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
OMAT1P015990	0.870227	-	AT1G58150	unknown protein	AT1G58140	transposable element gene
OMAT3P012780	0.851634	-	AT3G48680	GAMMA CAL2 (GAMMA CARBONIC ANHYDRASE-LIKE 2)	-	-
OMAT4P008880	0.851196	-	AT4G27690	VPS26B (VACUOLAR PROTEIN SORTING 26B)	-	-
OMAT5P006980	0.846352	-	AT5G20120	unknown protein	-	-
OMAT1P016375	0.845971	-	AT1G59900	AT-E1 ALPHA	-	-
OMAT3P017700	0.838259	-	AT3G62130	epimerase-related	-	-
OMAT1P014535	0.82579	-	AT1G52740	HTA9 (HISTONE H2A PROTEIN 9)	-	-
OMAT5P014100	0.819378	-	AT5G49400	zinc knuckle (CCHC-type) family protein	-	-
OMAT5P020580	0.818827	-	AT5G66360	ribosomal RNA adenine dimethylase family protein	-	-
OMAT3P010730	0.817259	-	AT3G28730	ATHMG (ARABIDOPSIS THALIANA HIGH MOBILITY GROUP)	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT5P100430	-0.760915	-	AT5G02380	MT2B (METALLOTHIONEIN 2B)	AT5G02370	kinesin motor protein-related
OMAT2P002950	-0.693724	-	-	-	AT2G18540	cupin family protein
OMAT3P012300	-0.681245	-	AT3G47540	chitinase, putative	-	-
OMAT1P111410	-0.649987	-	-	-	AT1G45688	unknown protein
OMAT2P004810	-0.649622	-	-	-	AT2G23810	TET8 (TETRASPANIN8)
OMAT4P101120	-0.646797	-	-	-	AT4G03280	PETC (PHOTOSYNTHETIC ELECTRON TRANSFER C)
OMAT5P103415	-0.638994	-	AT5G12140	ATCYS1 (A. thaliana cystatin-1)	-	-
OMAT3P109770	-0.638112	-	AT3G43190	SUS4	-	-
OMAT3P107880	-0.636183	-	-	-	AT3G23820	GAE6 (UDP-D-GLUCURONATE 4-EPIMERASE 6)
OMAT4P104150	-0.625127	-	-	-	AT4G16990	RLM3 (RESISTANCE TO LEPTOSPHAERIA MACULANS 3)

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.41e-26	:20 terms with high significance
1.41e-26 <	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	25/200	1.66	4.44e-03	-	no
B	5	GO:0016070	RNA metabolic process	16/200	1.88	5.39e-03	-	no
B	3	GO:0009056	catabolic process	10/200	2.10	8.89e-03	-	no

C	3	GO:0005622	intracellular	83/200	1.56	1.67e-06	-	yes
C	3	GO:0044424	intracellular part	78/200	1.53	8.97e-06	-	yes
C	4	GO:0043231	intracellular membrane-bounded organelle	69/200	1.57	1.61e-05	-	yes
C	3	GO:0043227	membrane-bounded organelle	69/200	1.57	1.62e-05	-	yes
C	3	GO:0043229	intracellular organelle	70/200	1.52	4.65e-05	-	yes
C	4	GO:0005737	cytoplasm	59/200	1.58	7.56e-05	-	yes
C	5	GO:0005634	nucleus	30/200	1.92	1.95e-04	-	no
C	4	GO:0044444	cytoplasmic part	53/200	1.53	4.30e-04	-	yes
C	5	GO:0005739	mitochondrion	14/200	2.19	2.06e-03	-	no
C	3	GO:0043234	protein complex	13/200	1.99	6.37e-03	-	no

M	3	GO:0003676	nucleic acid binding	41/200	1.73	1.57e-04	-	no
M	3	GO:0005515	protein binding	30/200	1.92	1.98e-04	-	no
M	4	GO:0003677	DNA binding	23/200	1.66	6.11e-03	-	no

