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
AT4G36710.1	0.932123	transcription factor	OMAT4P012560	-	-	-
AT1G29951.1	0.927782	CPuORF35 (Conserved peptide upstream open reading frame 35)	OMAT1P010490	-	-	-
AT1G29952.1	0.91893	CPuORF34 (Conserved peptide upstream open reading frame 34)	OMAT1P010490	-	-	-
AT1G27850.1	0.917833	unknown protein	OMAT1P009910	-	-	-
AT2G39340.1	0.917113	SAC3/GANP family protein	OMAT2P010380	-	-	-
AT4G34560.1	0.911703	unknown protein	OMAT4P011830	-	-	-
AT1G43850.1	0.90994	SEU (seuss)	OMAT1P012550	-	-	-
AT2G01680.1	0.907421	ankyrin repeat family protein	OMAT2P000180	-	-	-
AT1G37160.1	0.904988	transposable element gene	-	-	-	-
AT5G61190.1	0.90268	zinc finger protein-related	OMAT5P018650	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G13475.1	-0.865179	transposable element gene	-	-	-	-
AT2G06180.1	-0.758626	transposable element gene	-	-	-	-
AT1G62510.1	-0.753105	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	OMAT1P115300	-	OMAT1P017040	-
AT2G23673.1	-0.748947	Pseudogene of AT2G23680	-	-	-	-
AT1G15175.1	-0.737456	other RNA	OMAT1P105040	-	-	-
AT1G12669.1	-0.719453	Encodes a Plant thionin family protein [pseudogene]	-	-	-	-
AT2G22350.1	-0.693286	transposable element gene	-	-	-	-
AT3G52590.1	-0.689232	UBQ1 (UBIQUITIN EXTENSION PROTEIN 1)	OMAT3P014260	-	-	-
AT4G35090.1	-0.687601	CAT2 (CATALASE 2)	OMAT4P110330	-	OMAT4P012070	-
AT2G12190.1	-0.685869	cytochrome P450, putative	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.13e-17	:20 terms with high significance
1.13e-17 <	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:0010468	regulation of gene expression	28/200	2.63	9.63e-07	-	yes
B	4	GO:0060255	regulation of macromolecule metabolic process	28/200	2.56	1.64e-06	-	yes
B	5	GO:0090304	nucleic acid metabolic process	34/200	2.26	2.33e-06	-	yes
B	3	GO:0019222	regulation of metabolic process	29/200	2.46	2.35e-06	-	yes
B	3	GO:0050789	regulation of biological process	37/200	2.14	3.22e-06	-	yes
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	36/200	2.13	4.63e-06	-	yes
B	4	GO:0031323	regulation of cellular metabolic process	26/200	2.40	1.14e-05	-	yes
B	5	GO:0006350	transcription	25/200	2.45	1.19e-05	2.00E-14	yes
B	5	GO:0010556	regulation of macromolecule biosynthetic process	24/200	2.44	1.90e-05	-	yes
B	4	GO:0080090	regulation of primary metabolic process	25/200	2.37	2.04e-05	-	yes
B	4	GO:0044260	cellular macromolecule metabolic process	58/200	1.65	2.46e-05	-	yes
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	24/200	2.39	2.54e-05	-	yes
B	4	GO:0009889	regulation of biosynthetic process	24/200	2.39	2.61e-05	-	yes
B	5	GO:0031326	regulation of cellular biosynthetic process	24/200	2.39	2.61e-05	-	yes
B	4	GO:0051171	regulation of nitrogen compound metabolic process	24/200	2.37	3.00e-05	-	yes
B	4	GO:0034641	cellular nitrogen compound metabolic process	37/200	1.90	4.54e-05	-	yes
B	3	GO:0050794	regulation of cellular process	31/200	2.03	5.34e-05	-	yes
B	3	GO:0006807	nitrogen compound metabolic process	37/200	1.86	6.90e-05	-	yes
B	3	GO:0043170	macromolecule metabolic process	60/200	1.55	1.04e-04	-	yes
B	4	GO:0010467	gene expression	35/200	1.72	5.18e-04	-	yes
B	5	GO:0006464	protein modification process	21/200	2.02	7.83e-04	-	no
B	4	GO:0043412	macromolecule modification	22/200	1.94	1.03e-03	-	no
B	5	GO:0006796	phosphate metabolic process	15/200	2.26	1.11e-03	-	no
B	4	GO:0006793	phosphorus metabolic process	15/200	2.26	1.12e-03	-	no
B	3	GO:0022414	reproductive process	14/200	2.32	1.15e-03	-	yes
B	3	GO:0003006	reproductive developmental process	13/200	2.36	1.38e-03	-	yes
B	3	GO:0048856	anatomical structure development	18/200	2.01	1.70e-03	-	yes
B	3	GO:0044237	cellular metabolic process	64/200	1.35	2.60e-03	-	yes
B	4	GO:0048608	reproductive structure development	11/200	2.26	3.88e-03	-	yes
B	5	GO:0016070	RNA metabolic process	16/200	1.88	5.39e-03	-	no
B	3	GO:0009791	post-embryonic development	12/200	2.03	6.85e-03	-	yes

