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
AT5G55125.1	0.986129	unknown protein	OMAT5P016290	-	OMAT5P114360	-
AT5G64670.1	0.983172	ribosomal protein L15 family protein	OMAT5P117680	-	-	-
AT2G44510.1	0.982383	p21Cip1-binding protein-related	OMAT2P012390	-	-	-
AT5G61310.1	0.980489	cytochrome c oxidase subunit Vc, putative / COX5C, putative	OMAT5P116480	-	-	-
AtsnoR8b	0.980155	AtsnoR8b	OMAT3P010450	-	-	-
AT5G02610.1	0.980139	60S ribosomal protein L35 (RPL35D)	OMAT5P000650	-	-	-
AT3G55340.1	0.979365	PHIP1 (PHRAGMOPLASTIN INTERACTING PROTEIN 1)	OMAT3P015210	-	-	-
AtsnoR18a	0.978933	AtsnoR18a	-	-	-	-
AT3G58193.1	0.978933	snoRNA	-	-	-	-
AT1G03360.1	0.978862	ATRRP4 (ARABIDOPSIS THALIANA RIBOSOMAL RNA PROCESSING 4)	OMAT1P001010	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G17170.1	-0.749765	RABB1C (ARABIDOPSIS RAB GTPASE HOMOLOG B1C)	OMAT4P104230	-	-	-
AT1G20620.1	-0.729728	CAT3 (CATALASE 3)	OMAT1P007530,OMAT1P007540	[OMAT1P007530]-, [OMAT1P007540]-	OMAT1P106670	-
AT1G51402.1	-0.713798	unknown protein	OMAT1P014180	-	OMAT1P112450	-
AT3G03150.1	-0.688043	unknown protein	OMAT3P100900,OMAT3P100910	[OMAT3P100900]-, [OMAT3P100910]-	-	-
AT3G43640.1	-0.682758	transposable element gene	-	-	-	-
AT4G13460.1	-0.675546	SUVH9	OMAT4P102930	-	-	-
AT3G49460.1	-0.674694	60S acidic ribosomal protein-related	-	-	-	-
AT1G34220.1	-0.672345	unknown protein	OMAT1P110670	-	-	-
AT3G15450.1	-0.672155	unknown protein	OMAT3P005660	-	-	-
AT2G23810.1	-0.668214	TET8 (TETRASPANIN8)	OMAT2P104250	-	OMAT2P004810,OMAT2P004820	[OMAT2P004810]-, [OMAT2P004820]-

Get whole results

Over-Representation Analysis Result

	p-value	<= 7.86e-18	:20 terms with high significance
7.86e-18 <	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	4	GO:0042254	ribosome biogenesis	24/200	18.74	5.89e-25	-	no
B	3	GO:0022613	ribonucleoprotein complex biogenesis	24/200	18.14	1.34e-24	-	no
B	5	GO:0009451	RNA modification	16/200	21.11	2.30e-18	-	no
B	5	GO:0006364	rRNA processing	14/200	22.38	8.54e-17	-	no
B	5	GO:0006396	RNA processing	18/200	8.13	1.25e-12	-	no
B	5	GO:0006412	translation	30/200	4.14	9.47e-12	-	no
B	4	GO:0010467	gene expression	49/200	2.41	1.44e-09	-	no
B	3	GO:0043170	macromolecule metabolic process	66/200	1.71	1.53e-06	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	59/200	1.67	1.21e-05	-	no
B	4	GO:0019538	protein metabolic process	42/200	1.82	3.98e-05	-	no
B	5	GO:0016070	RNA metabolic process	21/200	2.47	4.69e-05	-	no
B	3	GO:0044238	primary metabolic process	71/200	1.43	2.58e-04	-	no
B	5	GO:0044267	cellular protein metabolic process	35/200	1.72	5.35e-04	-	no
B	5	GO:0034645	cellular macromolecule biosynthetic process	34/200	1.58	2.76e-03	-	no
B	4	GO:0009059	macromolecule biosynthetic process	34/200	1.57	2.90e-03	-	no
B	3	GO:0048856	anatomical structure development	17/200	1.90	3.97e-03	-	no
B	5	GO:0090304	nucleic acid metabolic process	24/200	1.60	8.50e-03	-	no