PS	4	PO:0009047	stem	165/200	1.96	1.11e-32	-	yes
PS	3	PO:0009013	meristem	159/200	1.98	8.42e-31	-	yes
PS	4	PO:0000230	inflorescence meristem	156/200	2.01	1.99e-30	-	yes
PS	5	PO:0009052	pedicel	158/200	1.94	2.41e-29	-	yes
PS	4	PO:0000037	shoot apex	162/200	1.88	4.32e-29	-	yes
PS	5	PO:0020039	leaf lamina	158/200	1.92	1.46e-28	-	yes
PS	4	PO:0009025	leaf	166/200	1.81	3.44e-28	-	yes
PS	5	PO:0000013	cauline leaf	152/200	1.97	8.69e-28	-	yes
PS	5	PO:0008037	seedling	161/200	1.82	7.62e-27	-	yes
PS	3	PO:0009005	root	162/200	1.80	1.85e-26	-	yes
PS	5	PO:0009027	megasporophyll	156/200	1.86	4.48e-26	-	yes
PS	3	PO:0009031	sepal	163/200	1.76	1.15e-25	-	yes
PS	4	PO:0020030	cotyledon	145/200	1.97	1.41e-25	-	no
PS	5	PO:0009028	microsporophyll	155/200	1.85	1.93e-25	-	yes
PS	4	PO:0009009	embryo	166/200	1.72	3.32e-25	-	yes
PS	3	PO:0009032	petal	158/200	1.80	4.26e-25	-	yes
PS	5	PO:0020038	petiole	147/200	1.93	4.32e-25	-	yes
PS	5	PO:0008034	leaf whorl	163/200	1.73	1.82e-24	-	yes
PS	4	PO:0008033	phyllome whorl	163/200	1.73	1.82e-24	-	yes
PS	3	PO:0009010	seed	166/200	1.70	1.82e-24	-	yes
PS	4	PO:0009001	fruit	166/200	1.69	3.71e-24	-	yes
PS	3	PO:0006342	infructescence	166/200	1.69	3.71e-24	-	yes
PS	3	PO:0006001	phyllome	169/200	1.65	8.00e-24	-	yes
PS	4	PO:0009026	sporophyll	157/200	1.74	5.95e-23	-	yes
PS	3	PO:0020091	male gametophyte	150/200	1.81	1.10e-22	-	no
PS	3	PO:0009006	shoot	171/200	1.57	8.33e-22	-	yes
PS	5	PO:0009046	flower	166/200	1.60	7.21e-21	-	yes
PS	4	PO:0009049	inflorescence	166/200	1.59	1.59e-20	-	yes
PS	3	PO:0000084	sperm cell	76/200	2.34	2.76e-14	-	no
PS	3	PO:0020097	generative cell	76/200	2.34	2.76e-14	-	no
PS	4	PO:0006345	pollen tube	52/200	1.78	7.40e-06	-	no
PS	3	PO:0000070	meristemoid	20/200	1.85	2.90e-03	-	no
PS	5	PO:0000349	epidermal initial	20/200	1.77	4.63e-03	-	no
PS	4	PO:0004011	initial cell	20/200	1.76	4.98e-03	-	no
PS	3	PO:0004010	meristematic cell	20/200	1.76	5.06e-03	-	no
PS	4	PO:0000293	guard cell	19/200	1.77	5.80e-03	-	no
PS	4	PO:0000351	guard mother cell	19/200	1.76	6.08e-03	-	no
PS	5	PO:0006016	leaf epidermis	19/200	1.71	8.22e-03	-	no
PS	3	PO:0004013	epidermal cell	20/200	1.68	8.57e-03	-	no
PS	5	PO:0006035	shoot epidermis	19/200	1.70	8.84e-03	-	no

PG	5	PO:0001081	F mature embryo stage	159/200	2.00	2.19e-31	-	yes
PG	5	PO:0001185	C globular stage	161/200	1.96	3.95e-31	-	yes
PG	5	PO:0004507	D bilateral stage	161/200	1.95	6.71e-31	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	160/200	1.93	1.13e-29	-	yes
PG	3	PO:0007134	A vegetative growth	160/200	1.89	1.75e-28	-	yes
PG	5	PO:0007133	leaf production	159/200	1.89	3.85e-28	-	yes
PG	4	PO:0007112	1 main shoot growth	159/200	1.89	3.96e-28	-	yes
PG	4	PO:0007631	embryo development stages	163/200	1.81	3.71e-27	-	yes
PG	3	PO:0001170	seed development stages	163/200	1.80	6.68e-27	-	yes
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:0007604	corolla developmental stages	165/200	1.67	3.21e-23	-	yes
PG	4	PO:0007616	4 anthesis	162/200	1.67	3.51e-22	-	yes
PG	4	PO:0007600	3 floral organ development stages	166/200	1.63	4.44e-22	-	yes
PG	3	PO:0007615	flower development stages	166/200	1.58	1.76e-20	-	yes
PG	5	PO:0007605	androecium developmental stages	65/200	2.22	4.86e-11	-	no

KW	0	complex	-	22/200	2.60	1.46e-05	-	no
KW	0	ligase	-	13/200	3.33	4.29e-05	-	no
KW	0	ubiquitin	-	14/200	3.12	5.15e-05	-	no
KW	0	cellular_component	-	69/200	1.42	4.70e-04	-	no
KW	0	finger	-	19/200	2.05	1.04e-03	-	no
KW	0	nucleus	-	24/200	1.86	1.18e-03	-	no
KW	0	containing	-	29/200	1.74	1.22e-03	-	no
KW	0	mitochondrion	-	13/200	2.37	1.33e-03	-	no
KW	0	intracellular	-	12/200	2.33	2.19e-03	-	no
KW	0	nucleic	-	14/200	2.14	2.52e-03	-	no
KW	0	biological_process	-	76/200	1.27	5.51e-03	-	yes
KW	0	transcription	-	24/200	1.65	5.60e-03	-	no
KW	0	subunit	-	14/200	1.91	7.15e-03	-	no
KW	0	encodes	-	37/200	1.45	7.61e-03	-	no
KW	0	cyclin	-	10/200	2.14	7.70e-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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