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
AT1G09710.1	0.877835	DNA binding	OMAT1P003350	-	-	-
AT1G15750.1	0.875515	TPL (TOPLESS)	OMAT1P105250	-	-	-
AT2G39435.1	0.874509	unknown protein	OMAT2P109630	-	-	-
AT2G03360.2	0.86338	transferase, transferring glycosyl groups	OMAT2P100710	-	-	-
AT2G29070.2	0.858878	ubiquitin fusion degradation UFD1 family protein	OMAT2P006650	-	-	-
AT2G16005.1	0.858377	MD-2-related lipid recognition domain-containing protein / ML domain-containing protein	OMAT2P101900	-	-	-
AT1G56700.1	0.846507	pyrrolidone-carboxylate peptidase family protein	OMAT1P015880	-	-	-
AT2G45330.1	0.841867	emb1067 (embryo defective 1067)	-	-	-	-
AT1G78660.1	0.838815	gamma-glutamyl hydrolase, putative / gamma-Glu-X carboxypeptidase, putative / conjugase, putative	OMAT1P023430	-	-	-
AT3G45242.1	0.838088	CPuORF61 (Conserved peptide upstream open reading frame 61)	OMAT3P110170	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G61050.1	-0.730497	histone deacetylase-related / HD-related	-	-	-	-
AT3G03456.1	-0.720136	unknown protein	-	-	-	-
AT4G04020.1	-0.713145	FIB (FIBRILLIN)	OMAT4P001380	-	-	-
AT5G02920.1	-0.702299	ubiquitin-protein ligase	-	-	-	-
AT5G46820.1	-0.702274	unknown protein	-	-	-	-
AT5G36080.1	-0.701556	unknown protein	-	-	-	-
AT2G04043.1	-0.683965	transposable element gene	-	-	-	-
AT5G64840.1	-0.675034	ATGCN5 (A. THALIANA GENERAL CONTROL NON-REPRESSIBLE 5)	OMAT5P117720	-	-	-
AT3G32130.1	-0.668682	FUNCTIONS IN: molecular_function unknown	-	-	-	-
AT1G12540.1	-0.661124	basic helix-loop-helix (bHLH) family protein	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.29e-08	:20 terms with high significance
2.29e-08 <	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	3	GO:0009628	response to abiotic stimulus	18/200	2.43	1.76e-04	-	no
B	3	GO:0042221	response to chemical stimulus	22/200	1.93	1.11e-03	-	no
B	3	GO:0006950	response to stress	22/200	1.77	3.23e-03	-	no
B	3	GO:0009056	catabolic process	11/200	2.31	3.25e-03	-	no
B	5	GO:0006508	proteolysis	10/200	2.39	3.49e-03	-	no
B	5	GO:0006464	protein modification process	18/200	1.73	8.56e-03	-	no

C	3	GO:0044464	cell part	126/200	1.38	3.10e-07	-	yes
C	3	GO:0016020	membrane	50/200	1.83	6.09e-06	-	yes
C	4	GO:0005886	plasma membrane	27/200	2.18	4.63e-05	-	no
C	3	GO:0012505	endomembrane system	39/200	1.61	9.98e-04	-	no
C	3	GO:0044425	membrane part	15/200	1.90	6.15e-03	-	no

M	3	GO:0016740	transferase activity	31/200	1.90	1.92e-04	-	no
M	5	GO:0016301	kinase activity	18/200	2.24	4.90e-04	-	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	15/200	2.42	5.45e-04	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	19/200	2.07	9.35e-04	-	no