C	4	GO:0005886	plasma membrane	27/200	2.18	4.63e-05	-	no
C	5	GO:0005634	nucleus	30/200	1.92	1.95e-04	-	no
C	3	GO:0044464	cell part	109/200	1.19	5.27e-03	-	no

M	3	GO:0005515	protein binding	34/200	2.17	5.70e-06	3.00E-15	no
M	4	GO:0003677	DNA binding	28/200	2.02	1.28e-04	3.00E-15	no
M	3	GO:0003700	transcription factor activity	22/200	2.18	2.08e-04	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	20/200	2.18	3.70e-04	-	no
M	3	GO:0003676	nucleic acid binding	39/200	1.64	6.25e-04	-	no
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	3	GO:0000166	nucleotide binding	22/200	1.67	6.83e-03	2.00E-09	no
M	5	GO:0016301	kinase activity	15/200	1.86	7.21e-03	-	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	12/200	1.93	9.97e-03	-	no

PS	3	PO:0009013	meristem	154/200	1.92	4.49e-27	-	yes
PS	4	PO:0000230	inflorescence meristem	150/200	1.93	4.50e-26	-	yes
PS	5	PO:0020039	leaf lamina	147/200	1.78	4.14e-21	-	yes
PS	4	PO:0009047	stem	148/200	1.75	1.40e-20	-	yes
PS	5	PO:0008037	seedling	150/200	1.70	1.49e-19	-	yes
PS	5	PO:0009052	pedicel	143/200	1.76	2.23e-19	-	yes
PS	5	PO:0000013	cauline leaf	138/200	1.79	7.59e-19	-	yes
PS	3	PO:0009005	root	149/200	1.66	4.95e-18	-	yes
PS	4	PO:0009009	embryo	155/200	1.60	5.51e-18	-	yes
PS	3	PO:0009010	seed	156/200	1.59	6.13e-18	-	yes
PS	5	PO:0009027	megasporophyll	143/200	1.70	6.68e-18	-	yes
PS	4	PO:0000037	shoot apex	145/200	1.69	6.88e-18	-	yes
PS	4	PO:0009001	fruit	156/200	1.59	1.13e-17	-	yes
PS	3	PO:0006342	infructescence	156/200	1.59	1.13e-17	-	yes
PS	4	PO:0009025	leaf	150/200	1.63	1.47e-17	-	yes
PS	5	PO:0009028	microsporophyll	142/200	1.69	2.09e-17	-	yes
PS	3	PO:0009032	petal	145/200	1.65	4.84e-17	-	yes
PS	3	PO:0009031	sepal	149/200	1.61	8.64e-17	-	yes
PS	3	PO:0006001	phyllome	157/200	1.53	3.94e-16	-	yes
PS	4	PO:0009026	sporophyll	145/200	1.61	7.75e-16	-	yes
PS	5	PO:0008034	leaf whorl	149/200	1.58	8.01e-16	-	yes
PS	4	PO:0008033	phyllome whorl	149/200	1.58	8.01e-16	-	yes
PS	3	PO:0009006	shoot	160/200	1.47	6.43e-15	-	yes
PS	5	PO:0009046	flower	156/200	1.50	7.06e-15	-	yes
PS	5	PO:0020038	petiole	129/200	1.69	9.93e-15	-	yes
PS	4	PO:0020030	cotyledon	126/200	1.72	1.21e-14	-	yes
PS	4	PO:0009049	inflorescence	156/200	1.49	1.38e-14	-	yes
PS	3	PO:0020091	male gametophyte	133/200	1.60	2.48e-13	-	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	5	PO:0006035	shoot epidermis	21/200	1.88	1.98e-03	-	no
PS	3	PO:0004013	epidermal cell	22/200	1.84	1.98e-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: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
PS	4	PO:0000293	guard cell	19/200	1.77	5.80e-03	-	no
PS	3	PO:0000084	sperm cell	45/200	1.39	7.87e-03	-	no
PS	3	PO:0020097	generative cell	45/200	1.39	7.87e-03	-	no

