Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.17.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.76761	0.033
27DAP/17DAP	1.04028	0.9
39DAP/27DAP	1.90989	0.101
41DAP/39DAP	0.65017	0.058
42DAP/41DAP	0.97077	1
43DAP/42DAP	1.20819	1
47DAP/43DAP	0.88106	0.603
52DAP/47DAP	0.98352	0.828
57DAP/52DAP	1.57939	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22281	0.48
17DAP/reference	1.26378	0.185
27DAP/reference	1.50496	0.055
39DAP/reference	1.45953	0.224
41DAP/reference	1.43902	0.085
42DAP/reference	2.40751	0.001
43DAP/reference	1.60009	0.01
47DAP/reference	2.27638	0.001
52DAP/reference	1.32156	0.302
57DAP/reference	1.50832	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.45497	0.036
27DAP/17DAP	0.97595	0.919
39DAP/27DAP	0.86753	0.456
41DAP/39DAP	1.38524	1
42DAP/41DAP	1.16712	0.8
43DAP/42DAP	0.88098	0.399
47DAP/43DAP	0.9193	0.41
52DAP/47DAP	1.09092	0.804
57DAP/52DAP	0.91881	0.457
57DAP/7DAP	1.25193	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26023	0.368
17DAP/reference	0.99978	0.599
27DAP/reference	0.8785	0.159
39DAP/reference	0.82255	0.083
41DAP/reference	1.19498	0.539
42DAP/reference	1.081	0.889
43DAP/reference	1.03562	0.974
47DAP/reference	2.80865	0.032
52DAP/reference	1.05505	1
57DAP/reference	1.20868	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66734	0.017
17DAP/reference	1.53696	0.065
27DAP/reference	2.29411	0.012
39DAP/reference	2.3176	0.011
41DAP/reference	1.90264	0.005
42DAP/reference	2.25038	0.007
43DAP/reference	1.41181	0.466
47DAP/reference	3.21637	0.008
52DAP/reference	1.93966	0.006
57DAP/reference	1.33914	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03853	0.846
17DAP/reference	0.96256	0.56
27DAP/reference	1.53121	0.037
39DAP/reference	1.23853	0.275
41DAP/reference	1.09233	0.867
42DAP/reference	1.92804	0.15
43DAP/reference	1.45932	0.71
47DAP/reference	2.02188	0.015
52DAP/reference	1.06875	0.99
57DAP/reference	2.52839	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22707	0.966
26DAP/20DAP	1.62464	0.106
34DAP/26DAP	1.09735	1
51DAP/34DAP	1.3859	0.115
52DAP/51DAP	0.60702	0.151
53DAP/52DAP	0.83893	0.259
55DAP/53DAP	0.70842	0.017
57DAP/55DAP	1.08985	0.997
62DAP/57DAP	0.74883	0.01
68DAP/62DAP	0.9124	0.7
68DAP/14DAP	1.52642	0.099

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.77774	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76436	0.226
Mature Green Tomato/Ripe Tomato	1.32863	0.053
Immature Eggplant/Mature Eggplant	1.56556	0.05
Ripe Pepper/Ripe Tomato	0.44026	0.224
Mature Eggplant/Ripe Tomato	0.85736	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8339	0.634
1-1-2/M82	1.28451	1
12-2/M82	0.55385
12-4/M82	1.26842	1
1-3/M82	1.82752	0.248
2-1-1/M82	0.96114	1
2-1/M82	0.93559	1
2-6/M82	0.77504	1
3-2/M82	1.17906
4-1-1/M82	1.08284	1
4-1/M82	1.13089
4-3-2/M82	1.15467	1
4-3/M82	0.96166	1
5-3/M82	0.9726	1
6-2/M82	1.16779	0.253
6-3/M82	1.06956	1
7-1/M82	1.32043	0.992
7-2/M82	1.2077	0.385
9-3-2/M82	1.00987	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.88097	0.277
IL2-6/WTpooled	0.52782	0.358
IL7-5/WTpooled	0.95409	1
IL7-3/WTpooled	1.54786	0.362
IL12-4/WTpooled	1.22388	0.646
IL1-4/WTpooled	0.9217	0.834
WT/WTpooled	0.98079	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.15083	0.853

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04736	0.921
DC3000/delta hrp 6h	0.98221	0.95
DC3000/delta hrp 12h	1.12497	1
DC3000/delta hrp 24h	1.09046	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11187	0.102
DC3000 delta B/DC3000 delta AB	1.27782	0.164

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02159	1
Exp 36h	1.27361	0.489
Exp 60h	1.2912	0.237

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.00377	1
Var 0h	0.86692	1
Var 12h I row2-row1	1.08339	0.736
Var 12h NI row2-row1	0.937	0.82
Var 36h I row2-row1	0.95067	1
Var 36h NI row2-row1	1.22328	1
Var 60h I row2-row1	0.90577	0.832
Var 60h NI row2-row1	0.96838	1
Time course 0hI-0hNI	0.98032	0.94
Time course 12hI-12hNI	1.01307	0.85
Time course 36hI-36hNI	1.11735	0.114
Time course 60hI-60hNI	1.12824	0.254

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.08689	0.541
transgenic ySAMdc/azygous control (breaker)	0.67981	0.15
transgenic ySAMdc/azygous control (red)	0.90033	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.27438	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69018	1
Manapal/WT (break)	1.12379	1
Manapal/WT (red)	1.23604	0.222