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
AT2G22530.1	0.863925	catalytic/ transferase	-	-	-	-
AT1G71696.2	0.82071	SOL1 (SUPPRESSOR OF LLP1 1)	-	-	-	-
AT5G18245.1	0.810854	other RNA	OMAT5P006320	-	-	-
AT2G39090.1	0.809033	tetratricopeptide repeat (TPR)-containing protein	-	-	-	-
AT3G47360.1	0.806763	AtHSD3 (hydroxysteroid dehydrogenase 3)	-	-	-	-
AT4G21530.1	0.798539	nucleotide binding	-	-	-	-
AT5G21950.1	0.789948	hydrolase, alpha/beta fold family protein	OMAT5P106360	-	-	-
AT5G47520.1	0.78637	AtRABA5a (Arabidopsis Rab GTPase homolog A5a)	-	-	-	-
AT3G19780.1	0.781776	LOCATED IN: endomembrane system	-	-	-	-
AT5G13300.1	0.7811	SFC (SCARFACE)	OMAT5P103680	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT2G03970.1	-0.738278	transposable element gene	-	-	-	-
AT4G08874.1	-0.733778	FUNCTIONS IN: molecular_function unknown	-	-	-	-
AT1G35650.1	-0.733756	transposable element gene	-	-	-	-
AT3G44605.1	-0.7267	transposable element gene	-	-	-	-
AT3G22710.1	-0.724404	F-box family protein	-	-	-	-
AT2G16019.1	-0.724233	unknown protein	-	-	OMAT2P101910	-
AT4G09143.1	-0.717206	pseudogene, type 2 peroxiredoxin -related, similar to type 2 peroxiredoxin, putative	-	-	-	-
AT1G43990.1	-0.714949	transposable element gene	-	-	-	-
AT3G32305.1	-0.699634	transposable element gene	-	-	-	-
AT2G12650.1	-0.698764	transposable element gene	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 5.11e-09	:20 terms with high significance
5.11e-09 <	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:0048856	anatomical structure development	21/200	2.35	9.85e-05	-	no
B	3	GO:0009653	anatomical structure morphogenesis	11/200	3.27	1.59e-04	-	no
B	4	GO:0048513	organ development	13/200	2.94	1.61e-04	-	no
B	4	GO:0048731	system development	13/200	2.93	1.63e-04	-	no
B	3	GO:0007275	multicellular organismal development	23/200	2.17	1.69e-04	-	no
B	3	GO:0050789	regulation of biological process	32/200	1.85	2.42e-04	-	no
B	5	GO:0090304	nucleic acid metabolic process	26/200	1.73	2.23e-03	-	no
B	4	GO:0043412	macromolecule modification	21/200	1.85	2.31e-03	-	no
B	3	GO:0009791	post-embryonic development	13/200	2.20	2.66e-03	-	no
B	3	GO:0022414	reproductive process	13/200	2.16	3.12e-03	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	50/200	1.42	3.22e-03	-	no
B	3	GO:0019222	regulation of metabolic process	21/200	1.78	3.63e-03	-	no
B	3	GO:0003006	reproductive developmental process	12/200	2.18	3.82e-03	-	no
B	4	GO:0048608	reproductive structure development	11/200	2.26	3.88e-03	-	no
B	5	GO:0006464	protein modification process	19/200	1.83	4.05e-03	-	no
B	3	GO:0044237	cellular metabolic process	63/200	1.33	4.17e-03	-	no
B	3	GO:0043170	macromolecule metabolic process	53/200	1.37	5.16e-03	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	27/200	1.60	5.58e-03	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	30/200	1.54	6.35e-03	-	no
B	5	GO:0006796	phosphate metabolic process	13/200	1.96	7.20e-03	-	no
B	4	GO:0006793	phosphorus metabolic process	13/200	1.96	7.26e-03	-	no
B	3	GO:0006807	nitrogen compound metabolic process	30/200	1.51	8.35e-03	-	no

M	3	GO:0016740	transferase activity	29/200	1.77	8.99e-04	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	19/200	2.07	9.35e-04	-	no
M	5	GO:0016301	kinase activity	17/200	2.11	1.27e-03	-	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	14/200	2.26	1.54e-03	-	no
M	3	GO:0000166	nucleotide binding	23/200	1.74	3.40e-03	-	no

