Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.10.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.65427	0.11
27DAP/17DAP	0.83638	0.606
39DAP/27DAP	0.90344	0.447
41DAP/39DAP	0.87577	0.555
42DAP/41DAP	1.03345	1
43DAP/42DAP	0.88687	0.801
47DAP/43DAP	0.89697	0.628
52DAP/47DAP	1.27735	0.509
57DAP/52DAP	1.00097	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0056	0.787
17DAP/reference	0.97368	0.664
27DAP/reference	0.93679	0.045
39DAP/reference	0.96888	0.624
41DAP/reference	0.97194	0.542
42DAP/reference	0.93	0.12
43DAP/reference	0.8805	0.067
47DAP/reference	0.92667	0.046
52DAP/reference	0.95532	0.405
57DAP/reference	1.05182	0.478

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78024	0.099
27DAP/17DAP	1.42615	0.045
39DAP/27DAP	0.74825	0.105
41DAP/39DAP	0.71301	0.049
42DAP/41DAP	1.1833	0.446
43DAP/42DAP	1.03263	0.83
47DAP/43DAP	0.99517	0.989
52DAP/47DAP	1.01172	0.969
57DAP/52DAP	1.05978	0.714
57DAP/7DAP	0.5881	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84295	0.168
17DAP/reference	0.80994	0.018
27DAP/reference	1.03489	1
39DAP/reference	0.79089	0.056
41DAP/reference	0.93829	0.259
42DAP/reference	1.0734	0.686
43DAP/reference	0.90785	0.082
47DAP/reference	0.84991	0.168
52DAP/reference	0.88777	0.196
57DAP/reference	1.02331	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14232	0.164
17DAP/reference	1.05244	0.557
27DAP/reference	1.11631	0.338
39DAP/reference	0.9471	0.404
41DAP/reference	0.83749	0.1
42DAP/reference	0.98195	0.534
43DAP/reference	1.35661	0.122
47DAP/reference	1.22241	0.024
52DAP/reference	1.08222	0.938
57DAP/reference	1.02103	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91249	0.104
17DAP/reference	1.03029	0.9
27DAP/reference	0.87386	0.102
39DAP/reference	1.00865	0.819
41DAP/reference	1.03598	1
42DAP/reference	0.92488	0.287
43DAP/reference	0.94306	0.398
47DAP/reference	1.14439	0.155
52DAP/reference	0.85324	0.303
57DAP/reference	1.17756	0.279

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10476	0.966
26DAP/20DAP	1.72772	0.099
34DAP/26DAP	0.8551	0.619
51DAP/34DAP	1.03906	0.795
52DAP/51DAP	0.94416	1
53DAP/52DAP	1.01435	1
55DAP/53DAP	0.76398	0.154
57DAP/55DAP	0.99143	0.93
62DAP/57DAP	1.07276	0.902
68DAP/62DAP	0.95837	0.722
68DAP/14DAP	1.24452	0.139

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62472	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.5984	0.209
Immature Eggplant/Mature Eggplant	2.51602	0.05
Ripe Pepper/Ripe Tomato	1.09412	1
Mature Eggplant/Ripe Tomato	0.97909	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96844	0.944
1-1-2/M82	0.85383	1
12-2/M82	1.35961
12-4/M82	0.88273	1
1-3/M82	1.02368	1
2-1-1/M82	0.92657
2-1/M82	1.00176
2-6/M82	1.00171	1
3-2/M82	0.95335
4-1-1/M82	0.91333	1
4-1/M82	1.36128
4-3-2/M82	0.95745	1
4-3/M82	0.83137	0.72
5-3/M82	0.99613	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.11707
7-2/M82	0.87579	0.881
9-3-2/M82	0.72056

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.67264	0.365
IL2-6/WTpooled	1.12701	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.19417	1
IL12-4/WTpooled	1.17608	0.432
IL1-4/WTpooled	1.09798	1
WT/WTpooled	0.97155	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	0.98882	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.089	0.846
DC3000/delta hrp 6h	1.21846	0.978
DC3000/delta hrp 12h	0.95487	1
DC3000/delta hrp 24h	1.12614	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51076	0.023
DC3000 delta B/DC3000 delta AB	0.53926	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90921	1
Exp 36h	1.0583	1
Exp 60h	1.15726	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98418	1
Var 0h	0.52492	0.374
Var 12h I row2-row1	0.87148	0.338
Var 12h NI row2-row1	0.94977	0.82
Var 36h I row2-row1	1.08346	0.41
Var 36h NI row2-row1	1.35919	0.482
Var 60h I row2-row1	0.88785	0.374
Var 60h NI row2-row1	1.03444	1
Time course 0hI-0hNI	1.01343	1
Time course 12hI-12hNI	0.90305	0.216
Time course 36hI-36hNI	0.83955	0.028
Time course 60hI-60hNI	0.25013	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)	0.96802	0.377
transgenic ySAMdc/azygous control (breaker)	0.54163	0.118
transgenic ySAMdc/azygous control (red)	0.88473	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04857	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77687	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77887	0.172
Manapal/WT (break)	0.90882	1
Manapal/WT (red)	0.93613	0.503