C	3	GO:0030529	ribonucleoprotein complex	43/200	12.33	2.72e-35	-	no
C	3	GO:0043228	non-membrane-bounded organelle	44/200	7.38	1.40e-26	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	44/200	7.38	1.40e-26	-	no
C	4	GO:0005840	ribosome	30/200	11.71	2.26e-24	-	no
C	4	GO:0033279	ribosomal subunit	21/200	12.93	1.34e-18	-	no
C	3	GO:0044424	intracellular part	103/200	2.02	8.65e-16	-	yes
C	5	GO:0022626	cytosolic ribosome	19/200	10.32	3.70e-15	-	no
C	3	GO:0044446	intracellular organelle part	49/200	3.42	3.72e-15	-	yes
C	3	GO:0044422	organelle part	49/200	3.41	3.84e-15	-	yes
C	3	GO:0005622	intracellular	104/200	1.95	6.25e-15	-	yes
C	5	GO:0015934	large ribosomal subunit	14/200	15.21	3.07e-14	-	no
C	4	GO:0070013	intracellular organelle lumen	20/200	7.37	5.63e-13	-	no
C	3	GO:0043233	organelle lumen	20/200	7.36	5.88e-13	-	no
C	3	GO:0043229	intracellular organelle	91/200	1.97	8.11e-13	-	yes
C	5	GO:0005730	nucleolus	16/200	9.33	2.02e-12	-	no
C	5	GO:0044445	cytosolic part	15/200	10.02	2.99e-12	-	no
C	4	GO:0044444	cytoplasmic part	73/200	2.10	2.60e-11	-	yes
C	4	GO:0005737	cytoplasm	75/200	2.00	1.30e-10	-	yes
C	5	GO:0031981	nuclear lumen	16/200	6.62	4.39e-10	-	no
C	5	GO:0005829	cytosol	19/200	4.59	7.87e-09	-	no
C	4	GO:0044428	nuclear part	17/200	5.11	8.19e-09	-	no
C	3	GO:0044464	cell part	130/200	1.42	1.34e-08	-	yes
C	5	GO:0005739	mitochondrion	23/200	3.59	3.12e-08	3.64E-21	yes
C	4	GO:0044429	mitochondrial part	10/200	7.17	1.84e-07	-	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	5	GO:0005634	nucleus	26/200	1.66	3.84e-03	-	no

M	3	GO:0003735	structural constituent of ribosome	29/200	13.39	2.50e-25	-	no
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	13/200	2.92	1.70e-04	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	13/200	2.89	1.88e-04	-	no
M	3	GO:0016787	hydrolase activity	28/200	1.79	9.16e-04	-	no

PS	4	PO:0000037	shoot apex	147/200	1.71	4.99e-19	-	yes
PS	5	PO:0009052	pedicel	142/200	1.75	8.37e-19	-	yes
PS	3	PO:0009005	root	145/200	1.61	7.59e-16	-	yes
PS	5	PO:0020038	petiole	131/200	1.72	1.01e-15	-	yes
PS	3	PO:0009032	petal	139/200	1.59	5.77e-14	-	yes
PS	4	PO:0009009	embryo	147/200	1.52	1.05e-13	-	yes
PS	3	PO:0009031	sepal	142/200	1.54	3.17e-13	-	yes
PS	3	PO:0009010	seed	147/200	1.50	3.65e-13	-	yes
PS	4	PO:0009025	leaf	141/200	1.53	6.08e-13	-	yes
PS	4	PO:0009001	fruit	147/200	1.49	6.13e-13	-	yes
PS	3	PO:0006342	infructescence	147/200	1.49	6.13e-13	-	yes
PS	5	PO:0008034	leaf whorl	143/200	1.52	7.79e-13	-	yes
PS	4	PO:0008033	phyllome whorl	143/200	1.52	7.79e-13	-	yes
PS	5	PO:0020039	leaf lamina	130/200	1.58	3.30e-12	-	yes
PS	5	PO:0009028	microsporophyll	131/200	1.56	5.14e-12	-	yes
PS	5	PO:0009046	flower	149/200	1.43	1.87e-11	-	yes
PS	4	PO:0009049	inflorescence	149/200	1.42	3.34e-11	-	yes
PS	3	PO:0006001	phyllome	147/200	1.43	3.60e-11	-	yes
PS	4	PO:0009026	sporophyll	135/200	1.50	4.03e-11	-	yes
PS	5	PO:0000013	cauline leaf	121/200	1.57	1.17e-10	-	yes
PS	3	PO:0009006	shoot	151/200	1.39	1.55e-10	-	yes
PS	5	PO:0009027	megasporophyll	127/200	1.51	2.63e-10	-	yes
PS	5	PO:0008037	seedling	130/200	1.47	8.61e-10	-	yes
PS	4	PO:0009047	stem	123/200	1.46	1.21e-08	-	yes
PS	4	PO:0020030	cotyledon	107/200	1.46	4.47e-07	-	no
PS	3	PO:0009013	meristem	114/200	1.42	5.30e-07	-	no
PS	4	PO:0000230	inflorescence meristem	111/200	1.43	6.32e-07	-	no

