Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.6.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99813	0.867
27DAP/17DAP	1.17363	0.822
39DAP/27DAP	0.89448	0.573
41DAP/39DAP	1.04569	0.386
42DAP/41DAP	0.99732	1
43DAP/42DAP	1.0436	1
47DAP/43DAP	0.9696	0.84
52DAP/47DAP	1.09638	0.869
57DAP/52DAP	1.04763	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99475	0.756
17DAP/reference	0.99061	0.858
27DAP/reference	1.06323	0.258
39DAP/reference	1.10675	0.301
41DAP/reference	1.06021	0.073
42DAP/reference	0.88547	0.012
43DAP/reference	0.9251	0.273
47DAP/reference	0.95048	0.09
52DAP/reference	1.01038	0.654
57DAP/reference	1.02971	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90628	0.496
27DAP/17DAP	1.02757	0.957
39DAP/27DAP	1.15236	0.779
41DAP/39DAP	1.09061	0.799
42DAP/41DAP	0.84522	0.093
43DAP/42DAP	0.89958	0.256
47DAP/43DAP	1.02825	0.948
52DAP/47DAP	1.13043	0.63
57DAP/52DAP	1.13415	0.703
57DAP/7DAP	1.38247	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20564	0.325
17DAP/reference	1.01678	0.599
27DAP/reference	1.1828	0.551
39DAP/reference	0.97256	0.474
41DAP/reference	1.09143	0.949
42DAP/reference	1.07821	1
43DAP/reference	1.07965	0.457
47DAP/reference	0.94283	0.504
52DAP/reference	1.09443	0.459
57DAP/reference	1.02596	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94081	0.548
17DAP/reference	0.92099	0.159
27DAP/reference	0.88348	0.181
39DAP/reference	0.84062	0.105
41DAP/reference	0.88348	0.137
42DAP/reference	0.87805	0.121
43DAP/reference	0.99038	0.692
47DAP/reference	0.95539	0.129
52DAP/reference	0.90368	0.06
57DAP/reference	0.98697	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09891	0.347
17DAP/reference	1.0001	0.739
27DAP/reference	1.24582	0.044
39DAP/reference	1.2208	0.203
41DAP/reference	1.30418	0.637
42DAP/reference	0.82575	0.172
43DAP/reference	0.85665	0.15
47DAP/reference	0.92272	0.286
52DAP/reference	0.90683	0.36
57DAP/reference	0.68815	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02179	0.966
26DAP/20DAP	1.3253	0.325
34DAP/26DAP	0.95151	0.944
51DAP/34DAP	1.23952	0.081
52DAP/51DAP	1.19248	0.492
53DAP/52DAP	1.20402	0.819
55DAP/53DAP	1.17012	0.562
57DAP/55DAP	1.2636	0.865
62DAP/57DAP	0.87221	0.871
68DAP/62DAP	0.85376	0.641
68DAP/14DAP	1.06598	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69506	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13025
Mature Green Tomato/Ripe Tomato	1.35243	0.166
Immature Eggplant/Mature Eggplant	1.39758	0.05
Ripe Pepper/Ripe Tomato	2.13852
Mature Eggplant/Ripe Tomato	1.7355	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.01699	1
1-3/M82	N/A	N/A
2-1-1/M82	0.7894
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.13375
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.84796
4-3/M82	N/A	N/A
5-3/M82	1.04811	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	0.90373	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00794	1
IL12-4/WTpooled	0.93983	0.566
IL1-4/WTpooled	1.13368	1
WT/WTpooled	1.00849	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	0.80866	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17762	0.875
DC3000/delta hrp 6h	1.20511	1
DC3000/delta hrp 12h	0.89574	1
DC3000/delta hrp 24h	0.99259	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78948
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.38207	1
Exp 60h	1.42921	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03823	1
Var 0h	0.95087	1
Var 12h I row2-row1	1.3824	0.473
Var 12h NI row2-row1	0.91878	0.82
Var 36h I row2-row1	0.84746	0.805
Var 36h NI row2-row1	1.16983	1
Var 60h I row2-row1	0.94905	0.285
Var 60h NI row2-row1	1.09597	0.5
Time course 0hI-0hNI	0.84482	0.386
Time course 12hI-12hNI	0.99229	1
Time course 36hI-36hNI	0.8513	0.102
Time course 60hI-60hNI	0.4734	0.006

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)	1.08452	0.431
transgenic ySAMdc/azygous control (breaker)	1.41292	0.248
transgenic ySAMdc/azygous control (red)	1.21395	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02578	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03103	1
Manapal/WT (break)	0.89544	1
Manapal/WT (red)	0.85975	0.242