ATTED-II : GeneCoexpression result

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Orthologous genes in OrthoFinder^**

Species	Gene	Description
ath-u.5	NRPD1A	nuclear RNA polymerase D1A
ath-r.7	NRPD1A	nuclear RNA polymerase D1A
ath-m.9	NRPD1A	nuclear RNA polymerase D1A
ath-e.2	NRPD1A	nuclear RNA polymerase D1A
ath-m.4.bio	NRPD1A	nuclear RNA polymerase D1A
ath-m.4.hor	NRPD1A	nuclear RNA polymerase D1A
ath-m.4.lig	NRPD1A	nuclear RNA polymerase D1A
ath-m.4.str	NRPD1A	nuclear RNA polymerase D1A
ath-m.4.tis	NRPD1A	nuclear RNA polymerase D1A
bra-r.6	117132791	DNA-directed RNA polymerase IV subunit 1
bra-r.6	103847833	DNA-directed RNA polymerase IV subunit 1
bra-r.6	103838307	DNA-directed RNA polymerase IV subunit 1
bna-r.1	106406243	DNA-directed RNA polymerase IV subunit 1
bna-r.1	106346632	DNA-directed RNA polymerase IV subunit 1-like
bna-r.1	106420995	DNA-directed RNA polymerase IV subunit 1
ghi-r.1	107926978	DNA-directed RNA polymerase IV subunit 1
ghi-r.1	107930048	DNA-directed RNA polymerase IV subunit 1
ghi-r.1	107904496	DNA-directed RNA polymerase IV subunit 1
cit-r.1	102607057	DNA-directed RNA polymerase IV subunit 1
gma-u.5	100810483	DNA-directed RNA polymerase IV subunit 1
gma-u.5	100796185	DNA-directed RNA polymerase IV subunit 1
vvi-u.5	100254724	DNA-directed RNA polymerase IV subunit 1
ppo-u.5	7490920	DNA-directed RNA polymerase IV subunit 1
mtr-u.5	11436803	DNA-directed RNA polymerase IV subunit 1
sly-u.5	778259	DNA-directed RNA polymerase IV subunit 1
sot-r.1	102603437	DNA-directed RNA polymerase IV subunit 1
nta-r.1	107794854	DNA-directed RNA polymerase IV subunit 1
nta-r.1	107766126	DNA-directed RNA polymerase IV subunit 1
osa-u.5	4336722	DNA-directed RNA polymerase IV subunit 1
osa-u.5	4347810	DNA-directed RNA polymerase IV subunit 1
zma-u.5	100501057	DNA dependent RNA polymerase D largest subunit
tae-r.2	123180590	DNA-directed RNA polymerase IV subunit 1
tae-r.2	123113199	DNA-directed RNA polymerase IV subunit 1
tae-r.2	123038976	DNA-directed RNA polymerase IV subunit 1
hvu-r.1	123426175	DNA-directed RNA polymerase IV subunit 1
sbi-r.1	8060411	DNA-directed RNA polymerase IV subunit 1
bdi-r.1	100842842	DNA-directed RNA polymerase IV subunit 1

Top 50 coexpressed genes to NRPD1A (ath-u.5 coexpression data)

KEGG ID	Pathway name	#genes in coex list	#genes in genome	-log10(p)	Link to the KEGG^* map (Multiple genes)

Top 50 enrichment test to NRPD1A (ath-u.5 coexpression data)

CoexMap"842605"

[Cytoscape]

Annotation

functional annotation

KEGG

ath03020 [list] [network] RNA polymerase (52 genes)

GO BP

GO:0010495 [list] [network] siRNA-mediated long-distance post-transcriptional gene silencing	(3 genes)	IMP
GO:0030422 [list] [network] siRNA processing	(31 genes)	IGI IMP
GO:0031047 [list] [network] regulatory ncRNA-mediated gene silencing	(179 genes)	IMP

GO CC

GO:0000418 [list] [network] RNA polymerase IV complex	(16 genes)	IDA
GO:0005654 [list] [network] nucleoplasm	(262 genes)	IDA
GO:0005634 [list] [network] nucleus	(10367 genes)	IDA ISM

GO MF

GO:0005515 [list] [network] protein binding

(5363 genes)

IPI

Protein

NP_001185298.1 [sequence] [blastp]
NP_001320708.1 [sequence] [blastp]
NP_001320709.1 [sequence] [blastp]
NP_001320710.1 [sequence] [blastp]
NP_176490.2 [sequence] [blastp]

Subcellular
localization
wolf

nucl 3, chlo 3, cysk_nucl 2, cyto 1, mito 1, plas 1, vacu 1, cyto_pero 1, mito_plas 1, cyto_E.R. 1	(predict for NP_001185298.1)
nucl 3, plas 2, E.R. 2, E.R._plas 2	(predict for NP_001320708.1)
nucl 3, chlo 3, cysk_nucl 2, cyto 1, mito 1, plas 1, vacu 1, cyto_pero 1, mito_plas 1, cyto_E.R. 1	(predict for NP_001320709.1)
chlo 3, nucl 2, E.R. 2, cysk_nucl 1, mito 1, plas 1, vacu 1, mito_plas 1	(predict for NP_001320710.1)
nucl 3, chlo 3, cysk_nucl 2, cyto 1, mito 1, plas 1, vacu 1, cyto_pero 1, mito_plas 1, cyto_E.R. 1	(predict for NP_176490.2)

