Specifically-expressed experiments

Gene ID	At1g09570
Gene name	PHYA (PHYTOCHROME A)
Functional description	Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation.

Click GSM ID or Assay name to show a list of genes that are specifically expressed in the GSM.

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title	Link to GEO
94.2	99.9	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
49.9	99.8	GSM282694	arf2_mock_rep1	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
46.7	99.8	GSM282703	arf2_brz_2	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
45.6	99.8	GSM133118	RIKEN-YAMAUCHI1B	GSE5687	AtGenExpress: Different temperature treatment of seeds
44.5	99.8	GSM282693	arf2_brz_1	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
41.5	99.8	GSM282695	arf2_mock_rep2	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
39.4	99.8	ArrayExpress	E-NASC-78-raw-cel-1463195187	-	-	-
38.9	99.8	GSM282696	arf2_mock_rep3	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
38.1	99.8	GSM282702	Col_mock_rep3	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
36.0	99.7	ArrayExpress	E-NASC-78-raw-cel-1463195235	-	-	-
35.2	99.7	GSM134305	Penfield_1-7_endosperm-PAC_Rep1_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
34.7	99.7	GSM282698	Col_BRZ_rep2	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
34.7	99.7	GSM282701	Col_mock_rep2	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
34.4	99.7	GSM282699	Col_BRZ_rep3	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
33.8	99.7	ArrayExpress	E-MEXP-1468-raw-cel-1591138919	-	-	-
32.5	99.7	ArrayExpress	E-MEXP-1468-raw-cel-1591138688	-	-	-
30.2	99.7	GSM282697	Col_BRZ_rep1	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
29.9	99.7	ArrayExpress	E-NASC-78-raw-cel-1463195203	-	-	-
29.8	99.7	GSM134307	Penfield_1-9_endosperm-PAC_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
28.3	99.7	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
28.2	99.7	GSM134299	Penfield_1-1_endosperm-control_Rep1_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
28.0	99.7	GSM226267	WT(Ler)_Dark_replicate1	GSE8951	A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks
27.7	99.7	GSM226268	WT(Ler)_Dark_replicate2	GSE8951	A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks
27.5	99.7	GSM133120	RIKEN-YAMAUCHI2B	GSE5687	AtGenExpress: Different temperature treatment of seeds
27.4	99.7	GSM134301	Penfield_1-3_endosperm-control_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
27.4	99.7	GSM134300	Penfield_1-2_endosperm-control_Rep2_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
27.1	99.7	ArrayExpress	E-NASC-78-raw-cel-1463195171	-	-	-
26.9	99.7	GSM245918	wild type dark replicate 3	GSE9728	COP9 signalosome (csn) mutant analysis
26.4	99.7	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
26.3	99.7	ArrayExpress	E-MEXP-1468-raw-cel-1591138820	-	-	-
25.8	99.7	GSM282700	Col_mock_rep1	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
25.2	99.6	GSM133119	RIKEN-YAMAUCHI2A	GSE5687	AtGenExpress: Different temperature treatment of seeds
24.5	99.6	GSM226269	WT(Ler)_Dark_replicate3	GSE8951	A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks
24.1	99.6	ArrayExpress	E-NASC-78-raw-cel-1463195219	-	-	-
23.9	99.6	ArrayExpress	E-MEXP-1299-raw-cel-1519902498	-	-	-
23.7	99.6	ArrayExpress	E-MEXP-1299-raw-cel-1519902871	-	-	-
23.6	99.6	ArrayExpress	E-MEXP-1468-raw-cel-1591138952	-	-	-