PG	5	PO:0001081	F mature embryo stage	143/200	1.80	2.11e-20	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	145/200	1.75	1.42e-19	-	yes
PG	5	PO:0004507	D bilateral stage	144/200	1.75	2.37e-19	-	yes
PG	5	PO:0001185	C globular stage	141/200	1.72	7.86e-18	-	yes
PG	4	PO:0007631	embryo development stages	146/200	1.62	2.42e-16	-	yes
PG	3	PO:0001170	seed development stages	146/200	1.61	3.81e-16	-	yes
PG	3	PO:0007134	A vegetative growth	135/200	1.59	1.96e-13	-	yes
PG	5	PO:0007133	leaf production	134/200	1.59	3.03e-13	-	yes
PG	4	PO:0007112	1 main shoot growth	134/200	1.59	3.09e-13	-	yes
PG	4	PO:0007616	4 anthesis	145/200	1.50	1.34e-12	-	yes
PG	5	PO:0007604	corolla developmental stages	146/200	1.48	2.62e-12	-	yes
PG	4	PO:0001054	4 leaf senescence stage	123/200	1.60	1.25e-11	-	yes
PG	3	PO:0001050	leaf development stages	123/200	1.60	1.31e-11	-	yes
PG	4	PO:0007600	3 floral organ development stages	146/200	1.43	5.30e-11	-	yes
PG	3	PO:0007615	flower development stages	148/200	1.41	9.81e-11	-	yes

KW	0	ribosome	-	31/200	11.74	3.67e-25	-	no
KW	0	ribosomal	-	32/200	10.60	1.66e-24	-	no
KW	0	constituent	-	29/200	10.35	4.52e-22	-	no
KW	0	structural	-	29/200	8.27	2.53e-19	-	no
KW	0	translation	-	33/200	6.66	7.80e-19	-	no
KW	0	cytosolic	-	20/200	9.34	5.65e-15	-	no
KW	0	subunit	-	32/200	4.36	4.56e-13	-	no
KW	0	large	-	15/200	9.78	4.30e-12	-	no
KW	0	nucleolus	-	14/200	10.30	9.21e-12	-	no
KW	0	mitochondrial	-	17/200	7.54	1.67e-11	0	yes
KW	0	biogenesis	-	12/200	8.83	1.35e-09	-	no
KW	0	ipr002885	-	15/200	5.35	2.74e-08	-	no
KW	0	pentatricopeptide	-	15/200	5.16	4.49e-08	-	no
KW	0	intracellular	-	19/200	3.68	2.83e-07	-	no
KW	0	mitochondrion	-	18/200	3.28	2.97e-06	3.64E-21	no
KW	0	defective	-	11/200	4.49	7.44e-06	-	no
KW	0	terminal	-	37/200	1.92	3.71e-05	-	no
KW	0	repeat	-	28/200	2.16	4.13e-05	-	no
KW	0	small	-	13/200	3.23	6.03e-05	-	no
KW	0	conserved	-	28/200	2.07	8.65e-05	-	no
KW	0	nucleic	-	17/200	2.60	1.10e-04	-	no
KW	0	embryo	-	17/200	2.45	2.31e-04	-	no
KW	0	nucleotide	-	15/200	2.36	7.11e-04	1.00E-15	yes
KW	0	motif	-	12/200	2.47	1.30e-03	-	no
KW	0	development	-	14/200	2.01	4.60e-03	-	no
KW	0	biological_process	-	75/200	1.25	8.35e-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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