Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.5.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86107	0.436
27DAP/17DAP	0.90897	0.787
39DAP/27DAP	0.98527	0.782
41DAP/39DAP	1.03862	0.949
42DAP/41DAP	0.95442	1
43DAP/42DAP	1.01086	0.937
47DAP/43DAP	1.20504	0.68
52DAP/47DAP	1.11206	0.773
57DAP/52DAP	0.77992	0.462

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19142	0.132
17DAP/reference	1.04474	0.492
27DAP/reference	1.05345	0.771
39DAP/reference	1.02224	0.92
41DAP/reference	1.02013	0.91
42DAP/reference	0.99207	0.484
43DAP/reference	1.15668	0.118
47DAP/reference	1.05971	0.989
52DAP/reference	0.807	0.021
57DAP/reference	1.01728	0.724

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74455	0.041
27DAP/17DAP	0.97096	0.724
39DAP/27DAP	0.89689	0.382
41DAP/39DAP	1.02191	0.914
42DAP/41DAP	0.8724	0.253
43DAP/42DAP	1.0755	0.351
47DAP/43DAP	1.04755	0.914
52DAP/47DAP	0.88333	0.565
57DAP/52DAP	0.99858	0.848
57DAP/7DAP	1.28797	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97967	0.55
17DAP/reference	0.87978	0.056
27DAP/reference	0.85422	0.028
39DAP/reference	0.74827	0.011
41DAP/reference	0.76729	0.04
42DAP/reference	0.72174	0.016
43DAP/reference	0.67712	0.013
47DAP/reference	0.84556	0.168
52DAP/reference	0.69189	0.017
57DAP/reference	0.62435	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0628	0.776
17DAP/reference	1.05316	0.806
27DAP/reference	1.10209	0.352
39DAP/reference	1.16286	0.389
41DAP/reference	1.15477	0.262
42DAP/reference	1.13189	0.794
43DAP/reference	1.48988	0.122
47DAP/reference	1.12045	0.12
52DAP/reference	0.95546	0.302
57DAP/reference	1.2094	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87358	0.127
17DAP/reference	1.11847	0.657
27DAP/reference	0.68008	0.023
39DAP/reference	0.72509	0.025
41DAP/reference	0.8141	0.027
42DAP/reference	0.77075	0.059
43DAP/reference	0.85667	0.206
47DAP/reference	0.92304	0.383
52DAP/reference	1.18233	0.876
57DAP/reference	4.07849	0.57

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99129	1
26DAP/20DAP	1.01675	1
34DAP/26DAP	1.19695	1
51DAP/34DAP	0.87788	0.504
52DAP/51DAP	0.93313	1
53DAP/52DAP	1.1614	0.797
55DAP/53DAP	1.08927	0.826
57DAP/55DAP	1.25256	0.164
62DAP/57DAP	1.74611
68DAP/62DAP	0.83204	0.7
68DAP/14DAP	1.4706

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.45427	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93964
Mature Green Tomato/Ripe Tomato	1.08278	0.399
Immature Eggplant/Mature Eggplant	0.72447	0.292
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94831	0.944
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.2399	1
1-3/M82	0.87166	1
2-1-1/M82	0.95837
2-1/M82	N/A	N/A
2-6/M82	0.90501	1
3-2/M82	0.83351	0.451
4-1-1/M82	1.00336	1
4-1/M82	1.27232	0.853
4-3-2/M82	0.91567
4-3/M82	0.82575
5-3/M82	1.03829	1
6-2/M82	0.87219	1
6-3/M82	0.96033	1
7-1/M82	0.98134	1
7-2/M82	0.82458	0.599
9-3-2/M82	0.9737	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88879	0.321
IL2-6/WTpooled	0.96406	1
IL7-5/WTpooled	0.75842	0.559
IL7-3/WTpooled	0.93046	1
IL12-4/WTpooled	1.09113	0.785
IL1-4/WTpooled	1.03376	1
WT/WTpooled	1.1418	0.777

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	0.93147	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.007	1
DC3000/delta hrp 6h	1.03693	1
DC3000/delta hrp 12h	1.16873	1
DC3000/delta hrp 24h	1.12824	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10635	0.515
DC3000 delta B/DC3000 delta AB	0.7821	0.063

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81376	0.328
Exp 36h	0.82947	0.623
Exp 60h	0.55955	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02653	1
Var 0h	1.00326	1
Var 12h I row2-row1	1.05341	0.58
Var 12h NI row2-row1	0.83392	0.384
Var 36h I row2-row1	1.05149	1
Var 36h NI row2-row1	1.04518	1
Var 60h I row2-row1	1.15709	0.543
Var 60h NI row2-row1	1.04145	0.904
Time course 0hI-0hNI	0.97269	0.863
Time course 12hI-12hNI	1.0549	0.762
Time course 36hI-36hNI	0.93906	0.077
Time course 60hI-60hNI	0.8726	0.081

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)	1.78554	0.541
transgenic ySAMdc/azygous control (breaker)	0.86981	0.142
transgenic ySAMdc/azygous control (red)	1.00434	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04075	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46763	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.67003	0.105
Manapal/WT (break)	1.53701	0.381
Manapal/WT (red)	1.33459	0.413