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
AT2G38020.1	0.929919	VCL1 (VACUOLELESS 1)	OMAT2P108990	-	-	-
AT5G53440.1	0.913413	unknown protein	OMAT5P113820	-	-	-
AT5G54310.1	0.9125	AGD5 (ARF-GAP domain 5)	OMAT5P114140	-	-	-
AT5G19450.1	0.912088	CDPK19 (CALCIUM-DEPENDENT PROTEIN KINASE 19)	OMAT5P105710	-	-	-
AT1G50640.1	0.909621	ERF3 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 3)	OMAT1P112380	-	-	-
AT1G09730.1	0.909383	Ulp1 protease family protein	-	-	-	-
AT5G64220.1	0.906149	calmodulin-binding protein	OMAT5P019710	-	-	-
AT2G13370.1	0.903673	CHR5 (chromatin remodeling 5)	OMAT2P101500	-	-	-
AT3G07100.1	0.900953	protein transport protein Sec24, putative	OMAT3P102450	-	-	-
AT4G30960.1	0.897917	SIP3 (SOS3-INTERACTING PROTEIN 3)	OMAT4P010210	-	OMAT4P108780	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G22990.1	-0.79723	zinc finger (C2H2 type) family protein	-	-	-	-
AT4G03790.1	-0.785134	transposable element gene	-	-	-	-
AT1G42280.1	-0.784469	transposable element gene	-	-	-	-
AT3G18750.1	-0.775341	WNK6 (WITH NO K (=LYSINE) 6)	OMAT3P106190	-	-	-
AT2G05082.1	-0.75559	transposable element gene	-	-	-	-
AT1G49110.1	-0.755356	unknown protein	-	-	-	-
AT3G26483.1	-0.755276	transposable element gene	-	-	-	-
AT3G49650.1	-0.748099	kinesin motor protein-related	-	-	-	-
AT5G02240.1	-0.744421	binding / catalytic/ coenzyme binding	OMAT5P000520	-	-	-
AT1G72480.1	-0.744062	FUNCTIONS IN: molecular_function unknown	OMAT1P118410	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 9.73e-33	:20 terms with high significance
9.73e-33 <	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:0023033	signaling pathway	16/200	4.73	6.23e-08	-	no
B	3	GO:0050789	regulation of biological process	39/200	2.25	4.59e-07	-	no
B	3	GO:0007275	multicellular organismal development	27/200	2.54	2.78e-06	-	no
B	3	GO:0007154	cell communication	10/200	5.38	3.06e-06	-	no
B	3	GO:0050794	regulation of cellular process	34/200	2.23	3.27e-06	-	no
B	3	GO:0048856	anatomical structure development	24/200	2.68	3.69e-06	-	no
B	3	GO:0009653	anatomical structure morphogenesis	13/200	3.87	8.31e-06	-	no
B	3	GO:0009791	post-embryonic development	18/200	3.04	8.74e-06	-	no
B	3	GO:0051716	cellular response to stimulus	15/200	3.39	1.08e-05	-	no
B	3	GO:0019222	regulation of metabolic process	27/200	2.29	1.88e-05	-	no
B	4	GO:0031323	regulation of cellular metabolic process	25/200	2.31	3.20e-05	-	no
B	5	GO:0006464	protein modification process	24/200	2.31	4.68e-05	-	yes
B	3	GO:0023046	signaling process	11/200	3.39	1.13e-04	-	no
B	3	GO:0023060	signal transmission	11/200	3.39	1.13e-04	-	no
B	5	GO:0006796	phosphate metabolic process	17/200	2.56	1.33e-04	-	yes
B	4	GO:0006793	phosphorus metabolic process	17/200	2.56	1.35e-04	-	yes
B	3	GO:0009628	response to abiotic stimulus	18/200	2.43	1.76e-04	-	no
B	4	GO:0043412	macromolecule modification	24/200	2.12	1.80e-04	-	yes
