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
AT4G24680.1	0.842064	FUNCTIONS IN: molecular_function unknown	OMAT4P007690	-	-	-
AT1G55860.1	0.828578	UPL1 (UBIQUITIN-PROTEIN LIGASE 1)	OMAT1P113880	-	-	-
AT5G49640.1	0.800714	unknown protein	-	-	OMAT5P112700	-
AT4G10940.1	0.790063	PHD finger family protein	-	-	-	-
AT4G00450.1	0.784926	CRP (CRYPTIC PRECOCIOUS)	OMAT4P000180	-	-	-
AT1G73960.1	0.782571	TAF2 (TBP-ASSOCIATED FACTOR 2)	OMAT1P118930	-	-	-
AT1G29240.1	0.779081	unknown protein	OMAT1P109230	-	-	-
AT3G32024.1	0.774745	transposable element gene	-	-	-	-
AT4G19040.2	0.773823	EDR2	-	-	-	-
AT1G71960.1	0.771295	ABC transporter family protein	OMAT1P118220,OMAT1P118230	[OMAT1P118220]-, [OMAT1P118230]-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G32610.1	-0.751828	transposable element gene	-	-	-	-
AT1G21510.1	-0.733691	unknown protein	-	-	-	-
AT2G04870.1	-0.708522	unknown protein	-	-	-	-
AT5G49200.1	-0.692522	WD-40 repeat family protein / zfwd4 protein (ZFWD4)	-	-	-	-
AT1G30950.1	-0.673926	UFO (UNUSUAL FLORAL ORGANS)	-	-	-	-
AT1G29620.1	-0.655672	unknown protein	-	-	-	-
AT2G17780.1	-0.652138	MCA2 (mid1-complementing activity 2)	OMAT2P102360	-	-	-
AT1G37669.1	-0.645959	transposable element gene	-	-	-	-
AT5G31919.1	-0.644534	transposable element gene	-	-	-	-
AT2G10105.1	-0.641996	transposable element gene	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 5.44e-12	:20 terms with high significance
5.44e-12 <	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:0016070	RNA metabolic process	18/200	2.12	9.46e-04	-	no
B	5	GO:0032774	RNA biosynthetic process	13/200	2.37	1.31e-03	-	no
B	4	GO:0048608	reproductive structure development	12/200	2.46	1.34e-03	-	no
B	3	GO:0048856	anatomical structure development	18/200	2.01	1.70e-03	-	no
B	3	GO:0009791	post-embryonic development	13/200	2.20	2.66e-03	-	no
B	3	GO:0022414	reproductive process	13/200	2.16	3.12e-03	-	no
B	3	GO:0003006	reproductive developmental process	12/200	2.18	3.82e-03	-	no
B	4	GO:0048513	organ development	10/200	2.26	5.21e-03	-	no
B	4	GO:0048731	system development	10/200	2.26	5.26e-03	-	no
B	5	GO:0051252	regulation of RNA metabolic process	11/200	2.10	6.63e-03	-	no
B	3	GO:0009628	response to abiotic stimulus	14/200	1.89	7.85e-03	-	no

C	5	GO:0005634	nucleus	34/200	2.17	5.61e-06	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	66/200	1.50	1.12e-04	-	yes
C	3	GO:0043227	membrane-bounded organelle	66/200	1.50	1.12e-04	-	yes
C	4	GO:0044428	nuclear part	11/200	3.31	1.44e-04	-	no
C	3	GO:0043229	intracellular organelle	66/200	1.43	5.01e-04	-	yes
C	3	GO:0044424	intracellular part	71/200	1.39	6.12e-04	-	yes
C	3	GO:0005622	intracellular	73/200	1.37	7.97e-04	-	yes
C	4	GO:0005886	plasma membrane	22/200	1.78	3.19e-03	4.72E-12	yes

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	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	12/200	2.70	5.83e-04	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	12/200	2.67	6.36e-04	-	no
M	4	GO:0003723	RNA binding	15/200	2.16	1.74e-03	-	no
M	3	GO:0000166	nucleotide binding	23/200	1.74	3.40e-03	-	no