PG	4	PO:0001054	4 leaf senescence stage	140/200	1.82	3.41e-20	-	yes
PG	3	PO:0001050	leaf development stages	140/200	1.82	3.61e-20	-	yes
PG	5	PO:0001185	C globular stage	144/200	1.75	1.56e-19	-	yes
PG	4	PO:0007631	embryo development stages	151/200	1.68	3.72e-19	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	144/200	1.73	5.40e-19	-	yes
PG	3	PO:0001170	seed development stages	151/200	1.67	6.09e-19	-	yes
PG	5	PO:0004507	D bilateral stage	142/200	1.72	3.27e-18	-	yes
PG	4	PO:0007600	3 floral organ development stages	159/200	1.56	1.31e-17	-	yes
PG	5	PO:0001081	F mature embryo stage	138/200	1.73	1.48e-17	-	yes
PG	3	PO:0007134	A vegetative growth	143/200	1.69	1.71e-17	-	yes
PG	5	PO:0007133	leaf production	142/200	1.69	2.89e-17	-	yes
PG	4	PO:0007112	1 main shoot growth	142/200	1.69	2.96e-17	-	yes
PG	5	PO:0007604	corolla developmental stages	155/200	1.57	6.58e-17	-	yes
PG	3	PO:0007615	flower development stages	159/200	1.52	3.47e-16	-	yes
PG	4	PO:0007616	4 anthesis	149/200	1.54	1.53e-14	-	yes
PG	5	PO:0007605	androecium developmental stages	43/200	1.47	3.30e-03	-	no

KW	0	regulation	-	36/200	2.72	1.14e-08	-	yes
KW	0	plasma	-	28/200	2.44	4.05e-06	-	no
KW	0	mutants	-	11/200	4.40	9.27e-06	2.76E-18	no
KW	0	nucleus	-	28/200	2.17	3.68e-05	-	no
KW	0	tyrosine	-	12/200	3.38	6.53e-05	-	no
KW	0	transcription	-	29/200	2.00	1.23e-04	2.00E-14	yes
KW	0	major	-	10/200	3.50	1.56e-04	-	no
KW	0	superfamily	-	11/200	2.90	4.68e-04	-	no
KW	0	threonine	-	17/200	2.27	5.72e-04	4.00E-09	no
KW	0	region	-	27/200	1.87	5.86e-04	-	yes
KW	0	ipr008271	-	12/200	2.46	1.35e-03	-	no
KW	0	ipr017441	-	11/200	2.56	1.37e-03	-	no
KW	0	ipr000719	-	14/200	2.25	1.59e-03	-	no
KW	0	membrane	-	41/200	1.54	1.68e-03	-	no
KW	0	ipr011009	-	14/200	2.17	2.27e-03	-	no
KW	0	amino	-	17/200	1.97	2.66e-03	-	no
KW	0	phosphorylation	-	13/200	2.12	3.72e-03	-	no
KW	0	associated	-	14/200	2.05	3.80e-03	4.00E-09	no
KW	0	serine	-	17/200	1.91	3.80e-03	4.00E-09	no
KW	0	finger	-	17/200	1.84	5.55e-03	-	no
KW	0	terminal	-	30/200	1.56	5.56e-03	4.00E-10	no
KW	0	repeat	-	22/200	1.69	5.61e-03	0	yes
KW	0	leucine	-	11/200	2.10	6.86e-03	-	no
KW	0	containing	-	26/200	1.56	8.82e-03	7.00E-122	yes

(*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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