Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97958	0.823
27DAP/17DAP	1.29956	0.793
39DAP/27DAP	1.15103	0.83
41DAP/39DAP	1.06123	0.985
42DAP/41DAP	1.1696	0.941
43DAP/42DAP	1.24301	0.698
47DAP/43DAP	1.13131	0.584
52DAP/47DAP	1.29699	0.791
57DAP/52DAP	1.2637	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79361	0.071
17DAP/reference	0.82803	0.085
27DAP/reference	0.84383	0.052
39DAP/reference	0.80954	0.054
41DAP/reference	0.71599	0.031
42DAP/reference	0.80743	0.022
43DAP/reference	0.94276	0.448
47DAP/reference	0.87111	0.071
52DAP/reference	0.92556	0.237
57DAP/reference	0.96535	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08275	0.581
27DAP/17DAP	0.85612	0.537
39DAP/27DAP	1.19114	0.262
41DAP/39DAP	0.87269	0.361
42DAP/41DAP	1.11414	0.708
43DAP/42DAP	1.38919	0.056
47DAP/43DAP	0.83547	0.339
52DAP/47DAP	1.14584	0.563
57DAP/52DAP	1.1491	0.388
57DAP/7DAP	1.1752	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8203	0.095
17DAP/reference	1.04006	1
27DAP/reference	0.90938	0.076
39DAP/reference	1.01005	1
41DAP/reference	0.89036	0.203
42DAP/reference	0.95872	0.355
43DAP/reference	0.81558	0.061
47DAP/reference	0.74517	0.04
52DAP/reference	0.89204	0.179
57DAP/reference	0.93779	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76121	0.096
17DAP/reference	0.62139	0.007
27DAP/reference	0.80579	0.084
39DAP/reference	0.66409	0.009
41DAP/reference	0.68726	0.012
42DAP/reference	0.92262	0.321
43DAP/reference	0.69952	0.024
47DAP/reference	0.72502	0.025
52DAP/reference	0.65286	0.004
57DAP/reference	0.76868	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90635	0.214
17DAP/reference	0.86193	0.239
27DAP/reference	0.92834	0.206
39DAP/reference	0.82348	0.018
41DAP/reference	1.00215	0.618
42DAP/reference	0.89414	0.172
43DAP/reference	0.84393	0.179
47DAP/reference	0.81236	0.054
52DAP/reference	0.81675	0.25
57DAP/reference	0.72479	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87482	0.787
26DAP/20DAP	0.90048	1
34DAP/26DAP	1.21641	1
51DAP/34DAP	1.74584	0.483
52DAP/51DAP	0.89883	1
53DAP/52DAP	1.31129	0.858
55DAP/53DAP	1.01134	0.876
57DAP/55DAP	0.88078	0.366
62DAP/57DAP	1.83349	0.515
68DAP/62DAP	1.13597	0.788
68DAP/14DAP	1.04176	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.7345	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.75704	0.2
Immature Eggplant/Mature Eggplant	0.94734	0.808
Ripe Pepper/Ripe Tomato	0.62752	0.224
Mature Eggplant/Ripe Tomato	1.27428	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79746	0.934
1-1-2/M82	1.31271	1
12-2/M82	0.84739
12-4/M82	1.04628	1
1-3/M82	N/A	N/A
2-1-1/M82	1.21924	1
2-1/M82	0.95387
2-6/M82	1.11884
3-2/M82	1.4208	0.461
4-1-1/M82	1.51377
4-1/M82	N/A	N/A
4-3-2/M82	1.17508
4-3/M82	1.63383	0.268
5-3/M82	0.75109	0.642
6-2/M82	1.58488	0.253
6-3/M82	1.15018	1
7-1/M82	0.94775	0.466
7-2/M82	1.13306	1
9-3-2/M82	1.38901

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.38161	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	2.04282	1
IL12-4/WTpooled	1.01529	0.557
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.97121	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	0.93571	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.71791	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01193	1
DC3000/delta hrp 24h	0.86826	0.198

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.78928

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07273	0.254
Exp 36h	1.18069	1
Exp 60h	1.20773	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9992	1
Var 0h	0.84581	0.933
Var 12h I row2-row1	0.98187	1
Var 12h NI row2-row1	0.98755	1
Var 36h I row2-row1	1.11444	0.41
Var 36h NI row2-row1	0.92741	0.432
Var 60h I row2-row1	0.91604	0.285
Var 60h NI row2-row1	0.96894	0.977
Time course 0hI-0hNI	1.04724	0.764
Time course 12hI-12hNI	1.02795	0.803
Time course 36hI-36hNI	1.04068	0.513
Time course 60hI-60hNI	1.52926	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)	0.95193	0.529
transgenic ySAMdc/azygous control (breaker)	1.73112	0.166
transgenic ySAMdc/azygous control (red)	1.13642	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9679	0.277

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17468	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64825	1
Manapal/WT (break)	0.7365	0.285
Manapal/WT (red)	1.1933	0.413