PS	4	PO:0000230	inflorescence meristem	135/200	1.74	5.88e-17	-	yes
PS	3	PO:0009013	meristem	137/200	1.71	1.36e-16	-	yes
PS	5	PO:0009052	pedicel	134/200	1.65	1.39e-14	-	yes
PS	4	PO:0009047	stem	137/200	1.62	1.47e-14	-	yes
PS	5	PO:0008037	seedling	139/200	1.57	1.13e-13	-	yes
PS	4	PO:0000037	shoot apex	136/200	1.58	2.75e-13	-	yes
PS	5	PO:0000013	cauline leaf	127/200	1.64	3.09e-13	-	yes
PS	4	PO:0020030	cotyledon	122/200	1.66	8.79e-13	-	yes
PS	5	PO:0020039	leaf lamina	131/200	1.59	1.19e-12	-	yes
PS	4	PO:0009025	leaf	140/200	1.52	1.75e-12	4.19E-17	yes
PS	3	PO:0009005	root	137/200	1.52	5.44e-12	-	yes
PS	5	PO:0020038	petiole	123/200	1.62	5.60e-12	-	yes
PS	5	PO:0009027	megasporophyll	130/200	1.55	1.53e-11	-	yes
PS	4	PO:0009009	embryo	142/200	1.47	2.13e-11	-	yes
PS	3	PO:0009032	petal	133/200	1.52	2.95e-11	-	yes
PS	5	PO:0008034	leaf whorl	139/200	1.47	4.67e-11	-	yes
PS	4	PO:0008033	phyllome whorl	139/200	1.47	4.67e-11	-	yes
PS	3	PO:0009010	seed	142/200	1.45	6.59e-11	-	yes
PS	5	PO:0009028	microsporophyll	128/200	1.53	9.47e-11	-	yes
PS	3	PO:0006001	phyllome	146/200	1.42	9.74e-11	-	yes
PS	4	PO:0009001	fruit	142/200	1.44	1.05e-10	-	yes
PS	3	PO:0006342	infructescence	142/200	1.44	1.05e-10	-	yes
PS	3	PO:0009031	sepal	136/200	1.47	1.40e-10	-	yes
PS	3	PO:0020091	male gametophyte	126/200	1.52	2.54e-10	-	yes
PS	3	PO:0009006	shoot	148/200	1.36	2.72e-09	-	yes
PS	4	PO:0009026	sporophyll	130/200	1.44	3.88e-09	-	yes
PS	5	PO:0009046	flower	143/200	1.37	5.73e-09	-	yes
PS	4	PO:0009049	inflorescence	143/200	1.37	9.53e-09	-	yes
PS	3	PO:0000084	sperm cell	62/200	1.91	6.20e-08	-	no
PS	3	PO:0020097	generative cell	62/200	1.91	6.20e-08	-	no
PS	4	PO:0006345	pollen tube	53/200	1.82	3.35e-06	-	no
PS	4	PO:0005679	epidermis	28/200	2.26	1.74e-05	-	yes
PS	3	PO:0009014	dermal tissue	28/200	2.26	1.76e-05	-	yes
PS	5	PO:0006016	leaf epidermis	26/200	2.34	1.87e-05	-	yes
PS	5	PO:0006035	shoot epidermis	26/200	2.32	2.12e-05	-	yes
PS	3	PO:0004013	epidermal cell	27/200	2.26	2.36e-05	-	yes
PS	4	PO:0000293	guard cell	25/200	2.32	2.94e-05	-	yes
PS	4	PO:0000351	guard mother cell	25/200	2.31	3.17e-05	-	yes
PS	3	PO:0000070	meristemoid	25/200	2.31	3.26e-05	-	yes
PS	5	PO:0000349	epidermal initial	25/200	2.22	6.40e-05	-	yes
PS	4	PO:0004011	initial cell	25/200	2.20	7.11e-05	-	yes
PS	3	PO:0004010	meristematic cell	25/200	2.20	7.29e-05	-	yes

PG	5	PO:0001081	F mature embryo stage	132/200	1.66	1.77e-14	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	135/200	1.63	3.04e-14	-	yes
PG	5	PO:0001185	C globular stage	134/200	1.63	3.21e-14	-	yes
PG	5	PO:0004507	D bilateral stage	134/200	1.63	4.57e-14	-	yes
PG	4	PO:0007631	embryo development stages	140/200	1.55	2.50e-13	-	yes
PG	3	PO:0001170	seed development stages	140/200	1.55	3.75e-13	-	yes
PG	3	PO:0007134	A vegetative growth	133/200	1.57	1.61e-12	-	yes
PG	5	PO:0007133	leaf production	132/200	1.57	2.44e-12	-	yes
PG	4	PO:0007112	1 main shoot growth	132/200	1.57	2.49e-12	-	yes
PG	4	PO:0001054	4 leaf senescence stage	122/200	1.59	3.29e-11	-	yes
PG	3	PO:0001050	leaf development stages	122/200	1.59	3.44e-11	-	yes
PG	5	PO:0007604	corolla developmental stages	142/200	1.44	1.48e-10	-	yes
PG	4	PO:0007616	4 anthesis	139/200	1.43	5.26e-10	-	yes
PG	4	PO:0007600	3 floral organ development stages	143/200	1.40	9.41e-10	-	yes
PG	3	PO:0007615	flower development stages	144/200	1.37	4.22e-09	-	yes
PG	5	PO:0007605	androecium developmental stages	54/200	1.84	1.74e-06	-	no

KW	0	ipr016024	-	16/200	8.67	6.62e-12	-	no
KW	0	armadillo	-	16/200	8.55	8.12e-12	-	no
KW	0	ipr011989	-	10/200	9.19	1.46e-08	-	no
KW	0	helical	-	12/200	3.98	1.21e-05	-	no
KW	0	nuclear	-	11/200	3.58	6.87e-05	-	no
KW	0	nucleic	-	16/200	2.45	3.32e-04	-	no
KW	0	nucleus	-	25/200	1.94	5.26e-04	-	no
KW	0	region	-	27/200	1.87	5.86e-04	5.00E-31	no
KW	0	dependent	-	25/200	1.87	9.12e-04	2.39E-15	no
KW	0	terminal	-	32/200	1.66	1.57e-03	-	no
KW	0	superfamily	-	10/200	2.64	1.61e-03	6.00E-56	yes
KW	0	associated	-	14/200	2.05	3.80e-03	-	no
KW	0	conserved	-	23/200	1.70	4.63e-03	4.72E-12	yes
KW	0	containing	-	26/200	1.56	8.82e-03	-	no
KW	0	expression	-	10/200	2.07	9.78e-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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