Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.6.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43937	0.348
27DAP/17DAP	1.15812	0.825
39DAP/27DAP	1.92223	0.064
41DAP/39DAP	1.00168	0.795
42DAP/41DAP	1.45689	0.672
43DAP/42DAP	1.45875	0.831
47DAP/43DAP	0.62003	0.102
52DAP/47DAP	0.94471	0.823
57DAP/52DAP	1.44081	0.589

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17765	0.334
17DAP/reference	2.18622	0.011
27DAP/reference	1.42594	0.087
39DAP/reference	1.4286	0.423
41DAP/reference	2.41469	0.013
42DAP/reference	1.02594	1
43DAP/reference	1.00542	0.84
47DAP/reference	0.65111	0.002
52DAP/reference	0.60932	0.029
57DAP/reference	0.73219	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.91642	0.036
27DAP/17DAP	0.78744	0.508
39DAP/27DAP	1.92667	0.063
41DAP/39DAP	0.82379	0.446
42DAP/41DAP	1.24182	0.291
43DAP/42DAP	1.20097	0.382
47DAP/43DAP	0.95632	0.796
52DAP/47DAP	1.0367	0.969
57DAP/52DAP	0.90535	0.466
57DAP/7DAP	1.49523

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.11285	0.024
17DAP/reference	1.5318	0.009
27DAP/reference	1.04601	0.664
39DAP/reference	3.12389	0.005
41DAP/reference	1.50322	0.018
42DAP/reference	1.98528	0.007
43DAP/reference	2.02938	0.006
47DAP/reference	2.30949	0.014
52DAP/reference	1.74336	0.007
57DAP/reference	2.05326	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88276	0.286
17DAP/reference	2.37338	0.008
27DAP/reference	2.38525	0.022
39DAP/reference	4.36859	0.011
41DAP/reference	1.56076	0.112
42DAP/reference	2.83447	0.008
43DAP/reference	1.92876	0.035
47DAP/reference	3.907	0.008
52DAP/reference	3.36027	0.014
57DAP/reference	3.22165	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05231	0.699
17DAP/reference	2.17826	0.07
27DAP/reference	1.2199	0.171
39DAP/reference	1.972	0.008
41DAP/reference	1.43259	0.008
42DAP/reference	1.351	0.063
43DAP/reference	1.20053	0.285
47DAP/reference	0.54171	0.006
52DAP/reference	0.68619	0.06
57DAP/reference	1.00298	0.718

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11029	0.631
26DAP/20DAP	0.9866	1
34DAP/26DAP	0.79622	0.174
51DAP/34DAP	1.35051	0.079
52DAP/51DAP	0.79939	0.151
53DAP/52DAP	1.3481	0.179
55DAP/53DAP	0.46505	0.017
57DAP/55DAP	0.94684	0.709
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.48217	0.464
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.27193	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.43474	0.058
Mature Green Tomato/Ripe Tomato	1.46272	0.185
Immature Eggplant/Mature Eggplant	0.25072	0.057
Ripe Pepper/Ripe Tomato	1.74654	1
Mature Eggplant/Ripe Tomato	3.09193	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96541	0.961
1-1-2/M82	1.32351	1
12-2/M82	1.07149	1
12-4/M82	1.34521	1
1-3/M82	2.29666	0.248
2-1-1/M82	0.71086	0.465
2-1/M82	0.76773
2-6/M82	0.89038	1
3-2/M82	1.19725	0.967
4-1-1/M82	0.96084	1
4-1/M82	1.6248	0.466
4-3-2/M82	1.59571	0.262
4-3/M82	1.05392	1
5-3/M82	0.94449	0.642
6-2/M82	1.28239	1
6-3/M82	1.18769	1
7-1/M82	1.03979	1
7-2/M82	0.97279	1
9-3-2/M82	1.48186

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71567	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.52303	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.88113	0.402
WT/WTpooled	1.22798

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	0.90534	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11637	0.894
DC3000/delta hrp 6h	0.48524	0.637
DC3000/delta hrp 12h	1.05057	1
DC3000/delta hrp 24h	1.11976	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.81759	0.413
DC3000 delta B/DC3000 delta AB	1.17056	0.389

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75894	0.265
Exp 36h	0.6005	0.406
Exp 60h	0.44212	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02773	1
Var 0h	1.05507	1
Var 12h I row2-row1	1.2595	0.473
Var 12h NI row2-row1	1.57823	0.649
Var 36h I row2-row1	1.25769	0.309
Var 36h NI row2-row1	0.73354	0.549
Var 60h I row2-row1	0.50576	0.285
Var 60h NI row2-row1	0.86798	0.818
Time course 0hI-0hNI	1.29673	0.537
Time course 12hI-12hNI	1.03253	0.85
Time course 36hI-36hNI	1.2852	0.01
Time course 60hI-60hNI	4.22671	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)	1.05415	0.612
transgenic ySAMdc/azygous control (breaker)	0.43584	0.15
transgenic ySAMdc/azygous control (red)	1.24233	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04748	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.36589	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0517	0.307
Manapal/WT (break)	0.85226	1
Manapal/WT (red)	0.90528	0.424