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
OMAT2P004420	0.970353	-	AT2G22840	AtGRF1 (GROWTH-REGULATING FACTOR 1)	-	-
OMAT4P109060	0.963331	-	AT4G31877,ath-MIR156c	[AT4G31877]MIR156C, [ath-MIR156c]ath-MIR156c	-	-
OMAT5P115020	0.960746	-	AT5G57390	AIL5 (AINTEGUMENTA-LIKE 5)	-	-
OMAT1P108660	0.959219	-	AT1G27530	FUNCTIONS IN: molecular_function unknown	-	-
OMAT1P019210	0.958178	-	-	-	AT1G68250	unknown protein
OMAT1P018690	0.957281	-	AT1G67100	LBD40 (LOB DOMAIN-CONTAINING PROTEIN 40)	-	-
OMAT2P008395	0.957227	-	AT2G34160	nucleic acid binding	-	-
OMAT5P012890	0.956883	-	AT5G45920	carboxylesterase/ hydrolase/ hydrolase, acting on ester bonds	-	-
OMAT5P110780	0.956455	-	AT5G44120	CRA1 (CRUCIFERINA)	-	-
OMAT5P114480	0.956151	-	-	-	AT5G55410,AT5G55420	[AT5G55410]protease inhibitor/seed storage/lipid transfer protein (LTP) family protein, [AT5G55420]Encodes a Protease inhibitor/seed storage/LTP family protein [pseudogene]
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT4P109700	-0.938569	-	AT4G33530	KUP5	-	-
OMAT3P113750	-0.92962	-	AT3G56240	CCH (COPPER CHAPERONE)	-	-
OMAT1P113460	-0.888323	-	AT1G54410	dehydrin family protein	-	-
OMAT1P007650	-0.886349	-	AT1G20850	XCP2 (xylem cysteine peptidase 2)	-	-
OMAT1P007430	-0.881869	-	AT1G20260	hydrogen ion transporting ATP synthase, rotational mechanism / hydrolase, acting on acid anhydrides, catalyzing transmembrane movement of substances / proton-transporting ATPase, rotational mechanism	-	-
OMAT4P002790	-0.857585	-	AT4G11211	unknown protein	-	-
OMAT1P011370	-0.841486	-	AT1G32440	PKp3 (plastidial pyruvate kinase 3)	-	-
OMAT3P113890	-0.840387	-	AT3G56760	calcium-dependent protein kinase, putative / CDPK, putative	-	-
OMAT5P004000	-0.840377	-	AT5G11710,AT5G11720	[AT5G11710]epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-related, [AT5G11720]alpha-glucosidase 1 (AGLU1)	-	-
OMAT5P117200	-0.838435	-	AT5G63380	4-coumarate--CoA ligase family protein / 4-coumaroyl-CoA synthase family protein	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.89e-09	:20 terms with high significance
2.89e-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:0033036	macromolecule localization	10/200	2.89	7.75e-04	-	no
B	3	GO:0007275	multicellular organismal development	21/200	1.98	1.02e-03	-	no
B	3	GO:0009791	post-embryonic development	12/200	2.03	6.85e-03	-	no
B	3	GO:0048856	anatomical structure development	16/200	1.79	8.75e-03	-	no

C	4	GO:0070013	intracellular organelle lumen	15/200	5.53	1.74e-08	-	no
C	3	GO:0043233	organelle lumen	15/200	5.52	1.80e-08	-	no
C	5	GO:0031981	nuclear lumen	11/200	4.55	6.57e-06	-	no
C	3	GO:0043229	intracellular organelle	71/200	1.54	2.44e-05	-	no
C	3	GO:0005622	intracellular	79/200	1.48	2.50e-05	-	no
C	3	GO:0044424	intracellular part	76/200	1.49	3.32e-05	-	no
C	4	GO:0044428	nuclear part	12/200	3.61	3.38e-05	-	no
C	3	GO:0044446	intracellular organelle part	29/200	2.02	9.81e-05	-	no
C	3	GO:0044422	organelle part	29/200	2.02	9.96e-05	-	no
C	3	GO:0043228	non-membrane-bounded organelle	16/200	2.68	1.13e-04	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	16/200	2.68	1.13e-04	-	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	5	GO:0005739	mitochondrion	15/200	2.34	7.55e-04	-	no
C	3	GO:0043234	protein complex	15/200	2.29	9.53e-04	-	no
C	4	GO:0005737	cytoplasm	52/200	1.39	4.20e-03	-	no
C	4	GO:0044444	cytoplasmic part	48/200	1.38	6.50e-03	-	no
C	5	GO:0005634	nucleus	25/200	1.60	7.34e-03	-	no