B	4	GO:0080090	regulation of primary metabolic process	22/200	2.09	3.77e-04	-	no
B	3	GO:0003006	reproductive developmental process	14/200	2.54	4.65e-04	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	21/200	2.07	5.45e-04	-	no
B	4	GO:0048513	organ development	12/200	2.71	5.55e-04	-	no
B	3	GO:0044237	cellular metabolic process	67/200	1.42	5.56e-04	-	yes
B	4	GO:0048731	system development	12/200	2.71	5.62e-04	-	no
B	4	GO:0044248	cellular catabolic process	10/200	2.77	1.09e-03	-	no
B	3	GO:0022414	reproductive process	14/200	2.32	1.15e-03	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	20/200	1.99	1.15e-03	-	no
B	4	GO:0048608	reproductive structure development	12/200	2.46	1.34e-03	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	32/200	1.64	1.82e-03	-	no
B	3	GO:0044238	primary metabolic process	67/200	1.35	2.12e-03	-	yes
B	3	GO:0006807	nitrogen compound metabolic process	32/200	1.61	2.50e-03	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	50/200	1.42	3.22e-03	-	yes
B	5	GO:0044267	cellular protein metabolic process	32/200	1.57	3.84e-03	-	yes
B	4	GO:0009889	regulation of biosynthetic process	18/200	1.79	5.94e-03	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	18/200	1.79	5.94e-03	-	no
B	3	GO:0009719	response to endogenous stimulus	11/200	2.13	5.96e-03	-	no
B	4	GO:0060255	regulation of macromolecule metabolic process	19/200	1.74	6.96e-03	-	no
B	5	GO:0006350	transcription	18/200	1.76	7.01e-03	-	no
B	4	GO:0010033	response to organic substance	13/200	1.94	7.65e-03	-	no
B	4	GO:0019538	protein metabolic process	34/200	1.47	7.97e-03	-	yes
B	4	GO:0009725	response to hormone stimulus	10/200	2.12	8.35e-03	-	no
B	3	GO:0009056	catabolic process	10/200	2.10	8.89e-03	-	no

C	3	GO:0044424	intracellular part	87/200	1.71	9.27e-09	-	yes
C	3	GO:0005622	intracellular	89/200	1.67	1.59e-08	-	yes
C	4	GO:0043231	intracellular membrane-bounded organelle	74/200	1.68	4.18e-07	-	yes
C	3	GO:0043227	membrane-bounded organelle	74/200	1.68	4.21e-07	-	yes
C	3	GO:0043229	intracellular organelle	75/200	1.62	1.49e-06	-	yes
C	4	GO:0044444	cytoplasmic part	59/200	1.70	7.55e-06	-	yes
C	4	GO:0005886	plasma membrane	28/200	2.26	1.76e-05	-	no
C	4	GO:0005737	cytoplasm	61/200	1.63	1.95e-05	-	yes
C	5	GO:0005634	nucleus	30/200	1.92	1.95e-04	3.64E-21	yes
C	5	GO:0005773	vacuole	10/200	2.90	7.64e-04	-	no
C	3	GO:0016020	membrane	40/200	1.46	4.98e-03	-	no
C	3	GO:0044464	cell part	108/200	1.18	7.86e-03	-	yes

M	3	GO:0005515	protein binding	35/200	2.24	2.16e-06	1.00E-25	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	16/200	2.58	1.82e-04	-	yes
M	5	GO:0046872	metal ion binding	27/200	1.99	2.17e-04	-	no
M	4	GO:0043169	cation binding	28/200	1.95	2.39e-04	-	no
M	3	GO:0043167	ion binding	28/200	1.95	2.39e-04	1.00E-25	no
M	3	GO:0000166	nucleotide binding	26/200	1.97	3.27e-04	-	yes
M	5	GO:0016301	kinase activity	17/200	2.11	1.27e-03	-	yes
