Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26184	0.709
27DAP/17DAP	1.09417	0.9
39DAP/27DAP	0.76072	0.376
41DAP/39DAP	1.34589	0.293
42DAP/41DAP	1.00142	1
43DAP/42DAP	0.93943	0.877
47DAP/43DAP	1.10749	0.825
52DAP/47DAP	0.99254	0.92
57DAP/52DAP	0.93996	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98166	0.601
17DAP/reference	1.04571	0.229
27DAP/reference	0.96119	0.395
39DAP/reference	1.03012	0.368
41DAP/reference	1.01217	0.759
42DAP/reference	0.90405	0.019
43DAP/reference	0.99938	0.924
47DAP/reference	0.92323	0.03
52DAP/reference	0.83898	0.047
57DAP/reference	0.79825	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01313	1
27DAP/17DAP	1.04873	0.885
39DAP/27DAP	0.98672	0.919
41DAP/39DAP	0.99391	1
42DAP/41DAP	1.0307	0.824
43DAP/42DAP	1.03942	0.513
47DAP/43DAP	0.98308	0.909
52DAP/47DAP	1.01147	0.973
57DAP/52DAP	0.96058	0.584
57DAP/7DAP	1.30172	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0807	0.6
17DAP/reference	1.11621	0.123
27DAP/reference	1.33459	0.009
39DAP/reference	1.49993	0.006
41DAP/reference	1.24678	0.109
42DAP/reference	1.46012	0.007
43DAP/reference	1.53549	0.007
47DAP/reference	1.33054	0.083
52DAP/reference	1.76965	0.007
57DAP/reference	1.69972	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08899	0.043
17DAP/reference	1.06002	0.584
27DAP/reference	0.98393	0.576
39DAP/reference	0.9749	0.455
41DAP/reference	0.8753	0.01
42DAP/reference	0.90119	0.039
43DAP/reference	1.01009	1
47DAP/reference	0.87128	0.028
52DAP/reference	1.02725	0.629
57DAP/reference	1.13588	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06072	0.469
17DAP/reference	0.97977	0.681
27DAP/reference	1.04885	0.408
39DAP/reference	1.40831	0.013
41DAP/reference	1.17911	0.115
42DAP/reference	1.15017	0.416
43DAP/reference	1.10452	0.617
47DAP/reference	0.9222	0.269
52DAP/reference	1.25968	0.257
57DAP/reference	0.80489	0.174

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01519	0.966
26DAP/20DAP	0.96633	1
34DAP/26DAP	0.90434	0.498
51DAP/34DAP	1.03544	0.869
52DAP/51DAP	0.98909	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.98341	0.886
57DAP/55DAP	1.05763	0.906
62DAP/57DAP	1.17081	0.081
68DAP/62DAP	0.97884	0.834
68DAP/14DAP	0.79123	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97567	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03515	1
Mature Green Tomato/Ripe Tomato	0.8253	0.256
Immature Eggplant/Mature Eggplant	1.15573
Ripe Pepper/Ripe Tomato	1.41924	1
Mature Eggplant/Ripe Tomato	1.74422	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97503	0.944
1-1-2/M82	0.91871	1
12-2/M82	0.99072	1
12-4/M82	1.0133	1
1-3/M82	0.75936	0.441
2-1-1/M82	1.0554	1
2-1/M82	N/A	N/A
2-6/M82	1.20266	0.505
3-2/M82	N/A	N/A
4-1-1/M82	0.89835	1
4-1/M82	0.8689	0.737
4-3-2/M82	0.80568	0.698
4-3/M82	0.72885	0.388
5-3/M82	0.97123	1
6-2/M82	1.07897	1
6-3/M82	0.97589	1
7-1/M82	1.01654
7-2/M82	1.00599	1
9-3-2/M82	0.78884	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.6841
IL2-6/WTpooled	0.97055	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.1616	1
IL12-4/WTpooled	1.11443	0.737
IL1-4/WTpooled	1.00818
WT/WTpooled	0.95232	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	1.03459	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06145	0.894
DC3000/delta hrp 6h	1.00502	1
DC3000/delta hrp 12h	0.95165	1
DC3000/delta hrp 24h	1.06884	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13217	0.183
DC3000 delta B/DC3000 delta AB	1.09847	0.318

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06512	1
Exp 36h	1.15923	1
Exp 60h	1.47416	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99168	1
Var 0h	0.96761	0.933
Var 12h I row2-row1	0.97538	0.948
Var 12h NI row2-row1	1.00316	1
Var 36h I row2-row1	0.87576	1
Var 36h NI row2-row1	0.91065	0.31
Var 60h I row2-row1	0.97708	0.832
Var 60h NI row2-row1	1.06896	0.904
Time course 0hI-0hNI	1.08822	0.764
Time course 12hI-12hNI	1.08603	0.409
Time course 36hI-36hNI	1.31089	0.005
Time course 60hI-60hNI	1.94332	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)	0.96583	0.485
transgenic ySAMdc/azygous control (breaker)	0.95093	1
transgenic ySAMdc/azygous control (red)	0.94605	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97454	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9096	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13915	0.105
Manapal/WT (break)	0.98468	1
Manapal/WT (red)	0.57463	0.181