23.3	99.6	GSM319209	Dark-grown WT control (vector#4)	GSE12729	Microarray analysis of MINI ZINC FINGER 1 (MIF1) overexpression transgenic Arabidopsis seedlings
23.1	99.6	GSM184912	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
22.9	99.6	ArrayExpress	E-MEXP-1468-raw-cel-1591139018	-	-	-
22.7	99.6	ArrayExpress	E-NASC-78-raw-cel-1463195283	-	-	-
22.3	99.6	ArrayExpress	E-MEXP-1468-raw-cel-1591138754	-	-	-
22.0	99.6	ArrayExpress	E-NASC-78-raw-cel-1463195267	-	-	-
21.9	99.6	GSM134514	Col-0_4day_dark_-lincomycin_rep2	GSE5759	red illumination w/o lincomycin
20.2	99.6	GSM134515	Col-0_4day_dark_+lincomycin_rep1	GSE5759	red illumination w/o lincomycin
20.1	99.6	GSM245916	wild type dark replicate 1	GSE9728	COP9 signalosome (csn) mutant analysis
20.1	99.6	ArrayExpress	E-ATMX-6-raw-cel-1308219121	-	-	-
20.1	99.6	GSM134306	Penfield_1-8_endosperm-PAC_Rep2_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
19.8	99.6	ArrayExpress	E-MEXP-849-raw-cel-1181980998	-	-	-
19.4	99.6	ArrayExpress	E-MEXP-1468-raw-cel-1591138853	-	-	-
19.1	99.6	GSM134518	Col-0_4day_red illumination_-lincomycin_rep2	GSE5759	red illumination w/o lincomycin
18.7	99.5	ArrayExpress	E-MEXP-1468-raw-cel-1591138985	-	-	-
18.5	99.5	ArrayExpress	E-MEXP-1299-raw-cel-1519902780	-	-	-
18.4	99.5	ArrayExpress	E-MEXP-1468-raw-cel-1591138721	-	-	-
17.9	99.5	ArrayExpress	E-MEXP-1468-raw-cel-1591138886	-	-	-
17.9	99.5	GSM245917	wild type dark replicate 2	GSE9728	COP9 signalosome (csn) mutant analysis
17.7	99.5	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
17.4	99.5	GSM253165	48h into an extended nightB	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
16.9	99.5	GSM134516	Col-0_4day_dark_+lincomycin_rep2	GSE5759	red illumination w/o lincomycin
16.8	99.5	GSM184911	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
16.7	99.5	ArrayExpress	E-MEXP-1468-raw-cel-1591138787	-	-	-
16.7	99.5	ArrayExpress	E-NASC-78-raw-cel-1463195251	-	-	-
16.6	99.5	ArrayExpress	E-MEXP-849-raw-cel-1181980990	-	-	-
16.0	99.5	ArrayExpress	E-MEXP-1468-raw-cel-1591138655	-	-	-
15.8	99.5	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
15.6	99.5	GSM158706	WT-ESTRADIOL-REP2	GSE6954	Identification of AGL24 downstream genes by using XVE inducible system
15.4	99.5	GSM134520	Col-0_4day_red illumination _+lincomycin_rep2	GSE5759	red illumination w/o lincomycin
14.8	99.4	GSM77180	04h low CO2 + dark replicate B	GSE3423	Carbon fixation (endogenous sugar) and light-dependent gene expression
14.6	99.4	GSM134302	Penfield_1-4_endosperm-ABA_Rep1_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
14.4	99.4	ArrayExpress	E-MEXP-1299-raw-cel-1519903415	-	-	-
14.3	99.4	GSM253161	8h into an extended nightA	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
14.0	99.4	GSM253163	24h into an extended nightB	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
13.1	99.4	GSM253160	6h into an extended night	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
12.9	99.3	ArrayExpress	E-MEXP-1304-raw-cel-1530618235	-	-	-
12.4	99.3	ArrayExpress	E-MEXP-1304-raw-cel-1530617935	-	-	-
12.3	99.3	GSM134519	Col-0_4day_red illumination_+lincomycin_rep1	GSE5759	red illumination w/o lincomycin
12.2	99.3	GSM319208	Dark-grown WT control (vector#1)	GSE12729	Microarray analysis of MINI ZINC FINGER 1 (MIF1) overexpression transgenic Arabidopsis seedlings
12.2	99.3	GSM253162	8h into an extended nightB	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