M	5	GO:0032555	purine ribonucleotide binding	19/200	1.94	2.09e-03	-	yes
M	4	GO:0032553	ribonucleotide binding	19/200	1.94	2.09e-03	-	yes
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	18/200	1.96	2.24e-03	-	yes
M	4	GO:0017076	purine nucleotide binding	19/200	1.83	3.93e-03	-	yes
M	3	GO:0016740	transferase activity	26/200	1.59	6.91e-03	-	yes
M	4	GO:0016788	hydrolase activity, acting on ester bonds	12/200	2.02	7.08e-03	-	no
M	3	GO:0016787	hydrolase activity	25/200	1.60	7.24e-03	-	no

PS	4	PO:0020030	cotyledon	164/200	2.23	1.60e-40	-	yes
PS	4	PO:0000230	inflorescence meristem	166/200	2.14	9.79e-39	-	yes
PS	3	PO:0009013	meristem	168/200	2.09	2.21e-38	-	yes
PS	5	PO:0000013	cauline leaf	163/200	2.11	1.89e-36	-	yes
PS	3	PO:0020091	male gametophyte	168/200	2.03	2.47e-36	-	yes
PS	4	PO:0009047	stem	169/200	2.00	4.08e-36	-	yes
PS	5	PO:0009027	megasporophyll	168/200	2.00	1.53e-35	-	yes
PS	5	PO:0020039	leaf lamina	165/200	2.00	4.02e-34	-	yes
PS	5	PO:0008037	seedling	170/200	1.93	4.63e-34	-	yes
PS	5	PO:0009028	microsporophyll	166/200	1.98	6.83e-34	-	yes
PS	5	PO:0009052	pedicel	163/200	2.00	2.70e-33	-	yes
PS	4	PO:0009025	leaf	171/200	1.86	2.84e-32	-	yes
PS	4	PO:0009026	sporophyll	169/200	1.88	5.98e-32	-	yes
PS	5	PO:0020038	petiole	156/200	2.05	1.36e-31	-	yes
PS	4	PO:0000037	shoot apex	165/200	1.92	1.84e-31	-	yes
PS	3	PO:0009032	petal	166/200	1.89	3.87e-31	-	yes
PS	3	PO:0009005	root	168/200	1.87	3.96e-31	-	yes
PS	3	PO:0009031	sepal	168/200	1.82	1.71e-29	-	yes
PS	5	PO:0008034	leaf whorl	169/200	1.79	5.29e-29	-	yes
PS	4	PO:0008033	phyllome whorl	169/200	1.79	5.29e-29	-	yes
PS	4	PO:0009009	embryo	170/200	1.76	2.82e-28	-	yes
PS	3	PO:0009010	seed	170/200	1.74	1.71e-27	-	yes
PS	4	PO:0009001	fruit	170/200	1.73	3.62e-27	-	yes
PS	3	PO:0006342	infructescence	170/200	1.73	3.62e-27	-	yes
PS	3	PO:0006001	phyllome	171/200	1.67	2.53e-25	-	yes
PS	4	PO:0009049	inflorescence	171/200	1.63	4.68e-24	-	yes
PS	5	PO:0009046	flower	170/200	1.63	1.11e-23	-	yes
PS	3	PO:0009006	shoot	173/200	1.59	2.85e-23	-	yes
PS	4	PO:0006345	pollen tube	72/200	2.47	1.14e-14	-	yes
PS	3	PO:0000084	sperm cell	62/200	1.91	6.20e-08	-	yes
PS	3	PO:0020097	generative cell	62/200	1.91	6.20e-08	-	yes
PS	5	PO:0006016	leaf epidermis	26/200	2.34	1.87e-05	-	no
PS	5	PO:0006035	shoot epidermis	26/200	2.32	2.12e-05	-	no
PS	4	PO:0000293	guard cell	25/200	2.32	2.94e-05	-	no
PS	4	PO:0000351	guard mother cell	25/200	2.31	3.17e-05	-	no
PS	3	PO:0000070	meristemoid	25/200	2.31	3.26e-05	-	no
PS	4	PO:0005679	epidermis	27/200	2.18	4.59e-05	-	no
PS	3	PO:0009014	dermal tissue	27/200	2.18	4.63e-05	-	no
PS	5	PO:0000349	epidermal initial	25/200	2.22	6.40e-05	-	no
PS	4	PO:0004011	initial cell	25/200	2.20	7.11e-05	-	no
PS	3	PO:0004010	meristematic cell	25/200	2.20	7.29e-05	-	no
PS	3	PO:0004013	epidermal cell	25/200	2.10	1.58e-04	-	no

PG	5	PO:0007133	leaf production	168/200	2.00	2.04e-35	-	yes
