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
AT3G06620.1	0.940755	protein kinase family protein	OMAT3P102290	-	-	-
AT5G11700.2	0.9233	glycine-rich protein	OMAT5P103260	-	-	-
AT5G18525.1	0.914004	ATP binding / protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase	OMAT5P105420	-	-	-
AT1G07200.2	0.906536	ATP-dependent Clp protease ClpB protein-related	OMAT1P102110	-	-	-
AT3G48050.1	0.906364	DNA binding / protein binding / transcription regulator	OMAT3P110950	-	-	-
AT1G03080.1	0.903756	FUNCTIONS IN: molecular_function unknown	OMAT1P100670	-	OMAT1P000840	-
AT3G13870.1	0.900056	RHD3 (ROOT HAIR DEFECTIVE 3)	OMAT3P104610	-	-	-
AT2G38020.1	0.897988	VCL1 (VACUOLELESS 1)	OMAT2P108990	-	-	-
AT1G08800.1	0.887907	unknown protein	OMAT1P102710	-	-	-
AT5G06600.1	0.885863	UBP12 (UBIQUITIN-SPECIFIC PROTEASE 12)	OMAT5P101750	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G10750.1	-0.81006	HpcH/HpaI aldolase family protein	OMAT4P002630	-	-	-
AT1G69680.1	-0.793422	FUNCTIONS IN: molecular_function unknown	OMAT1P019790	-	-	-
AT1G27870.1	-0.790344	nucleic acid binding	-	-	-	-
AT4G01820.1	-0.78453	PGP3 (P-GLYCOPROTEIN 3)	-	-	-	-
AT3G26483.1	-0.781297	transposable element gene	-	-	-	-
AT2G19820.1	-0.77851	LBD9 (LOB DOMAIN-CONTAINING PROTEIN 9)	-	-	-	-
AT3G42203.1	-0.775558	transposable element gene	-	-	-	-
AT1G29870.1	-0.77269	tRNA synthetase class II (G, H, P and S) family protein	-	-	-	-
AT5G02240.1	-0.771944	binding / catalytic/ coenzyme binding	OMAT5P000520	-	-	-
AT3G46030.1	-0.770893	HTB11	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.30e-24	:20 terms with high significance
2.30e-24 <	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:0046907	intracellular transport	10/200	4.21	3.03e-05	-	no
B	3	GO:0048856	anatomical structure development	22/200	2.46	3.45e-05	-	no
B	3	GO:0009653	anatomical structure morphogenesis	12/200	3.57	3.78e-05	-	no
B	3	GO:0051649	establishment of localization in cell	10/200	3.71	9.34e-05	-	no
B	3	GO:0019222	regulation of metabolic process	25/200	2.12	1.29e-04	-	no
B	3	GO:0006996	organelle organization	11/200	3.30	1.49e-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:0051641	cellular localization	10/200	3.40	2.00e-04	6.86E-17	no
B	4	GO:0031323	regulation of cellular metabolic process	23/200	2.13	2.21e-04	-	no
B	3	GO:0050789	regulation of biological process	32/200	1.85	2.42e-04	-	no
B	3	GO:0050794	regulation of cellular process	29/200	1.90	2.88e-04	-	no
B	5	GO:0006508	proteolysis	12/200	2.86	3.33e-04	-	no
B	3	GO:0051707	response to other organism	10/200	2.99	5.97e-04	-	no
B	3	GO:0006810	transport	21/200	2.05	6.37e-04	-	no
B	3	GO:0051234	establishment of localization	21/200	2.04	6.62e-04	-	no
B	3	GO:0033036	macromolecule localization	10/200	2.89	7.75e-04	-	no
B	4	GO:0080090	regulation of primary metabolic process	21/200	1.99	9.09e-04	-	no
B	3	GO:0007275	multicellular organismal development	21/200	1.98	1.02e-03	-	no
B	3	GO:0009607	response to biotic stimulus	10/200	2.77	1.11e-03	-	no
B	3	GO:0022414	reproductive process	14/200	2.32	1.15e-03	-	no
B	4	GO:0009889	regulation of biosynthetic process	20/200	1.99	1.18e-03	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	20/200	1.99	1.18e-03	-	no
B	4	GO:0010033	response to organic substance	15/200	2.24	1.19e-03	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	20/200	1.97	1.31e-03	-	no
B	3	GO:0065008	regulation of biological quality	10/200	2.68	1.43e-03	-	no
B	5	GO:0006350	transcription	20/200	1.96	1.44e-03	-	no
B	4	GO:0060255	regulation of macromolecule metabolic process	21/200	1.92	1.49e-03	-	no
B	5	GO:0010556	regulation of macromolecule biosynthetic process	19/200	1.93	2.18e-03	-	no
B	5	GO:0010468	regulation of gene expression	20/200	1.88	2.41e-03	1.01E-15	no
B	5	GO:0051252	regulation of RNA metabolic process	12/200	2.30	2.45e-03	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	19/200	1.90	2.66e-03	-	no
B	3	GO:0009628	response to abiotic stimulus	15/200	2.02	3.32e-03	-	yes
B	5	GO:0032774	RNA biosynthetic process	12/200	2.19	3.65e-03	-	no
B	3	GO:0003006	reproductive developmental process	12/200	2.18	3.82e-03	-	no
B	3	GO:0009056	catabolic process	10/200	2.10	8.89e-03	-	no