Subcellular
localization
TargetP

other 8	(predict for NP_001185298.1)
other 8	(predict for NP_001320708.1)
other 8	(predict for NP_001320709.1)
other 8	(predict for NP_001320710.1)
other 8	(predict for NP_176490.2)

Gene expression

All samples

[Expression pattern]

Tissue specificity^*

Coexpression

	Gene	Function	KEGG					Entrez Gene ID	Other ID	Link	Target				Condition-specific^*					Reference
	Gene	Function	KEGG					Entrez Gene ID	Other ID	Link	ath-u.5 for NRPD1A	ath-r.7 for NRPD1A	ath-m.9 for NRPD1A	ath-e.2 for NRPD1A	ath-m.4.bio for NRPD1A	ath-m.4.hor for NRPD1A	ath-m.4.lig for NRPD1A	ath-m.4.str for NRPD1A	ath-m.4.tis for NRPD1A	bra-r.6 for 117132791	bra-r.6 for 103847833	bra-r.6 for 103838307	bna-r.1 for 106406243	bna-r.1 for 106346632	bna-r.1 for 106420995	ghi-r.1 for 107926978	ghi-r.1 for 107930048	ghi-r.1 for 107904496	cit-r.1 for 102607057	gma-u.5 for 100810483	gma-u.5 for 100796185	vvi-u.5 for 100254724	ppo-u.5 for 7490920	mtr-u.5 for 11436803	sly-u.5 for 778259	sot-r.1 for 102603437	nta-r.1 for 107794854	nta-r.1 for 107766126	osa-u.5 for 4336722	osa-u.5 for 4347810	zma-u.5 for 100501057	tae-r.2 for 123180590	tae-r.2 for 123113199	tae-r.2 for 123038976	hvu-r.1 for 123426175	sbi-r.1 for 8060411	bdi-r.1 for 100842842

Ortholog

Ortholog ID: 7845

Species

ath

bra

bna

ghi

cit

gma

vvi

ppo

mtr

sly

sot

nta

osa

zma

tae

hvu

sbi

bdi

Symbol

NRPD1A

Function^*

nuclear RNA polymerase D1A

DNA-directed RNA polymerase IV subunit 1

DNA-directed RNA polymerase IV subunit 1-like

DNA-directed RNA polymerase IV subunit 1

DNA dependent RNA polymerase D largest subunit

DNA-directed RNA polymerase IV subunit 1

Coexmap

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Coexpression

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KEGG Info

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ath03020	RNA polymerase	3

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bra00620	Pyruvate metabolism	3
bra01200	Carbon metabolism	3
bra03020	RNA polymerase	3
bra00010	Glycolysis / Gluconeogenesis	2
bra00020	Citrate cycle (TCA cycle)	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bra03020	RNA polymerase	3
bra00906	Carotenoid biosynthesis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bra03020	RNA polymerase	3
bra04075	Plant hormone signal transduction	2
bra00906	Carotenoid biosynthesis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bna03020	RNA polymerase	5

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bna03020	RNA polymerase	5

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bna03020	RNA polymerase	5

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ghi03020	RNA polymerase	3
ghi00100	Steroid biosynthesis	2
ghi03440	Homologous recombination	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ghi03020	RNA polymerase	3
ghi00100	Steroid biosynthesis	2
ghi03440	Homologous recombination	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ghi03020	RNA polymerase	3
ghi00100	Steroid biosynthesis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
cit03020	RNA polymerase	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
gma03020	RNA polymerase	3
gma03440	Homologous recombination	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
gma03020	RNA polymerase	4

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ppo04142	Lysosome	2
ppo03082	ATP-dependent chromatin remodeling	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
sot03013	Nucleocytoplasmic transport	3

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
nta03020	RNA polymerase	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
nta03020	RNA polymerase	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
osa04120	Ubiquitin mediated proteolysis	3
osa03013	Nucleocytoplasmic transport	3
osa03020	RNA polymerase	2
osa03008	Ribosome biogenesis in eukaryotes	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
zma03013	Nucleocytoplasmic transport	3

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
tae03013	Nucleocytoplasmic transport	5
tae03040	Spliceosome	4
tae03083	Polycomb repressive complex	3
tae03020	RNA polymerase	2
tae03015	mRNA surveillance pathway	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
tae03040	Spliceosome	2
tae03010	Ribosome	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
tae03013	Nucleocytoplasmic transport	3
tae03015	mRNA surveillance pathway	3
tae03020	RNA polymerase	2
tae03082	ATP-dependent chromatin remodeling	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
hvu03020	RNA polymerase	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
sbi03018	RNA degradation	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bdi03440	Homologous recombination	2
bdi03013	Nucleocytoplasmic transport	2
bdi03460	Fanconi anemia pathway	2

Expression

Expression pattern

Entrez Gene ID^*

842605

117132791

103847833

103838307

106406243

106346632

106420995

107926978

107930048

107904496

102607057

100810483

100796185

100254724

7490920

11436803

778259

102603437

107794854

107766126

4336722

4347810

100501057

123180590

123113199

123038976

123426175

8060411

100842842

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Species	ath	bra	bna	ghi	cit	gma	vvi	ppo	mtr	sly	sot	nta	osa	zma	tae	hvu	sbi	bdi	cre
Paralog	9	3	3	3	1	2	1	1	1	1	1	2	2	1	3	1	1	1	0

Select Species**

Orthologous genes in OrthoFinder**

Top 50 coexpressed genes to NRPD1A (ath-u.5 coexpression data)

Top 50 enrichment test to NRPD1A (ath-u.5 coexpression data)

Select Species^**

Orthologous genes in OrthoFinder^**