PG	4	PO:0007112	1 main shoot growth	168/200	2.00	2.11e-35	-	yes
PG	4	PO:0001054	4 leaf senescence stage	161/200	2.09	5.10e-35	-	yes
PG	3	PO:0001050	leaf development stages	161/200	2.09	5.50e-35	-	yes
PG	3	PO:0007134	A vegetative growth	168/200	1.98	5.78e-35	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	165/200	1.99	1.09e-33	-	yes
PG	5	PO:0004507	D bilateral stage	164/200	1.99	2.52e-33	-	yes
PG	5	PO:0001081	F mature embryo stage	161/200	2.02	5.53e-33	-	yes
PG	5	PO:0001185	C globular stage	163/200	1.99	9.73e-33	-	yes
PG	4	PO:0007631	embryo development stages	166/200	1.84	1.82e-29	-	yes
PG	3	PO:0001170	seed development stages	166/200	1.84	3.36e-29	-	yes
PG	4	PO:0007600	3 floral organ development stages	174/200	1.71	3.94e-28	-	yes
PG	4	PO:0007616	4 anthesis	169/200	1.74	2.93e-27	-	yes
PG	5	PO:0007604	corolla developmental stages	170/200	1.72	6.31e-27	-	yes
PG	3	PO:0007615	flower development stages	174/200	1.66	2.46e-26	-	yes
PG	5	PO:0007605	androecium developmental stages	77/200	2.63	2.42e-17	-	yes

KW	0	finger	-	27/200	2.92	1.83e-07	-	no
KW	0	ipr016024	-	11/200	5.96	4.03e-07	-	no
KW	0	armadillo	-	11/200	5.88	4.63e-07	-	no
KW	0	processes	-	14/200	4.62	4.69e-07	-	no
KW	0	mediated	-	15/200	4.24	6.31e-07	-	no
KW	0	ubiquitin	-	17/200	3.78	7.16e-07	-	no
KW	0	plasma	-	27/200	2.36	1.16e-05	-	no
KW	0	regulator	-	11/200	3.76	4.26e-05	-	no
KW	0	ligase	-	13/200	3.33	4.29e-05	-	no
KW	0	helical	-	11/200	3.65	5.69e-05	-	no
KW	0	phosphatase	-	10/200	3.91	5.86e-05	-	no
KW	0	nucleus	-	27/200	2.09	9.28e-05	3.64E-21	yes
KW	0	regulation	-	27/200	2.04	1.40e-04	-	no
KW	0	encodes	-	43/200	1.68	1.94e-04	-	yes
KW	0	ipr002290	-	10/200	3.39	2.04e-04	-	yes
KW	0	vacuole	-	10/200	3.17	3.60e-04	-	no
KW	0	signaling	-	11/200	2.95	4.00e-04	-	no
KW	0	amino	-	19/200	2.21	4.29e-04	1.00E-25	yes
KW	0	ipr008271	-	13/200	2.66	4.34e-04	-	no
KW	0	threonine	-	17/200	2.27	5.72e-04	0	yes
KW	0	containing	-	30/200	1.80	5.86e-04	2.00E-49	no
KW	0	region	-	27/200	1.87	5.86e-04	-	yes
KW	0	ipr011009	-	15/200	2.32	8.41e-04	-	yes
KW	0	nucleic	-	15/200	2.29	9.44e-04	-	no
KW	0	tyrosine	-	10/200	2.82	9.54e-04	-	yes
KW	0	phosphorylation	-	14/200	2.28	1.40e-03	-	yes
KW	0	ipr000719	-	14/200	2.25	1.59e-03	-	yes
KW	0	serine	-	18/200	2.02	1.63e-03	0	yes
KW	0	development	-	15/200	2.15	1.84e-03	-	no
KW	0	ipr017442	-	12/200	2.28	2.62e-03	-	yes
KW	0	transcription	-	25/200	1.72	2.82e-03	-	no
KW	0	alpha	-	15/200	2.06	2.86e-03	-	no
KW	0	active	-	16/200	1.95	3.70e-03	-	no
KW	0	motif	-	11/200	2.26	3.77e-03	-	no
KW	0	dependent	-	22/200	1.64	8.03e-03	2.00E-23	no
KW	0	associated	-	13/200	1.90	9.12e-03	6.00E-21	no
KW	0	transport	-	17/200	1.75	9.14e-03	-	no
KW	0	kinase	-	18/200	1.71	9.82e-03	0	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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label http://www.w3.org/2000/01/rdf-schema#label