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
OMAT1P106820	0.928441	-	AT1G21190	small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative	-	-
OMAT4P102400	0.913952	-	AT4G11920	CCS52A2	-	-
OMAT5P100120	0.893621	-	AT5G01350,AtsnoR112	[AT5G01350]unknown protein, [AtsnoR112]AtsnoR112	-	-
OMAT3P101720	0.883414	-	AT3G05290	PNC1 (PEROXISOMAL ADENINE NUCLEOTIDE CARRIER 1)	-	-
OMAT5P013530	0.872183	-	AT5G47710	C2 domain-containing protein	-	-
OMAT1P101160	0.865527	-	AT1G04590	FUNCTIONS IN: molecular_function unknown	-	-
OMAT2P111670	0.864258	-	AT2G45460	forkhead-associated domain-containing protein / FHA domain-containing protein	-	-
OMAT1P013320	0.862388	-	AT1G48560	unknown protein	-	-
OMAT1P116330	0.861125	-	AT1G66080	unknown protein	-	-
OMAT1P021770	0.860631	-	AT1G74700	TRZ1 (TRNASE Z 1)	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT3P000660	-0.81923	-	AT3G02470,AT3G02468	[AT3G02470]SAMDC (S-ADENOSYLMETHIONINE DECARBOXYLASE), [AT3G02468]CPuORF9 (Conserved peptide upstream open reading frame 9)	-	-
OMAT2P002950	-0.757656	-	-	-	AT2G18540	cupin family protein
OMAT2P013445	-0.744153	-	AT2G46910	plastid-lipid associated protein PAP / fibrillin family protein	-	-
OMAT4P105880	-0.728592	-	AT4G22505	INVOLVED IN: lipid transport	-	-
OMAT4P008480	-0.703643	-	AT4G26710	ATP synthase subunit H family protein	-	-
OMAT4P011550	-0.701218	-	AT4G34120	LEJ1 (LOSS OF THE TIMING OF ET AND JA BIOSYNTHESIS 1)	AT4G34131	UGT73B3 (UDP-glucosyl transferase 73B3)
OMAT4P104970	-0.700636	-	AT4G19410	pectinacetylesterase, putative	-	-
OMAT5P011680	-0.69675	-	AT5G42270	VAR1 (VARIEGATED 1)	-	-
OMAT2P013930	-0.693517	-	AT2G48020	sugar transporter, putative	-	-
OMAT2P007330	-0.68599	-	AT2G30950	VAR2 (VARIEGATED 2)	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.74e-13	:20 terms with high significance
1.74e-13 <	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:0090304	nucleic acid metabolic process	36/200	2.40	2.97e-07	-	yes
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	36/200	2.13	4.63e-06	-	yes
B	4	GO:0044260	cellular macromolecule metabolic process	59/200	1.67	1.21e-05	-	yes
B	4	GO:0034641	cellular nitrogen compound metabolic process	38/200	1.95	1.98e-05	-	yes
B	3	GO:0006807	nitrogen compound metabolic process	38/200	1.92	3.07e-05	-	yes
B	5	GO:0016070	RNA metabolic process	21/200	2.47	4.69e-05	-	yes
B	3	GO:0043170	macromolecule metabolic process	60/200	1.55	1.04e-04	-	yes
B	4	GO:0010467	gene expression	35/200	1.72	5.18e-04	-	yes
B	3	GO:0044237	cellular metabolic process	67/200	1.42	5.56e-04	-	yes
B	5	GO:0006350	transcription	21/200	2.06	6.04e-04	0	yes
B	3	GO:0009791	post-embryonic development	13/200	2.20	2.66e-03	-	no
B	3	GO:0007275	multicellular organismal development	19/200	1.79	5.05e-03	-	no
B	3	GO:0044238	primary metabolic process	65/200	1.31	5.38e-03	-	yes

C	5	GO:0005634	nucleus	39/200	2.49	3.15e-08	-	yes
C	4	GO:0044428	nuclear part	14/200	4.21	1.49e-06	-	yes
C	3	GO:0043234	protein complex	20/200	3.06	2.89e-06	-	yes
C	4	GO:0043231	intracellular membrane-bounded organelle	70/200	1.59	8.09e-06	-	yes
C	3	GO:0043227	membrane-bounded organelle	70/200	1.59	8.13e-06	-	yes
C	3	GO:0043229	intracellular organelle	72/200	1.56	1.25e-05	-	yes
C	3	GO:0005622	intracellular	80/200	1.50	1.31e-05	-	yes
C	3	GO:0044424	intracellular part	77/200	1.51	1.74e-05	-	yes

M	3	GO:0003676	nucleic acid binding	40/200	1.69	3.17e-04	-	no
M	4	GO:0003677	DNA binding	23/200	1.66	6.11e-03	-	no

