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
AT5G12050.1	0.971265	unknown protein	OMAT5P004130	-	-	-
AT1G18400.1	0.955049	BEE1 (BR Enhanced Expression 1)	OMAT1P006750	-	-	-
AT4G02330.1	0.93866	ATPMEPCRB	OMAT4P000840,OMAT4P000850	[OMAT4P000840]-, [OMAT4P000850]-	-	-
AT3G02250.1	0.923023	unknown protein	OMAT3P100560	-	-	-
AT5G08760.1	0.916581	unknown protein	OMAT5P003090	-	OMAT5P102450	-
AT3G45260.1	0.911965	zinc finger (C2H2 type) family protein	OMAT3P110180	-	-	-
AT5G62280.1	0.911402	unknown protein	OMAT5P018950	-	OMAT5P116820	-
AT5G44568.1	0.91075	unknown protein	OMAT5P111010	-	-	-
AT2G29680.1	0.906606	CDC6 (CELL DIVISION CONTROL 6)	-	-	-	-
AT3G25717.1	0.897559	RTFL16 (ROTUNDIFOLIA LIKE 16)	OMAT3P108370	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G14600.1	-0.789112	FUNCTIONS IN: molecular_function unknown	-	-	-	-
AT2G04880.1	-0.777641	ZAP1 (ZINC-DEPENDENT ACTIVATOR PROTEIN-1)	OMAT2P001130	-	-	-
AT2G01220.2	-0.768541	nucleotidyltransferase	OMAT2P000070	-	-	-
AT1G15240.2	-0.763669	phox (PX) domain-containing protein	OMAT1P005440	-	-	-
AT1G57540.1	-0.760113	unknown protein	-	-	-	-
AT5G15170.1	-0.756688	tyrosyl-DNA phosphodiesterase-related	-	-	-	-
AT4G29490.1	-0.756513	aminopeptidase/ manganese ion binding	OMAT4P009710	-	-	-
AT5G21030.1	-0.755877	PAZ domain-containing protein / piwi domain-containing protein	-	-	-	-
AT1G55310.1	-0.748965	SR33	OMAT1P015420	-	-	-
AT1G08460.1	-0.746543	HDA08	OMAT1P002780	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.85e-17	:20 terms with high significance
1.85e-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:0009733	response to auxin stimulus	16/200	9.47	1.61e-12	-	no
B	3	GO:0009719	response to endogenous stimulus	23/200	4.46	4.76e-10	-	no
B	4	GO:0009725	response to hormone stimulus	22/200	4.65	4.85e-10	-	no
B	4	GO:0010033	response to organic substance	26/200	3.89	8.20e-10	-	no
B	3	GO:0042221	response to chemical stimulus	28/200	2.46	3.65e-06	-	no
B	5	GO:0009416	response to light stimulus	12/200	4.17	7.36e-06	-	no
B	4	GO:0009314	response to radiation	12/200	4.04	1.04e-05	-	no
B	3	GO:0033036	macromolecule localization	13/200	3.76	1.14e-05	-	no
B	3	GO:0009628	response to abiotic stimulus	16/200	2.16	1.32e-03	-	no
B	4	GO:0080090	regulation of primary metabolic process	20/200	1.90	2.10e-03	-	no
B	5	GO:0010556	regulation of macromolecule biosynthetic process	19/200	1.93	2.18e-03	-	no
B	4	GO:0009889	regulation of biosynthetic process	19/200	1.89	2.71e-03	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	19/200	1.89	2.71e-03	-	no
B	3	GO:0050794	regulation of cellular process	26/200	1.70	2.75e-03	-	no
B	4	GO:0031323	regulation of cellular metabolic process	20/200	1.85	2.86e-03	-	no
B	5	GO:0006796	phosphate metabolic process	14/200	2.11	2.92e-03	-	no
B	4	GO:0006793	phosphorus metabolic process	14/200	2.11	2.95e-03	-	no
