Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.11.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08104	0.893
27DAP/17DAP	1.36681	0.86
39DAP/27DAP	1.08673	0.985
41DAP/39DAP	1.09816	1
42DAP/41DAP	0.88619	1
43DAP/42DAP	0.87621	0.743
47DAP/43DAP	1.01974	0.804
52DAP/47DAP	1.56744	0.662
57DAP/52DAP	1.07966	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21462	0.089
17DAP/reference	1.17071	0.013
27DAP/reference	1.13381	0.165
39DAP/reference	0.91767	0.455
41DAP/reference	0.92166	0.267
42DAP/reference	1.40258	0.002
43DAP/reference	1.00135	0.942
47DAP/reference	0.77151	0.011
52DAP/reference	0.70004	0.018
57DAP/reference	0.63264	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.21142	0.02
27DAP/17DAP	1.71306	0.053
39DAP/27DAP	1.59523	0.11
41DAP/39DAP	2.65711	0.044
42DAP/41DAP	0.67453	0.066
43DAP/42DAP	4.91815	0.013
47DAP/43DAP	1.32201	0.026
52DAP/47DAP	0.86633	0.553
57DAP/52DAP	6.83658	0.029
57DAP/7DAP	2.5237	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70356	0.03
17DAP/reference	0.98221	0.518
27DAP/reference	0.75847	0.023
39DAP/reference	1.39826	0.032
41DAP/reference	1.1828	0.314
42DAP/reference	1.26899	0.405
43DAP/reference	2.68276	0.008
47DAP/reference	1.42244	0.025
52DAP/reference	1.14677	0.375
57DAP/reference	0.83935	0.074

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13119	0.438
17DAP/reference	1.16405	0.089
27DAP/reference	0.89593	0.22
39DAP/reference	1.59594	0.024
41DAP/reference	1.99926	0.005
42DAP/reference	1.34637	0.105
43DAP/reference	1.18666	0.457
47DAP/reference	1.00323	0.714
52DAP/reference	0.72419	0.008
57DAP/reference	0.63333	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39993	0.066
17DAP/reference	0.99131	0.763
27DAP/reference	1.35935	0.096
39DAP/reference	0.91125	0.199
41DAP/reference	0.85068	0.02
42DAP/reference	0.90369	0.287
43DAP/reference	0.90039	0.294
47DAP/reference	0.65334	0.004
52DAP/reference	1.03533	0.876
57DAP/reference	0.70095	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89567	0.807
26DAP/20DAP	1.00161	1
34DAP/26DAP	0.82397	0.078
51DAP/34DAP	1.20116	0.215
52DAP/51DAP	1.56261	0.035
53DAP/52DAP	1.034	1
55DAP/53DAP	0.9285	0.282
57DAP/55DAP	0.79519	0.238
62DAP/57DAP	2.92232	0.115
68DAP/62DAP	1.20417	0.7
68DAP/14DAP	1.20337	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.38924	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.4495	0.058
Mature Green Tomato/Ripe Tomato	0.16134
Immature Eggplant/Mature Eggplant	0.52139	0.254
Ripe Pepper/Ripe Tomato	0.1046	0.224
Mature Eggplant/Ripe Tomato	0.11863	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78195	0.605
1-1-2/M82	1.12835	1
12-2/M82	0.68665	0.721
12-4/M82	0.87947	0.619
1-3/M82	1.89134	0.248
2-1-1/M82	0.98175	1
2-1/M82	0.64926	0.74
2-6/M82	0.77482	1
3-2/M82	1.48205
4-1-1/M82	0.53486	0.926
4-1/M82	0.77531	0.665
4-3-2/M82	0.75179	0.698
4-3/M82	0.33687	0.578
5-3/M82	1.46576	0.572
6-2/M82	1.88155	0.235
6-3/M82	0.91022	1
7-1/M82	2.17885	0.87
7-2/M82	1.47336	0.324
9-3-2/M82	0.89997	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77037	0.243
IL2-6/WTpooled	0.95845	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.06572	1
IL12-4/WTpooled	1.05352	0.891
IL1-4/WTpooled	0.9521
WT/WTpooled	0.95747	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	1.43145	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99743	1
DC3000/delta hrp 6h	0.8343	0.95
DC3000/delta hrp 12h	0.95279	1
DC3000/delta hrp 24h	0.93775	0.654

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23468	0.073
DC3000 delta B/DC3000 delta AB	1.18086	0.415

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04554	1
Var 0h	1.1281	0.936
Var 12h I row2-row1	1.91894	0.406
Var 12h NI row2-row1	0.89277	0.82
Var 36h I row2-row1	1.00297	1
Var 36h NI row2-row1	1.08014	1
Var 60h I row2-row1	1.49768	1
Var 60h NI row2-row1	1.11295	0.904
Time course 0hI-0hNI	1.13025	0.799
Time course 12hI-12hNI	1.09776	0.668
Time course 36hI-36hNI	1.00707	0.826
Time course 60hI-60hNI	1.5973	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)	1.57731	0.325
transgenic ySAMdc/azygous control (breaker)	0.85252	0.173
transgenic ySAMdc/azygous control (red)	0.91975	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86051	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87378	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16671	0.105
Manapal/WT (break)	0.49942	0.333
Manapal/WT (red)	0.81708	0.184