PS	4	PO:0000037	shoot apex	146/200	1.70	1.88e-18	-	yes
PS	4	PO:0009047	stem	144/200	1.71	3.05e-18	-	yes
PS	5	PO:0009052	pedicel	140/200	1.72	1.09e-17	-	yes
PS	3	PO:0009005	root	146/200	1.62	2.24e-16	-	yes
PS	3	PO:0009031	sepal	147/200	1.59	1.02e-15	-	yes
PS	4	PO:0009001	fruit	152/200	1.55	1.89e-15	-	yes
PS	3	PO:0006342	infructescence	152/200	1.55	1.89e-15	-	yes
PS	3	PO:0009010	seed	151/200	1.54	3.62e-15	-	yes
PS	5	PO:0008034	leaf whorl	147/200	1.56	8.79e-15	-	yes
PS	4	PO:0008033	phyllome whorl	147/200	1.56	8.79e-15	-	yes
PS	4	PO:0009009	embryo	149/200	1.54	1.05e-14	-	yes
PS	5	PO:0008037	seedling	140/200	1.59	3.73e-14	-	yes
PS	4	PO:0000230	inflorescence meristem	128/200	1.65	1.74e-13	-	yes
PS	4	PO:0009026	sporophyll	140/200	1.56	2.38e-13	-	yes
PS	5	PO:0009027	megasporophyll	134/200	1.60	2.55e-13	-	yes
PS	3	PO:0009032	petal	137/200	1.56	5.06e-13	-	yes
PS	3	PO:0006001	phyllome	151/200	1.47	5.18e-13	-	yes
PS	5	PO:0009028	microsporophyll	133/200	1.59	6.60e-13	-	yes
PS	3	PO:0009006	shoot	156/200	1.44	7.63e-13	-	yes
PS	4	PO:0009049	inflorescence	152/200	1.45	1.40e-12	-	yes
PS	4	PO:0009025	leaf	140/200	1.52	1.75e-12	-	yes
PS	5	PO:0009046	flower	151/200	1.45	2.25e-12	-	yes
PS	3	PO:0009013	meristem	128/200	1.59	2.95e-12	-	yes
PS	5	PO:0000013	cauline leaf	124/200	1.61	6.62e-12	-	yes
PS	5	PO:0020039	leaf lamina	127/200	1.54	6.22e-11	-	yes
PS	3	PO:0020091	male gametophyte	127/200	1.53	1.01e-10	-	yes
PS	5	PO:0020038	petiole	116/200	1.52	3.51e-09	-	yes
PS	4	PO:0020030	cotyledon	113/200	1.54	4.01e-09	-	yes
PS	3	PO:0000084	sperm cell	63/200	1.94	2.51e-08	-	no
PS	3	PO:0020097	generative cell	63/200	1.94	2.51e-08	-	no

PG	5	PO:0001078	E expanded cotyledon stage	147/200	1.77	9.09e-21	-	yes
PG	5	PO:0004507	D bilateral stage	146/200	1.77	1.56e-20	-	yes
PG	5	PO:0001081	F mature embryo stage	143/200	1.80	2.11e-20	-	yes
PG	4	PO:0007631	embryo development stages	148/200	1.64	1.96e-17	-	yes
PG	3	PO:0001170	seed development stages	148/200	1.64	3.14e-17	-	yes
PG	5	PO:0001185	C globular stage	139/200	1.69	9.50e-17	-	yes
PG	5	PO:0007604	corolla developmental stages	151/200	1.53	9.54e-15	-	yes
PG	4	PO:0007600	3 floral organ development stages	151/200	1.48	2.63e-13	-	yes
PG	4	PO:0007616	4 anthesis	146/200	1.51	4.56e-13	-	yes
PG	3	PO:0007615	flower development stages	151/200	1.44	4.46e-12	-	yes
PG	5	PO:0007133	leaf production	131/200	1.56	6.70e-12	-	yes
PG	4	PO:0007112	1 main shoot growth	131/200	1.56	6.82e-12	-	yes
PG	3	PO:0007134	A vegetative growth	131/200	1.55	1.21e-11	-	yes
PG	4	PO:0001054	4 leaf senescence stage	120/200	1.56	2.13e-10	-	yes
PG	3	PO:0001050	leaf development stages	120/200	1.56	2.22e-10	-	yes

KW	0	polymerase	-	10/200	6.79	3.17e-07	-	yes
KW	0	nucleus	-	29/200	2.25	1.40e-05	-	no
KW	0	complex	-	22/200	2.60	1.46e-05	-	yes
KW	0	subunit	-	19/200	2.59	5.12e-05	0	yes
KW	0	cellular_component	-	71/200	1.46	1.51e-04	-	no
KW	0	transcription	-	28/200	1.93	2.86e-04	0	yes
KW	0	molecular_function	-	71/200	1.41	4.61e-04	-	no
KW	0	nucleic	-	15/200	2.29	9.44e-04	-	no
KW	0	dependent	-	24/200	1.79	1.96e-03	-	yes
KW	0	ubiquitin	-	11/200	2.45	2.00e-03	-	no
KW	0	biological_process	-	77/200	1.29	3.57e-03	-	no
KW	0	associated	-	14/200	2.05	3.80e-03	-	no
KW	0	containing	-	26/200	1.56	8.82e-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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