020030	cotyledon	118/200	1.61	4.56e-11	-	no
PS	3	PO:0020091	male gametophyte	101/200	1.22	3.97e-03	-	no

PG	5	PO:0001081	F mature embryo stage	152/200	1.91	3.32e-26	-	yes
PG	5	PO:0004507	D bilateral stage	153/200	1.86	4.99e-25	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	152/200	1.83	5.98e-24	-	yes
PG	5	PO:0001185	C globular stage	148/200	1.80	5.93e-22	-	yes
PG	4	PO:0007631	embryo development stages	153/200	1.70	2.31e-20	-	yes
PG	3	PO:0001170	seed development stages	153/200	1.69	3.85e-20	-	yes
PG	3	PO:0007134	A vegetative growth	147/200	1.74	8.92e-20	-	yes
PG	5	PO:0007133	leaf production	145/200	1.72	6.07e-19	-	yes
PG	4	PO:0007112	1 main shoot growth	145/200	1.72	6.21e-19	-	yes
PG	4	PO:0001054	4 leaf senescence stage	136/200	1.77	6.32e-18	-	no
PG	3	PO:0001050	leaf development stages	136/200	1.77	6.68e-18	-	no
PG	5	PO:0007604	corolla developmental stages	154/200	1.56	2.38e-16	-	yes
PG	4	PO:0007600	3 floral organ development stages	156/200	1.53	6.67e-16	-	yes
PG	4	PO:0007616	4 anthesis	150/200	1.55	4.68e-15	-	yes
PG	3	PO:0007615	flower development stages	156/200	1.49	1.50e-14	-	yes

KW	0	ribosome	-	36/200	13.64	2.56e-31	-	no
KW	0	ribosomal	-	37/200	12.26	2.02e-30	2.00E-08	no
KW	0	constituent	-	28/200	9.99	5.94e-21	-	no
KW	0	translation	-	35/200	7.06	1.01e-20	-	no
KW	0	nucleolus	-	20/200	14.71	5.56e-19	-	no
KW	0	structural	-	28/200	7.99	2.61e-18	-	no
KW	0	mitochondrial	-	22/200	9.75	1.15e-16	-	no
KW	0	mitochondrion	-	31/200	5.65	9.19e-16	-	no
KW	0	cytosolic	-	19/200	8.87	6.45e-14	-	no
KW	0	subunit	-	33/200	4.50	8.27e-14	-	no
KW	0	large	-	14/200	9.13	5.11e-11	-	no
KW	0	biogenesis	-	13/200	9.56	1.16e-10	-	no
KW	0	intracellular	-	21/200	4.07	1.30e-08	-	no
KW	0	nucleotide	-	23/200	3.61	2.81e-08	-	no
KW	0	processing	-	10/200	7.05	2.18e-07	-	yes
KW	0	ipr015943	-	10/200	6.65	3.87e-07	-	no
KW	0	complex	-	25/200	2.95	4.02e-07	-	no
KW	0	ipr011046	-	10/200	6.44	5.29e-07	-	no
KW	0	eukaryotic	-	10/200	5.08	5.24e-06	-	no
KW	0	motif	-	16/200	3.29	8.86e-06	-	no
KW	0	conserved	-	29/200	2.14	3.47e-05	-	no
KW	0	small	-	13/200	3.23	6.03e-05	-	no
KW	0	terminal	-	35/200	1.82	1.83e-04	-	no
KW	0	atpase	-	11/200	3.12	2.45e-04	-	no
KW	0	nucleic	-	16/200	2.45	3.32e-04	3.00E-43	yes
KW	0	ubiquitin	-	11/200	2.45	2.00e-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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