C	3	GO:0044424	intracellular part	75/200	1.47	6.18e-05	-	no
C	4	GO:0044444	cytoplasmic part	56/200	1.61	6.33e-05	-	no
C	3	GO:0005622	intracellular	77/200	1.45	8.59e-05	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	65/200	1.48	2.04e-04	-	no
C	3	GO:0043227	membrane-bounded organelle	65/200	1.48	2.05e-04	-	no
C	4	GO:0005737	cytoplasm	57/200	1.52	2.67e-04	-	no
C	3	GO:0043229	intracellular organelle	65/200	1.41	8.62e-04	-	no
C	5	GO:0005829	cytosol	11/200	2.66	1.00e-03	-	no
C	4	GO:0005886	plasma membrane	22/200	1.78	3.19e-03	-	no
C	5	GO:0005634	nucleus	26/200	1.66	3.84e-03	-	no
C	3	GO:0044464	cell part	108/200	1.18	7.86e-03	-	no
C	3	GO:0016020	membrane	39/200	1.42	8.38e-03	1.96E-15	no

M	3	GO:0005515	protein binding	35/200	2.24	2.16e-06	0	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	17/200	2.74	5.71e-05	-	no
M	4	GO:0003677	DNA binding	26/200	1.88	6.78e-04	0	no
M	5	GO:0016301	kinase activity	17/200	2.11	1.27e-03	-	no
M	3	GO:0000166	nucleotide binding	23/200	1.74	3.40e-03	-	no
M	5	GO:0032555	purine ribonucleotide binding	18/200	1.83	4.67e-03	-	no
M	4	GO:0032553	ribonucleotide binding	18/200	1.83	4.67e-03	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	17/200	1.85	5.10e-03	-	no
M	3	GO:0022892	substrate-specific transporter activity	11/200	2.13	6.07e-03	-	no
M	4	GO:0017076	purine nucleotide binding	18/200	1.73	8.32e-03	-	no
M	5	GO:0030554	adenyl nucleotide binding	16/200	1.77	9.66e-03	-	no
M	4	GO:0001883	purine nucleoside binding	16/200	1.77	9.66e-03	-	no
M	3	GO:0001882	nucleoside binding	16/200	1.76	9.90e-03	-	no

PS	3	PO:0009013	meristem	159/200	1.98	8.42e-31	-	yes
PS	4	PO:0020030	cotyledon	152/200	2.07	1.45e-30	-	yes
PS	3	PO:0020091	male gametophyte	161/200	1.94	1.69e-30	-	yes
PS	4	PO:0009047	stem	161/200	1.91	1.73e-29	-	yes
PS	4	PO:0000230	inflorescence meristem	154/200	1.98	6.29e-29	-	yes
PS	5	PO:0020039	leaf lamina	158/200	1.92	1.46e-28	-	yes
PS	5	PO:0009028	microsporophyll	159/200	1.90	2.54e-28	-	yes
PS	4	PO:0009025	leaf	165/200	1.79	2.02e-27	-	yes
PS	3	PO:0009005	root	163/200	1.81	3.36e-27	-	yes
PS	5	PO:0000013	cauline leaf	151/200	1.95	4.47e-27	-	yes
PS	5	PO:0008037	seedling	161/200	1.82	7.62e-27	-	yes
PS	5	PO:0020038	petiole	149/200	1.96	1.88e-26	-	yes
PS	5	PO:0009027	megasporophyll	156/200	1.86	4.48e-26	-	yes
PS	4	PO:0009026	sporophyll	160/200	1.78	5.23e-25	-	yes
PS	5	PO:0009052	pedicel	151/200	1.86	2.30e-24	-	yes
PS	4	PO:0000037	shoot apex	155/200	1.80	4.80e-24	-	yes
PS	5	PO:0008034	leaf whorl	161/200	1.71	4.50e-23	-	yes
PS	4	PO:0008033	phyllome whorl	161/200	1.71	4.50e-23	-	yes
PS	3	PO:0009031	sepal	159/200	1.72	7.16e-23	-	yes
PS	3	PO:0006001	phyllome	167/200	1.63	2.16e-22	-	yes
PS	3	PO:0009032	petal	153/200	1.75	9.26e-22	-	yes
PS	4	PO:0009009	embryo	161/200	1.67	1.03e-21	-	yes
PS	3	PO:0009010	seed	161/200	1.65	4.99e-21	-	yes
PS	4	PO:0009001	fruit	161/200	1.64	9.67e-21	-	yes
PS	3	PO:0006342	infructescence	161/200	1.64	9.67e-21	-	yes
PS	3	PO:0009006	shoot	169/200	1.56	2.07e-20	-	yes
PS	4	PO:0009049	inflorescence	163/200	1.56	1.35e-18	-	yes
PS	5	PO:0009046	flower	162/200	1.56	2.65e-18	-	yes
PS	4	PO:0006345	pollen tube	71/200	2.44	3.89e-14	-	yes
PS	3	PO:0000084	sperm cell	56/200	1.73	8.61e-06	-	no
PS	3	PO:0020097	generative cell	56/200	1.73	8.61e-06	-	no
PS	4	PO:0005679	epidermis	26/200	2.10	1.16e-04	-	no
PS	3	PO:0009014	dermal tissue	26/200	2.10	1.17e-04	-	no
PS	5	PO:0006016	leaf epidermis	23/200	2.07	3.32e-04	-	no
PS	5	PO:0006035	shoot epidermis	23/200	2.05	3.67e-04	-	no
PS	3	PO:0004013	epidermal cell	24/200	2.01	3.82e-04	-	no
PS	5	PO:0000349	epidermal initial	23/200	2.04	4.06e-04	-	no
PS	4	PO:0004011	initial cell	23/200	2.03	4.44e-04	-	no
PS	3	PO:0004010	meristematic cell	23/200	2.02	4.54e-04	-	no
PS	4	PO:0000293	guard cell	22/200	2.04	5.07e-04	-	no
PS	4	PO:0000351	guard mother cell	22/200	2.04	5.39e-04	-	no
PS	3	PO:0000070	meristemoid	22/200	2.03	5.51e-04	-	no