PS	5	PO:0009052	pedicel	127/200	1.56	2.09e-11	-	no
PS	5	PO:0008037	seedling	132/200	1.50	1.38e-10	-	no
PS	4	PO:0009009	embryo	140/200	1.45	1.51e-10	-	no
PS	4	PO:0000037	shoot apex	129/200	1.50	2.87e-10	-	no
PS	5	PO:0008034	leaf whorl	137/200	1.45	3.14e-10	-	no
PS	4	PO:0008033	phyllome whorl	137/200	1.45	3.14e-10	-	no
PS	3	PO:0009010	seed	140/200	1.43	4.44e-10	-	no
PS	3	PO:0009005	root	132/200	1.47	6.57e-10	-	no
PS	4	PO:0009001	fruit	140/200	1.42	6.95e-10	-	no
PS	3	PO:0006342	infructescence	140/200	1.42	6.95e-10	-	no
PS	4	PO:0000230	inflorescence meristem	119/200	1.53	1.08e-09	-	no
PS	5	PO:0020039	leaf lamina	123/200	1.49	2.31e-09	-	no
PS	3	PO:0009013	meristem	120/200	1.49	4.86e-09	-	no
PS	3	PO:0009031	sepal	132/200	1.43	5.11e-09	-	no
PS	3	PO:0009032	petal	127/200	1.45	6.77e-09	-	no
PS	5	PO:0009027	megasporophyll	123/200	1.46	8.65e-09	-	no
PS	3	PO:0006001	phyllome	141/200	1.37	9.76e-09	-	no
PS	5	PO:0009046	flower	141/200	1.36	3.18e-08	-	no
PS	4	PO:0009025	leaf	129/200	1.40	4.37e-08	-	no
PS	4	PO:0009026	sporophyll	127/200	1.41	4.63e-08	-	no
PS	4	PO:0009049	inflorescence	141/200	1.35	5.15e-08	-	no
PS	5	PO:0000013	cauline leaf	113/200	1.46	1.02e-07	-	no
PS	3	PO:0009006	shoot	142/200	1.31	4.22e-07	-	no
PS	4	PO:0020030	cotyledon	106/200	1.44	9.16e-07	-	no
PS	5	PO:0009028	microsporophyll	115/200	1.37	3.24e-06	-	no
PS	4	PO:0009047	stem	115/200	1.36	4.57e-06	-	no
PS	5	PO:0020038	petiole	106/200	1.39	6.30e-06	-	no
PS	3	PO:0020091	male gametophyte	104/200	1.25	1.03e-03	-	no

PG	5	PO:0001078	E expanded cotyledon stage	133/200	1.60	2.68e-13	-	no
PG	5	PO:0004507	D bilateral stage	131/200	1.59	1.12e-12	-	no
PG	4	PO:0007631	embryo development stages	137/200	1.52	5.81e-12	-	no
PG	3	PO:0001170	seed development stages	137/200	1.51	8.53e-12	-	no
PG	5	PO:0001081	F mature embryo stage	126/200	1.58	9.59e-12	-	no
PG	5	PO:0001185	C globular stage	125/200	1.52	2.80e-10	-	no
PG	5	PO:0007604	corolla developmental stages	138/200	1.40	5.71e-09	-	no
PG	4	PO:0001054	4 leaf senescence stage	115/200	1.50	1.59e-08	-	no
PG	3	PO:0001050	leaf development stages	115/200	1.49	1.65e-08	-	no
PG	4	PO:0007616	4 anthesis	134/200	1.38	3.99e-08	-	no
PG	4	PO:0007600	3 floral organ development stages	138/200	1.35	7.02e-08	-	no
PG	5	PO:0007133	leaf production	120/200	1.43	1.08e-07	-	no
PG	4	PO:0007112	1 main shoot growth	120/200	1.43	1.10e-07	-	no
PG	3	PO:0007134	A vegetative growth	120/200	1.42	1.72e-07	-	no
PG	3	PO:0007615	flower development stages	138/200	1.32	5.73e-07	-	no

KW	0	regulation	-	30/200	2.27	8.38e-06	-	no
KW	0	cytoplasm	-	11/200	3.55	7.39e-05	-	no
KW	0	development	-	18/200	2.58	8.12e-05	-	no
KW	0	processes	-	10/200	3.30	2.59e-04	-	no
KW	0	small	-	11/200	2.73	8.00e-04	-	no
KW	0	repeat	-	24/200	1.85	1.29e-03	-	no
KW	0	ipr008271	-	12/200	2.46	1.35e-03	-	no
KW	0	cyclin	-	11/200	2.35	2.76e-03	1.00E-101	yes
KW	0	ipr000719	-	13/200	2.09	4.19e-03	-	no
KW	0	kinase	-	19/200	1.80	4.71e-03	-	no
KW	0	complex	-	16/200	1.89	5.17e-03	-	no
KW	0	nucleus	-	22/200	1.71	5.19e-03	-	no
KW	0	finger	-	17/200	1.84	5.55e-03	-	no
KW	0	ipr011009	-	13/200	2.01	5.76e-03	-	no
KW	0	amino	-	16/200	1.86	6.09e-03	-	no
KW	0	hydrolase	-	14/200	1.92	6.85e-03	-	no
KW	0	ipr017442	-	11/200	2.09	7.04e-03	-	no
KW	0	encodes	-	37/200	1.45	7.61e-03	-	no

(*1)	[B]:Biological process(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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