Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98747	0.847
27DAP/17DAP	0.75605	0.304
39DAP/27DAP	0.80577	0.414
41DAP/39DAP	0.8016	0.271
42DAP/41DAP	0.69433	0.774
43DAP/42DAP	1.16871	0.823
47DAP/43DAP	0.64838	0.147
52DAP/47DAP	1.00748	0.976
57DAP/52DAP	1.11792	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02831	1
17DAP/reference	1.24682	0.057
27DAP/reference	1.13411	0.277
39DAP/reference	1.20714	0.059
41DAP/reference	1.07748	0.516
42DAP/reference	0.9197	0.033
43DAP/reference	0.90552	0.063
47DAP/reference	0.79728	0.004
52DAP/reference	0.63663	0.014
57DAP/reference	0.86574	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03804	1
27DAP/17DAP	1.03072	0.954
39DAP/27DAP	0.57976	0.035
41DAP/39DAP	0.99851	1
42DAP/41DAP	1.03596	1
43DAP/42DAP	0.70809	0.026
47DAP/43DAP	0.70599	0.018
52DAP/47DAP	1.05591	0.826
57DAP/52DAP	0.82156	0.317
57DAP/7DAP	0.36602	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.80562	0.025
17DAP/reference	1.39889	0.008
27DAP/reference	0.91876	0.117
39DAP/reference	1.15061	0.351
41DAP/reference	0.90915	0.058
42DAP/reference	0.91141	0.06
43DAP/reference	0.92295	0.126
47DAP/reference	0.84888	0.128
52DAP/reference	0.90453	0.106
57DAP/reference	1.22141	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13306	0.424
17DAP/reference	1.07547	0.25
27DAP/reference	1.04465	0.822
39DAP/reference	0.84005	0.117
41DAP/reference	0.76239	0.017
42DAP/reference	0.93133	0.321
43DAP/reference	0.79636	0.06
47DAP/reference	0.86817	0.039
52DAP/reference	0.73397	0.009
57DAP/reference	0.76136	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69544	0.019
17DAP/reference	1.40607	0.179
27DAP/reference	1.23155	0.03
39DAP/reference	1.21963	0.097
41DAP/reference	1.06131	0.621
42DAP/reference	0.88861	0.361
43DAP/reference	1.02091	0.973
47DAP/reference	1.0842	0.127
52DAP/reference	0.94946	0.573
57DAP/reference	1.21986	0.175

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94313	1
26DAP/20DAP	1.35313	0.249
34DAP/26DAP	0.9664	0.972
51DAP/34DAP	0.85161	0.158
52DAP/51DAP	0.88456	1
53DAP/52DAP	0.84979	0.116
55DAP/53DAP	0.57408	0.022
57DAP/55DAP	1.02459	0.955
62DAP/57DAP	1.02597	1
68DAP/62DAP	1.12766	0.936
68DAP/14DAP	0.65279	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.29334	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09603	0.287
Mature Green Tomato/Ripe Tomato	5.20016	0.026
Immature Eggplant/Mature Eggplant	0.71659	0.082
Ripe Pepper/Ripe Tomato	9.33069	0.256
Mature Eggplant/Ripe Tomato	12.0627	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15785	0.877
1-1-2/M82	1.19311	1
12-2/M82	1.052	1
12-4/M82	0.84044	1
1-3/M82	1.02236	1
2-1-1/M82	1.03391	1
2-1/M82	N/A	N/A
2-6/M82	1.33269	0.505
3-2/M82	0.79069
4-1-1/M82	0.84861	1
4-1/M82	1.55632
4-3-2/M82	1.83276	0.284
4-3/M82	0.98348	1
5-3/M82	0.89955	1
6-2/M82	0.85992	0.481
6-3/M82	0.90853	1
7-1/M82	0.84601
7-2/M82	1.17616
9-3-2/M82	1.65274	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84624	0.247
IL2-6/WTpooled	0.89822	1
IL7-5/WTpooled	1.12519	1
IL7-3/WTpooled	1.39484	1
IL12-4/WTpooled	0.99561	1
IL1-4/WTpooled	0.9585	1
WT/WTpooled	0.99053	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	0.93167	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1938	0.671
DC3000/delta hrp 6h	0.89278	0.95
DC3000/delta hrp 12h	0.96871	1
DC3000/delta hrp 24h	0.66907	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54	0.023
DC3000 delta B/DC3000 delta AB	0.58634	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9862	1
Exp 36h	0.84848	0.699
Exp 60h	0.79601	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99103	1
Var 0h	0.801	0.933
Var 12h I row2-row1	0.84206	0.338
Var 12h NI row2-row1	0.98387	0.906
Var 36h I row2-row1	1.09415	0.908
Var 36h NI row2-row1	1.35246	0.482
Var 60h I row2-row1	1.06433	0.562
Var 60h NI row2-row1	1.0684	0.904
Time course 0hI-0hNI	0.95544	0.751
Time course 12hI-12hNI	1.00809	0.892
Time course 36hI-36hNI	0.88311	0.042
Time course 60hI-60hNI	0.14741	0.005

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)	0.90988	0.529
transgenic ySAMdc/azygous control (breaker)	1.56669	1
transgenic ySAMdc/azygous control (red)	2.16998	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92779	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.71035	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.86272	0.083
Manapal/WT (break)	5.41817	0.123
Manapal/WT (red)	5.72767	0.134