PS	3	PO:0009005	root	149/200	1.66	4.95e-18	-	yes
PS	3	PO:0020091	male gametophyte	131/200	1.58	2.00e-12	-	yes
PS	4	PO:0009047	stem	132/200	1.56	3.12e-12	-	yes
PS	5	PO:0009028	microsporophyll	127/200	1.51	2.39e-10	-	yes
PS	4	PO:0009026	sporophyll	133/200	1.48	2.68e-10	-	yes
PS	3	PO:0009031	sepal	134/200	1.45	8.84e-10	-	yes
PS	5	PO:0008037	seedling	129/200	1.46	2.08e-09	-	yes
PS	5	PO:0009027	megasporophyll	124/200	1.48	3.73e-09	-	yes
PS	4	PO:0009025	leaf	131/200	1.42	8.47e-09	-	yes
PS	3	PO:0009013	meristem	119/200	1.48	1.12e-08	-	yes
PS	4	PO:0009001	fruit	136/200	1.38	2.29e-08	-	yes
PS	3	PO:0006342	infructescence	136/200	1.38	2.29e-08	-	yes
PS	4	PO:0009009	embryo	134/200	1.39	3.04e-08	-	yes
PS	4	PO:0000230	inflorescence meristem	115/200	1.48	3.07e-08	-	yes
PS	3	PO:0009010	seed	135/200	1.38	3.47e-08	-	yes
PS	4	PO:0020030	cotyledon	110/200	1.50	4.63e-08	-	yes
PS	5	PO:0000013	cauline leaf	114/200	1.48	4.69e-08	-	yes
PS	5	PO:0009046	flower	140/200	1.35	7.21e-08	-	yes
PS	3	PO:0009032	petal	124/200	1.41	7.69e-08	-	yes
PS	4	PO:0009049	inflorescence	140/200	1.34	1.16e-07	-	yes
PS	3	PO:0006001	phyllome	138/200	1.35	1.16e-07	-	yes
PS	5	PO:0020039	leaf lamina	118/200	1.43	1.33e-07	-	yes
PS	5	PO:0020038	petiole	110/200	1.45	3.98e-07	-	yes
PS	5	PO:0009052	pedicel	115/200	1.41	5.26e-07	-	yes
PS	5	PO:0008034	leaf whorl	128/200	1.36	5.48e-07	-	yes
PS	4	PO:0008033	phyllome whorl	128/200	1.36	5.48e-07	-	yes
PS	3	PO:0009006	shoot	141/200	1.30	8.98e-07	-	yes
PS	4	PO:0000037	shoot apex	117/200	1.36	3.77e-06	-	yes
PS	4	PO:0006345	pollen tube	47/200	1.61	2.69e-04	-	yes
PS	3	PO:0000084	sperm cell	50/200	1.54	5.13e-04	-	yes
PS	3	PO:0020097	generative cell	50/200	1.54	5.13e-04	-	yes

PG	5	PO:0007133	leaf production	128/200	1.52	1.21e-10	-	yes
PG	4	PO:0007112	1 main shoot growth	128/200	1.52	1.24e-10	-	yes
PG	3	PO:0007134	A vegetative growth	128/200	1.51	2.12e-10	-	yes
PG	4	PO:0007616	4 anthesis	138/200	1.42	1.31e-09	-	yes
PG	3	PO:0007615	flower development stages	145/200	1.38	1.71e-09	-	yes
PG	4	PO:0007600	3 floral organ development stages	142/200	1.39	2.34e-09	-	yes
PG	4	PO:0001054	4 leaf senescence stage	115/200	1.50	1.59e-08	-	yes
PG	3	PO:0001050	leaf development stages	115/200	1.49	1.65e-08	-	yes
PG	5	PO:0001081	F mature embryo stage	116/200	1.46	6.37e-08	-	yes
PG	5	PO:0007604	corolla developmental stages	135/200	1.37	6.92e-08	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	118/200	1.42	2.08e-07	-	yes
PG	5	PO:0001185	C globular stage	115/200	1.40	9.09e-07	-	yes
PG	4	PO:0007631	embryo development stages	123/200	1.37	9.73e-07	-	yes
PG	5	PO:0004507	D bilateral stage	115/200	1.40	1.14e-06	-	yes
PG	3	PO:0001170	seed development stages	123/200	1.36	1.28e-06	-	yes
PG	5	PO:0007605	androecium developmental stages	52/200	1.78	8.59e-06	-	yes

KW	0	membrane	-	47/200	1.77	2.90e-05	-	yes
KW	0	ipr017441	-	14/200	3.26	3.09e-05	-	no
KW	0	plasma	-	26/200	2.27	3.17e-05	-	no
KW	0	response	-	33/200	1.84	2.15e-04	-	no
KW	0	active	-	19/200	2.32	2.24e-04	-	no
KW	0	serine	-	20/200	2.24	2.54e-04	-	no
KW	0	kinase	-	21/200	1.99	9.37e-04	-	no
KW	0	threonine	-	16/200	2.13	1.50e-03	-	no
KW	0	ipr000719	-	14/200	2.25	1.59e-03	-	no
KW	0	regulation	-	24/200	1.82	1.65e-03	-	no
KW	0	ipr011009	-	14/200	2.17	2.27e-03	-	no
KW	0	system	-	37/200	1.53	3.22e-03	-	no
KW	0	transferase	-	13/200	2.12	3.66e-03	-	no
KW	0	motif	-	11/200	2.26	3.77e-03	-	no
KW	0	endomembrane	-	36/200	1.52	3.79e-03	-	no
KW	0	ipr008271	-	11/200	2.25	3.92e-03	-	no
KW	0	amino	-	16/200	1.86	6.09e-03	-	no
KW	0	ipr017442	-	11/200	2.09	7.04e-03	-	no
KW	0	stress	-	10/200	2.13	7.91e-03	-	no
KW	0	terminal	-	29/200	1.50	9.96e-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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