B	5	GO:0006350	transcription	19/200	1.86	3.25e-03	-	no
B	4	GO:0060255	regulation of macromolecule metabolic process	20/200	1.83	3.30e-03	-	no
B	5	GO:0010468	regulation of gene expression	19/200	1.78	5.23e-03	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	18/200	1.80	5.83e-03	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	18/200	1.78	6.47e-03	-	no
B	3	GO:0019222	regulation of metabolic process	20/200	1.70	7.47e-03	-	no
B	3	GO:0050789	regulation of biological process	27/200	1.56	7.75e-03	-	no

C	3	GO:0044464	cell part	132/200	1.44	2.43e-09	-	yes
C	5	GO:0042651	thylakoid membrane	12/200	6.63	4.12e-08	-	no
C	4	GO:0034357	photosynthetic membrane	12/200	6.54	4.81e-08	-	no
C	4	GO:0044436	thylakoid part	12/200	5.82	1.87e-07	-	no
C	5	GO:0055035	plastid thylakoid membrane	11/200	6.35	2.04e-07	-	no
C	4	GO:0044435	plastid part	20/200	3.52	3.12e-07	-	no
C	5	GO:0044434	chloroplast part	19/200	3.43	8.53e-07	-	no
C	5	GO:0031976	plastid thylakoid	11/200	5.53	8.92e-07	-	no
C	4	GO:0031984	organelle subcompartment	11/200	5.49	9.50e-07	-	no
C	4	GO:0009579	thylakoid	12/200	4.82	1.55e-06	-	no
C	5	GO:0009532	plastid stroma	10/200	4.05	4.34e-05	-	no
C	5	GO:0009536	plastid	35/200	1.90	7.79e-05	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	66/200	1.50	1.12e-04	-	no
C	3	GO:0043227	membrane-bounded organelle	66/200	1.50	1.12e-04	-	no
C	4	GO:0005618	cell wall	11/200	3.31	1.41e-04	-	no
C	3	GO:0030312	external encapsulating structure	11/200	3.29	1.51e-04	-	no
C	3	GO:0005622	intracellular	75/200	1.41	2.72e-04	-	no
C	3	GO:0016020	membrane	44/200	1.61	4.68e-04	-	yes
C	3	GO:0043229	intracellular organelle	66/200	1.43	5.01e-04	-	no
C	3	GO:0044424	intracellular part	71/200	1.39	6.12e-04	-	no
C	4	GO:0044444	cytoplasmic part	52/200	1.50	7.76e-04	-	no
C	4	GO:0031967	organelle envelope	11/200	2.64	1.07e-03	-	no
C	3	GO:0031975	envelope	11/200	2.64	1.07e-03	-	no
C	4	GO:0005737	cytoplasm	54/200	1.44	1.49e-03	-	no
C	4	GO:0005886	plasma membrane	22/200	1.78	3.19e-03	-	no

M	3	GO:0003700	transcription factor activity	23/200	2.28	7.88e-05	-	no
M	4	GO:0003677	DNA binding	25/200	1.80	1.47e-03	-	no

PS	4	PO:0009025	leaf	162/200	1.76	3.31e-25	-	yes
PS	5	PO:0020039	leaf lamina	151/200	1.83	1.19e-23	-	yes
PS	4	PO:0020030	cotyledon	142/200	1.93	1.32e-23	-	yes
PS	5	PO:0020038	petiole	144/200	1.89	3.95e-23	-	yes
PS	5	PO:0000013	cauline leaf	143/200	1.85	8.54e-22	-	yes
PS	3	PO:0006001	phyllome	165/200	1.61	5.05e-21	-	yes
PS	5	PO:0008034	leaf whorl	154/200	1.63	1.26e-18	-	yes
PS	4	PO:0008033	phyllome whorl	154/200	1.63	1.26e-18	-	yes
PS	4	PO:0009009	embryo	156/200	1.61	1.42e-18	-	yes
PS	3	PO:0009006	shoot	166/200	1.53	1.92e-18	-	yes
PS	5	PO:0008037	seedling	148/200	1.68	2.20e-18	-	yes
