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
AT1G31010.1	0.952843	OSB4 (organellar single-stranded DNA binding protein 4)	-	-	-	-
AT3G63400.1	0.947808	peptidyl-prolyl cis-trans isomerase cyclophilin-type family protein	OMAT3P018140	-	-	-
AT4G38440.1	0.945986	LOCATED IN: chloroplast	OMAT4P013380	-	-	-
AT3G04020.1	0.942815	unknown protein	-	-	-	-
AT2G41945.3	0.938078	unknown protein	-	-	-	-
AT2G19490.1	0.937937	recA family protein	OMAT2P003265	-	-	-
AT5G44170.1	0.931985	FUNCTIONS IN: molecular_function unknown	OMAT5P012270	-	-	-
AT2G06040.1	0.929825	FUNCTIONS IN: molecular_function unknown	OMAT2P101240	-	-	-
AT2G32070.1	0.929722	CCR4-NOT transcription complex protein, putative	OMAT2P106850	-	-	-
AT1G04945.2	0.929642	FUNCTIONS IN: molecular_function unknown	OMAT1P001550	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT3G02470.1	-0.873454	SAMDC (S-ADENOSYLMETHIONINE DECARBOXYLASE)	OMAT3P000660	-	OMAT3P100630	-
AT3G15810.1	-0.870089	unknown protein	OMAT3P105310	-	-	-
AT3G02468.1	-0.863292	CPuORF9 (Conserved peptide upstream open reading frame 9)	OMAT3P000660	-	OMAT3P100630	-
AT1G07600.1	-0.856233	MT1A (METALLOTHIONEIN 1A)	OMAT1P102300	-	-	-
AT5G02380.1	-0.826978	MT2B (METALLOTHIONEIN 2B)	OMAT5P100430	-	-	-
AT3G47540.1	-0.808005	chitinase, putative	OMAT3P012300	-	-	-
AT3G43640.1	-0.789694	transposable element gene	-	-	-	-
AT3G05935.1	-0.768808	unknown protein	OMAT3P101980	-	-	-
AT1G29930.1	-0.760885	CAB1 (CHLOROPHYLL A/B BINDING PROTEIN 1)	OMAT1P010480	-	-	-
AT4G14910.2	-0.759788	imidazoleglycerol-phosphate dehydratase, putative	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.33e-13	:20 terms with high significance
2.33e-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:0006396	RNA processing	11/200	4.97	2.68e-06	3.82E-16	yes
B	5	GO:0090304	nucleic acid metabolic process	32/200	2.13	1.61e-05	-	yes
B	4	GO:0034641	cellular nitrogen compound metabolic process	38/200	1.95	1.98e-05	-	yes
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	34/200	2.01	2.84e-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	18/200	2.12	9.46e-04	-	yes
B	3	GO:0007275	multicellular organismal development	20/200	1.88	2.32e-03	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	49/200	1.39	5.33e-03	-	yes
B	4	GO:0010467	gene expression	31/200	1.52	6.76e-03	1.77E-15	yes

C	5	GO:0005634	nucleus	41/200	2.62	3.19e-09	-	yes
C	4	GO:0044428	nuclear part	17/200	5.11	8.19e-09	-	no
C	3	GO:0005622	intracellular	82/200	1.54	3.38e-06	-	yes
C	5	GO:0031981	nuclear lumen	11/200	4.55	6.57e-06	-	no
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:0044424	intracellular part	77/200	1.51	1.74e-05	-	yes
C	4	GO:0070013	intracellular organelle lumen	11/200	4.06	2.06e-05	-	no
C	3	GO:0043233	organelle lumen	11/200	4.05	2.11e-05	-	no
C	3	GO:0043234	protein complex	14/200	2.14	2.55e-03	-	no
C	3	GO:0043228	non-membrane-bounded organelle	13/200	2.18	2.83e-03	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	13/200	2.18	2.83e-03	-	no
C	3	GO:0044446	intracellular organelle part	24/200	1.67	4.76e-03	-	no
C	3	GO:0044422	organelle part	24/200	1.67	4.81e-03	-	no
C	5	GO:0005739	mitochondrion	13/200	2.03	5.27e-03	-	no

