Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.1.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96474	0.713
27DAP/17DAP	1.36384	0.697
39DAP/27DAP	0.93364	0.663
41DAP/39DAP	0.79612	0.419
42DAP/41DAP	1.3878	0.752
43DAP/42DAP	1.26831	0.894
47DAP/43DAP	0.71243	0.221
52DAP/47DAP	1.31672	0.786
57DAP/52DAP	1.56843	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14383	0.097
17DAP/reference	1.12149	0.154
27DAP/reference	1.09466	0.118
39DAP/reference	1.03611	0.059
41DAP/reference	1.05557	0.667
42DAP/reference	1.01968	0.731
43DAP/reference	1.13334	0.031
47DAP/reference	0.97796	0.445
52DAP/reference	0.88244	0.152
57DAP/reference	0.91757	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45184	0.107
27DAP/17DAP	1.23239	0.587
39DAP/27DAP	0.6074	0.076
41DAP/39DAP	1.02418	0.968
42DAP/41DAP	0.69039	0.016
43DAP/42DAP	1.1669	0.627
47DAP/43DAP	1.20762	0.873
52DAP/47DAP	1.15121	0.713
57DAP/52DAP	1.41047	0.457
57DAP/7DAP	2.70288	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09653	0.555
17DAP/reference	1.0655	0.896
27DAP/reference	1.02849	1
39DAP/reference	0.95926	0.411
41DAP/reference	1.01918	0.709
42DAP/reference	0.92715	0.355
43DAP/reference	0.86993	0.132
47DAP/reference	1.09879	0.804
52DAP/reference	0.96958	0.435
57DAP/reference	0.96771	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17294	0.181
17DAP/reference	1.38485	0.009
27DAP/reference	1.33714	0.024
39DAP/reference	1.17824	0.08
41DAP/reference	1.11433	0.194
42DAP/reference	1.01145	1
43DAP/reference	1.30412	0.076
47DAP/reference	1.10803	0.264
52DAP/reference	1.17498	0.034
57DAP/reference	1.08392	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10564	0.74
17DAP/reference	1.06644	0.689
27DAP/reference	1.00235	0.763
39DAP/reference	1.09035	0.451
41DAP/reference	1.07769	0.383
42DAP/reference	1.00493	1
43DAP/reference	1.2538	0.314
47DAP/reference	0.98869	0.574
52DAP/reference	1.75783	0.216
57DAP/reference	0.97542	0.564

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.38802	0.56
26DAP/20DAP	1.2943	0.319
34DAP/26DAP	0.6433	0.431
51DAP/34DAP	1.12215	0.55
52DAP/51DAP	1.02978	0.888
53DAP/52DAP	1.38918	0.274
55DAP/53DAP	1.10187	0.886
57DAP/55DAP	0.91299	0.698
62DAP/57DAP	1.13042	0.767
68DAP/62DAP	0.69474	0.227
68DAP/14DAP	0.76506	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84299	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87686	0.41
Mature Green Tomato/Ripe Tomato	0.58379
Immature Eggplant/Mature Eggplant	0.66939	0.062
Ripe Pepper/Ripe Tomato	1.15298	1
Mature Eggplant/Ripe Tomato	1.20212	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.87617
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.3616
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04798	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.89367	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.78967
IL1-4/WTpooled	0.97181	0.834
WT/WTpooled	1.12296	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	0.91806	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97876	1
DC3000/delta hrp 6h	0.90684	0.95
DC3000/delta hrp 12h	0.96386	1
DC3000/delta hrp 24h	0.90911	0.464

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50778	0.436
DC3000 delta B/DC3000 delta AB	0.46013

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91164	1
Exp 36h	0.94391	0.943
Exp 60h	0.89921	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99115
Var 0h	N/A	N/A
Var 12h I row2-row1	0.5926	0.39
Var 12h NI row2-row1	0.83313
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	1.04457
Var 60h NI row2-row1	0.87856	1
Time course 0hI-0hNI	1.0522	0.603
Time course 12hI-12hNI	0.95526	0.795
Time course 36hI-36hNI	0.76944	0.023
Time course 60hI-60hNI	0.17672	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)	0.93956	0.324
transgenic ySAMdc/azygous control (breaker)	1.10803	0.172
transgenic ySAMdc/azygous control (red)	1.17264	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07453	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06288	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93177	1
Manapal/WT (break)	1.06812	1
Manapal/WT (red)	0.86827	0.503