Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53716	0.061
27DAP/17DAP	1.20953	0.833
39DAP/27DAP	1.21146	0.583
41DAP/39DAP	1.24503	0.203
42DAP/41DAP	1.46228	0.169
43DAP/42DAP	1.4247	0.304
47DAP/43DAP	0.90779	0.667
52DAP/47DAP	0.93448	0.683
57DAP/52DAP	0.8917	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67497	0.036
17DAP/reference	0.65582	0.01
27DAP/reference	0.74279	0.028
39DAP/reference	0.91175	0.35
41DAP/reference	0.63142	0.016
42DAP/reference	1.0989	1
43DAP/reference	0.87096	0.077
47DAP/reference	1.00439	0.636
52DAP/reference	0.9663	0.438
57DAP/reference	1.16116	0.202

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6994	0.251
27DAP/17DAP	1.25287	0.399
39DAP/27DAP	0.74451	0.243
41DAP/39DAP	0.76792	0.446
42DAP/41DAP	0.81806	0.434
43DAP/42DAP	1.06646	0.788
47DAP/43DAP	1.07637	1
52DAP/47DAP	1.02897	0.979
57DAP/52DAP	0.80486	0.331
57DAP/7DAP	0.8545	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82178	0.067
17DAP/reference	0.87467	0.167
27DAP/reference	1.38058	0.008
39DAP/reference	0.94037	0.146
41DAP/reference	1.25658	0.041
42DAP/reference	1.35214	0.014
43DAP/reference	1.19264	0.537
47DAP/reference	0.90047	0.293
52DAP/reference	0.99593	0.679
57DAP/reference	0.79783	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76532	0.01
17DAP/reference	0.73036	0.013
27DAP/reference	0.78092	0.134
39DAP/reference	0.86987	0.136
41DAP/reference	0.96678	0.432
42DAP/reference	0.77912	0.016
43DAP/reference	0.78767	0.108
47DAP/reference	1.90989	0.028
52DAP/reference	0.79717	0.066
57DAP/reference	1.05442	0.314

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77324	0.032
17DAP/reference	0.83533	0.268
27DAP/reference	1.08432	0.34
39DAP/reference	0.89548	0.122
41DAP/reference	0.90903	0.086
42DAP/reference	1.19847	0.321
43DAP/reference	1.03655	0.767
47DAP/reference	1.12886	1
52DAP/reference	1.41409	0.393
57DAP/reference	1.38903	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15103	1
26DAP/20DAP	6.47994	0.04
34DAP/26DAP	1.60109	0.542
51DAP/34DAP	0.81754	0.305
52DAP/51DAP	0.88274	1
53DAP/52DAP	0.89431	0.715
55DAP/53DAP	0.47799	0.026
57DAP/55DAP	0.42443	0.01
62DAP/57DAP	1.3344	0.445
68DAP/62DAP	0.8708	0.505
68DAP/14DAP	1.40331	0.069

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.18141	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	9.07644	0.058
Mature Green Tomato/Ripe Tomato	0.44728
Immature Eggplant/Mature Eggplant	42.581	0.05
Ripe Pepper/Ripe Tomato	6.23495	0.256
Mature Eggplant/Ripe Tomato	1.8746	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.71763
1-1-2/M82	0.86997	1
12-2/M82	N/A	N/A
12-4/M82	0.8517	0.282
1-3/M82	2.1285	0.255
2-1-1/M82	0.23482
2-1/M82	3.47156
2-6/M82	1.86591	0.695
3-2/M82	2.32424
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.92296	1
5-3/M82	2.46515	0.37
6-2/M82	2.89438
6-3/M82	1.24049	1
7-1/M82	1.67257
7-2/M82	4.46018	0.291
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00711	1
IL2-6/WTpooled	1.05247	0.788
IL7-5/WTpooled	1.0791	0.792
IL7-3/WTpooled	0.87896	0.418
IL12-4/WTpooled	0.99342	1
IL1-4/WTpooled	0.98404	0.834
WT/WTpooled	1.03774	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	1.79466	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95556
DC3000/delta hrp 6h	0.97671	0.95
DC3000/delta hrp 12h	1.22387	1
DC3000/delta hrp 24h	1.67305	0.129

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92017	1
DC3000 delta B/DC3000 delta AB	1.94571	0.139

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22826	1
Exp 36h	1.36323	1
Exp 60h	1.01889	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98583	1
Var 0h	0.51554	0.936
Var 12h I row2-row1	0.85403	0.705
Var 12h NI row2-row1	2.13581	0.34
Var 36h I row2-row1	1.12374	1
Var 36h NI row2-row1	0.66669	0.549
Var 60h I row2-row1	0.78854	0.374
Var 60h NI row2-row1	0.44011	0.292
Time course 0hI-0hNI	1.10876	0.662
Time course 12hI-12hNI	1.41271	0.158
Time course 36hI-36hNI	5.59025	0.004
Time course 60hI-60hNI	51.642	0.008

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)	0.9896	0.614
transgenic ySAMdc/azygous control (breaker)	0.21807	0.137
transgenic ySAMdc/azygous control (red)	1.7272	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08845	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76724	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	16.6095	0.14
Manapal/WT (break)	1.29529	1
Manapal/WT (red)	2.35251	0.413