PS	4	PO:0000037	shoot apex	148/200	1.72	1.29e-19	-	no
PS	5	PO:0009052	pedicel	140/200	1.72	1.09e-17	-	no
PS	3	PO:0009010	seed	154/200	1.57	8.56e-17	-	no
PS	4	PO:0009001	fruit	154/200	1.57	1.54e-16	-	no
PS	3	PO:0006342	infructescence	154/200	1.57	1.54e-16	-	no
PS	4	PO:0009009	embryo	149/200	1.54	1.05e-14	-	no
PS	3	PO:0009031	sepal	145/200	1.57	1.09e-14	-	no
PS	5	PO:0008034	leaf whorl	146/200	1.55	2.80e-14	-	no
PS	4	PO:0008033	phyllome whorl	146/200	1.55	2.80e-14	-	no
PS	4	PO:0009049	inflorescence	154/200	1.47	1.47e-13	-	no
PS	3	PO:0009005	root	140/200	1.56	2.33e-13	-	no
PS	5	PO:0009046	flower	153/200	1.47	2.44e-13	-	no
PS	3	PO:0006001	phyllome	150/200	1.46	1.55e-12	-	no
PS	4	PO:0009047	stem	132/200	1.56	3.12e-12	-	no
PS	3	PO:0009006	shoot	154/200	1.42	6.96e-12	-	no
PS	4	PO:0009025	leaf	137/200	1.49	3.63e-11	-	no
PS	5	PO:0008037	seedling	132/200	1.50	1.38e-10	-	no
PS	3	PO:0009032	petal	131/200	1.49	1.97e-10	-	no
PS	4	PO:0000230	inflorescence meristem	117/200	1.51	6.00e-09	-	no
PS	5	PO:0009027	megasporophyll	123/200	1.46	8.65e-09	-	no
PS	4	PO:0009026	sporophyll	129/200	1.43	9.06e-09	-	no
PS	5	PO:0009028	microsporophyll	122/200	1.45	1.81e-08	-	no
PS	5	PO:0020038	petiole	114/200	1.50	1.84e-08	-	no
PS	3	PO:0009013	meristem	118/200	1.47	2.52e-08	-	no
PS	5	PO:0020039	leaf lamina	120/200	1.46	2.80e-08	-	no
PS	5	PO:0000013	cauline leaf	114/200	1.48	4.69e-08	-	no
PS	3	PO:0020091	male gametophyte	117/200	1.41	4.12e-07	-	no
PS	4	PO:0020030	cotyledon	104/200	1.42	3.62e-06	-	no
PS	3	PO:0000084	sperm cell	57/200	1.76	4.01e-06	-	no
PS	3	PO:0020097	generative cell	57/200	1.76	4.01e-06	-	no

PG	5	PO:0001081	F mature embryo stage	146/200	1.84	3.10e-22	-	no
PG	5	PO:0001078	E expanded cotyledon stage	149/200	1.80	5.25e-22	-	no
PG	5	PO:0004507	D bilateral stage	146/200	1.77	1.56e-20	-	no
PG	4	PO:0007631	embryo development stages	151/200	1.68	3.72e-19	-	no
PG	3	PO:0001170	seed development stages	151/200	1.67	6.09e-19	-	no
PG	5	PO:0007604	corolla developmental stages	152/200	1.54	2.87e-15	-	no
PG	4	PO:0007600	3 floral organ development stages	153/200	1.50	2.62e-14	-	no
PG	5	PO:0001185	C globular stage	134/200	1.63	3.21e-14	-	no
PG	3	PO:0007615	flower development stages	154/200	1.47	1.59e-13	-	no
PG	4	PO:0007616	4 anthesis	144/200	1.48	3.86e-12	-	no
PG	5	PO:0007133	leaf production	126/200	1.50	7.53e-10	-	no
PG	4	PO:0007112	1 main shoot growth	126/200	1.50	7.65e-10	-	no
PG	3	PO:0007134	A vegetative growth	126/200	1.49	1.28e-09	-	no
PG	4	PO:0001054	4 leaf senescence stage	117/200	1.52	3.02e-09	-	no
PG	3	PO:0001050	leaf development stages	117/200	1.52	3.13e-09	-	no

KW	0	cellular_component	-	80/200	1.64	3.29e-07	-	no
KW	0	complex	-	25/200	2.95	4.02e-07	-	no
KW	0	biological_process	-	91/200	1.52	1.06e-06	-	no
KW	0	pentatricopeptide	-	13/200	4.48	1.56e-06	-	no
KW	0	repeat	-	31/200	2.39	2.09e-06	-	no
KW	0	molecular_function	-	77/200	1.52	1.22e-05	-	no
KW	0	ipr002885	-	11/200	3.92	2.84e-05	-	no
KW	0	nucleus	-	27/200	2.09	9.28e-05	-	yes
KW	0	nucleic	-	17/200	2.60	1.10e-04	-	no
KW	0	expanded	-	13/200	2.98	1.40e-04	-	no
KW	0	nucleotide	-	16/200	2.51	2.43e-04	-	no
KW	0	subunit	-	17/200	2.32	4.39e-04	4.21E-16	no
KW	0	containing	-	30/200	1.80	5.86e-04	5.00E-20	no
KW	0	transcription	-	27/200	1.86	6.37e-04	1.02E-15	no
KW	0	embryo	-	16/200	2.30	6.56e-04	-	no
KW	0	cotyledon	-	13/200	2.47	8.96e-04	-	no
KW	0	bilateral	-	10/200	2.74	1.20e-03	-	no
KW	0	region	-	25/200	1.73	2.63e-03	-	no
KW	0	ubiquitin	-	10/200	2.23	5.81e-03	-	no
KW	0	intracellular	-	11/200	2.13	6.01e-03	-	no
KW	0	mitochondrion	-	11/200	2.01	9.51e-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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