PS	3	PO:0009010	seed	156/200	1.59	6.13e-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:0009026	sporophyll	148/200	1.64	1.85e-17	-	yes
PS	4	PO:0009049	inflorescence	161/200	1.54	2.21e-17	-	yes
PS	4	PO:0009047	stem	142/200	1.68	3.88e-17	-	yes
PS	5	PO:0009046	flower	160/200	1.54	4.16e-17	-	yes
PS	4	PO:0000037	shoot apex	142/200	1.65	2.92e-16	-	yes
PS	3	PO:0009031	sepal	146/200	1.58	3.39e-15	-	yes
PS	3	PO:0009032	petal	139/200	1.59	5.77e-14	-	yes
PS	3	PO:0009013	meristem	130/200	1.62	3.74e-13	-	yes
PS	5	PO:0009028	microsporophyll	133/200	1.59	6.60e-13	-	yes
PS	5	PO:0009027	megasporophyll	133/200	1.58	7.35e-13	-	no
PS	4	PO:0000230	inflorescence meristem	125/200	1.61	3.87e-12	-	yes
PS	5	PO:0009052	pedicel	120/200	1.48	1.11e-08	-	yes
PS	3	PO:0020091	male gametophyte	109/200	1.31	7.49e-05	-	no
PS	3	PO:0009005	root	114/200	1.27	2.48e-04	-	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	4	PO:0001054	4 leaf senescence stage	143/200	1.86	5.28e-22	-	yes
PG	3	PO:0001050	leaf development stages	143/200	1.86	5.60e-22	-	yes
PG	5	PO:0007604	corolla developmental stages	154/200	1.56	2.38e-16	-	yes
PG	3	PO:0007615	flower development stages	158/200	1.51	1.25e-15	-	yes
PG	4	PO:0007600	3 floral organ development stages	155/200	1.52	2.33e-15	-	yes
PG	4	PO:0007616	4 anthesis	150/200	1.55	4.68e-15	-	yes
PG	4	PO:0007631	embryo development stages	137/200	1.52	5.81e-12	-	yes
PG	3	PO:0001170	seed development stages	137/200	1.51	8.53e-12	-	yes
PG	5	PO:0004507	D bilateral stage	127/200	1.54	5.90e-11	-	yes
PG	5	PO:0001081	F mature embryo stage	122/200	1.53	4.15e-10	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	124/200	1.49	1.62e-09	-	yes
PG	5	PO:0001185	C globular stage	123/200	1.50	1.66e-09	-	yes

KW	0	stimulus	-	27/200	6.27	4.71e-15	-	no
KW	0	responsive	-	21/200	7.01	4.38e-13	-	no
KW	0	auxin	-	18/200	8.02	1.58e-12	-	no
KW	0	response	-	47/200	2.62	1.97e-10	-	no
KW	0	basic	-	11/200	6.18	2.73e-07	-	no
KW	0	lipid	-	14/200	4.08	2.20e-06	-	no
KW	0	light	-	12/200	4.49	3.33e-06	-	no
KW	0	thylakoid	-	10/200	4.70	1.10e-05	-	no
KW	0	inhibitor	-	12/200	4.01	1.11e-05	-	no
KW	0	chloroplast	-	35/200	1.98	3.10e-05	-	no
KW	0	protease	-	12/200	3.59	3.58e-05	-	no
KW	0	helical	-	11/200	3.65	5.69e-05	-	no
KW	0	amino	-	19/200	2.21	4.29e-04	-	no
KW	0	plasma	-	23/200	2.01	5.12e-04	-	no
KW	0	transcription	-	27/200	1.86	6.37e-04	-	no
KW	0	active	-	17/200	2.08	1.53e-03	-	no
KW	0	membrane	-	41/200	1.54	1.68e-03	-	yes
KW	0	subgroup	-	10/200	2.46	2.74e-03	-	no
KW	0	regulation	-	23/200	1.74	3.44e-03	-	no
KW	0	ipr000719	-	13/200	2.09	4.19e-03	-	no
KW	0	related	-	41/200	1.46	4.55e-03	-	no
KW	0	ipr011009	-	13/200	2.01	5.76e-03	-	no
KW	0	putative	-	34/200	1.47	8.00e-03	-	no
KW	0	serine	-	16/200	1.80	8.42e-03	-	no
KW	0	threonine	-	14/200	1.87	8.71e-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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