PS	4	PO:0000037	shoot apex	134/200	1.56	2.24e-12	-	yes
PS	5	PO:0009052	pedicel	126/200	1.55	5.46e-11	-	yes
PS	3	PO:0009006	shoot	152/200	1.40	5.67e-11	-	yes
PS	5	PO:0009027	megasporophyll	128/200	1.52	1.04e-10	-	yes
PS	3	PO:0006001	phyllome	145/200	1.41	2.57e-10	-	yes
PS	5	PO:0009028	microsporophyll	126/200	1.50	5.93e-10	-	no
PS	5	PO:0020038	petiole	118/200	1.55	6.17e-10	-	no
PS	3	PO:0009005	root	132/200	1.47	6.57e-10	-	yes
PS	4	PO:0009026	sporophyll	132/200	1.47	6.67e-10	-	yes
PS	5	PO:0020039	leaf lamina	124/200	1.50	9.67e-10	-	no
PS	4	PO:0009025	leaf	133/200	1.45	1.50e-09	-	yes
PS	5	PO:0008034	leaf whorl	135/200	1.43	1.93e-09	-	yes
PS	4	PO:0008033	phyllome whorl	135/200	1.43	1.93e-09	-	yes
PS	3	PO:0009032	petal	128/200	1.46	2.89e-09	-	yes
PS	3	PO:0009031	sepal	131/200	1.42	1.19e-08	-	yes
PS	4	PO:0009001	fruit	136/200	1.38	2.29e-08	-	yes
PS	3	PO:0006342	infructescence	136/200	1.38	2.29e-08	-	yes
PS	4	PO:0009047	stem	122/200	1.45	2.73e-08	-	no
PS	3	PO:0009010	seed	135/200	1.38	3.47e-08	-	yes
PS	4	PO:0009009	embryo	133/200	1.38	6.79e-08	-	yes
PS	5	PO:0000013	cauline leaf	113/200	1.46	1.02e-07	-	no
PS	4	PO:0009049	inflorescence	140/200	1.34	1.16e-07	-	yes
PS	5	PO:0008037	seedling	124/200	1.40	1.25e-07	-	yes
PS	5	PO:0009046	flower	139/200	1.34	1.60e-07	-	yes
PS	3	PO:0009013	meristem	115/200	1.43	2.55e-07	-	no
PS	4	PO:0020030	cotyledon	106/200	1.44	9.16e-07	-	no
PS	4	PO:0000230	inflorescence meristem	107/200	1.38	9.50e-06	-	no
PS	3	PO:0020091	male gametophyte	109/200	1.31	7.49e-05	-	yes
PS	3	PO:0000084	sperm cell	51/200	1.57	2.76e-04	-	yes
PS	3	PO:0020097	generative cell	51/200	1.57	2.76e-04	-	yes
PS	4	PO:0006345	pollen tube	41/200	1.41	8.53e-03	-	no

PG	3	PO:0001170	seed development stages	139/200	1.54	1.09e-12	-	yes
PG	5	PO:0001081	F mature embryo stage	128/200	1.61	1.28e-12	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	131/200	1.58	2.16e-12	-	yes
PG	5	PO:0004507	D bilateral stage	129/200	1.57	8.50e-12	-	yes
PG	4	PO:0007631	embryo development stages	133/200	1.48	2.80e-10	-	yes
PG	5	PO:0001185	C globular stage	125/200	1.52	2.80e-10	-	yes
PG	5	PO:0007604	corolla developmental stages	137/200	1.39	1.34e-08	-	yes
PG	3	PO:0007134	A vegetative growth	123/200	1.45	1.63e-08	-	no
PG	4	PO:0007616	4 anthesis	135/200	1.39	1.76e-08	-	yes
PG	4	PO:0001054	4 leaf senescence stage	113/200	1.47	7.78e-08	-	no
PG	3	PO:0001050	leaf development stages	113/200	1.47	8.04e-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	4	PO:0007600	3 floral organ development stages	137/200	1.34	1.55e-07	-	yes
PG	3	PO:0007615	flower development stages	138/200	1.32	5.73e-07	-	yes

KW	0	storage	-	10/200	8.80	2.28e-08	-	no
KW	0	complex	-	22/200	2.60	1.46e-05	-	no
KW	0	transcriptional	-	10/200	4.15	3.47e-05	-	no
KW	0	subunit	-	19/200	2.59	5.12e-05	-	no
KW	0	ubiquitin	-	13/200	2.89	1.88e-04	-	no
KW	0	nuclear	-	10/200	3.25	2.91e-04	-	no
KW	0	alpha	-	17/200	2.33	4.14e-04	-	no
KW	0	mitochondrion	-	14/200	2.55	4.44e-04	-	no
KW	0	translation	-	12/200	2.42	1.54e-03	-	no
KW	0	development	-	15/200	2.15	1.84e-03	-	no
KW	0	cellular_component	-	65/200	1.33	3.56e-03	-	yes
KW	0	biological_process	-	77/200	1.29	3.57e-03	-	no

(*1)	[B]:Biological process(Gene ontology), [C]:Cellular component(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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