12.1	99.3	GSM184892	Arabidopsis, root cells, columella root cap, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
12.1	99.3	GSM253166	48h into an extended nightC	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
11.9	99.3	GSM77177	04h low CO2 + dark replicate A	GSE3423	Carbon fixation (endogenous sugar) and light-dependent gene expression
11.4	99.3	ArrayExpress	E-MEXP-1304-raw-cel-1530618136	-	-	-
11.3	99.3	GSM131199	AtGen_D-33_3-DL_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
11.3	99.3	ArrayExpress	E-MEXP-1304-raw-cel-1530618033	-	-	-
11.3	99.3	GSM131189	AtGen_D-22_2-AL_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
11.0	99.2	ArrayExpress	E-MEXP-849-raw-cel-1181981046	-	-	-
11.0	99.2	ArrayExpress	E-MEXP-1304-raw-cel-1530618275	-	-	-
11.0	99.2	ArrayExpress	E-MEXP-1304-raw-cel-1530618171	-	-	-
10.8	99.2	GSM252688	Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep2	GSE9996	Organ regeneration in plants is independent of stem cell niche activity
10.5	99.2	GSM266666	Arabidopsis, root cells, columella root cap, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
10.4	99.2	GSM292076	Wt, dark sample, biological rep1	GSE11594	Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings
10.1	99.2	ArrayExpress	E-MEXP-1299-raw-cel-1519902994	-	-	-
10.1	99.2	ArrayExpress	E-MEXP-1304-raw-cel-1530617971	-	-	-
10.1	99.2	ArrayExpress	E-MEXP-849-raw-cel-1181981022	-	-	-
10.1	99.2	GSM292081	pif1-2, dark sample, biological rep3	GSE11594	Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings
9.7	99.1	GSM131190	AtGen_D-23_2-UL_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
9.7	99.1	GSM134513	Col-0_4day_dark_-lincomycin_rep1	GSE5759	red illumination w/o lincomycin
9.5	99.1	ArrayExpress	E-MEXP-1304-raw-cel-1530617900	-	-	-
9.4	99.1	GSM292080	pif1-2, dark sample, biological rep2	GSE11594	Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings
9.4	99.1	GSM319210	Dark-grown WT control (vector#7)	GSE12729	Microarray analysis of MINI ZINC FINGER 1 (MIF1) overexpression transgenic Arabidopsis seedlings
9.1	99.1	GSM134304	Penfield_1-6_endosperm-ABA_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
9.1	99.1	GSM131169	AtGen_D-1_1-DL_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
9.0	99.1	GSM131215	AtGen_D-17_2-DL_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
8.9	99.0	ArrayExpress	E-MEXP-1304-raw-cel-1530618104	-	-	-
8.9	99.0	GSM158701	HY213-MOCK-REP1	GSE6954	Identification of AGL24 downstream genes by using XVE inducible system
8.9	99.0	ArrayExpress	E-MEXP-1299-raw-cel-1519903848	-	-	-
8.9	99.0	GSM133309	RIKEN-NAKABAYASHI4B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
8.9	99.0	ArrayExpress	E-MEXP-1304-raw-cel-1530618068	-	-	-
8.9	99.0	ArrayExpress	E-MEXP-1304-raw-cel-1530618003	-	-	-
8.8	99.0	GSM131193	AtGen_D-27_2-PS_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
8.8	99.0	GSM131216	AtGen_D-26_1-FS_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
8.8	99.0	GSM253164	24h into an extended nightC	GSE10016	Expression data of Arabidopsis thaliana rosettes in an extended night
8.8	99.0	ArrayExpress	E-MEXP-1299-raw-cel-1519901992	-	-	-
8.7	99.0	GSM133307	RIKEN-NAKABAYASHI3A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
8.6	99.0	GSM292079	pif1-2, dark sample, biological rep1	GSE11594	Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings
8.6	99.0	ArrayExpress	E-MEXP-849-raw-cel-1181980982	-	-	-

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