PG	4	PO:0001054	4 leaf senescence stage	150/200	1.95	1.32e-26	-	yes
PG	3	PO:0001050	leaf development stages	150/200	1.95	1.41e-26	-	yes
PG	5	PO:0007133	leaf production	156/200	1.85	5.73e-26	-	yes
PG	4	PO:0007112	1 main shoot growth	156/200	1.85	5.89e-26	-	yes
PG	3	PO:0007134	A vegetative growth	156/200	1.84	1.40e-25	-	yes
PG	5	PO:0004507	D bilateral stage	151/200	1.83	1.10e-23	-	yes
PG	5	PO:0001081	F mature embryo stage	148/200	1.86	1.63e-23	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	151/200	1.82	2.73e-23	-	yes
PG	4	PO:0007600	3 floral organ development stages	167/200	1.64	8.91e-23	-	yes
PG	5	PO:0001185	C globular stage	149/200	1.82	1.38e-22	-	yes
PG	4	PO:0007616	4 anthesis	162/200	1.67	3.51e-22	-	yes
PG	5	PO:0007604	corolla developmental stages	162/200	1.64	3.51e-21	-	yes
PG	3	PO:0007615	flower development stages	167/200	1.59	3.73e-21	-	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	5	PO:0007605	androecium developmental stages	74/200	2.53	1.22e-15	-	yes

KW	0	ipr016024	-	13/200	7.04	6.16e-09	-	no
KW	0	armadillo	-	13/200	6.95	7.26e-09	-	no
KW	0	golgi	-	10/200	6.02	1.03e-06	-	no
KW	0	helical	-	13/200	4.31	2.38e-06	-	no
KW	0	ubiquitin	-	15/200	3.34	1.32e-05	-	no
KW	0	mediated	-	13/200	3.68	1.46e-05	-	yes
KW	0	region	-	31/200	2.15	1.85e-05	1.08E-15	no
KW	0	transcription	-	29/200	2.00	1.23e-04	-	no
KW	0	regulator	-	10/200	3.42	1.90e-04	-	no
KW	0	processes	-	10/200	3.30	2.59e-04	-	no
KW	0	ipr013083	-	10/200	3.19	3.43e-04	-	no
KW	0	finger	-	20/200	2.16	4.14e-04	-	no
KW	0	nucleus	-	25/200	1.94	5.26e-04	-	no
KW	0	containing	-	30/200	1.80	5.86e-04	0	no
KW	0	ligase	-	11/200	2.82	6.07e-04	-	no
KW	0	transport	-	20/200	2.06	7.94e-04	-	no
KW	0	motif	-	12/200	2.47	1.30e-03	1.28E-16	no
KW	0	regulation	-	24/200	1.82	1.65e-03	1.97E-15	no
KW	0	kinase	-	20/200	1.89	2.15e-03	-	no
KW	0	dependent	-	23/200	1.72	4.06e-03	-	no
KW	0	plasma	-	20/200	1.74	5.56e-03	-	no
KW	0	ipr011009	-	13/200	2.01	5.76e-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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