Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.13.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.30469	0.014
27DAP/17DAP	1.68027	1
39DAP/27DAP	1.04327	0.798
41DAP/39DAP	1.34734	0.413
42DAP/41DAP	0.98076	1
43DAP/42DAP	0.78949	0.695
47DAP/43DAP	1.11452	0.95
52DAP/47DAP	1.33536	0.957
57DAP/52DAP	0.83669	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81237	0.054
17DAP/reference	0.97041	0.597
27DAP/reference	0.84975	0.031
39DAP/reference	0.86992	0.088
41DAP/reference	0.96327	0.667
42DAP/reference	0.84361	0.002
43DAP/reference	0.98716	0.785
47DAP/reference	0.9218	0.065
52DAP/reference	0.79991	0.035
57DAP/reference	0.95054	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80415	0.289
27DAP/17DAP	1.4026	0.632
39DAP/27DAP	1.04978	0.844
41DAP/39DAP	1.11295	0.705
42DAP/41DAP	0.94378	0.654
43DAP/42DAP	0.75224	0.558
47DAP/43DAP	2.79608	0.873
52DAP/47DAP	1.19261	0.939
57DAP/52DAP	0.92082	0.457
57DAP/7DAP	2.41041

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9225	0.361
17DAP/reference	1.14795	0.361
27DAP/reference	0.95781	0.303
39DAP/reference	0.9571	0.354
41DAP/reference	0.89244	0.153
42DAP/reference	0.97302	0.506
43DAP/reference	0.95059	0.351
47DAP/reference	0.80108	0.034
52DAP/reference	0.83566	0.057
57DAP/reference	0.6555	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97079	0.655
17DAP/reference	0.8084	0.004
27DAP/reference	0.84193	0.079
39DAP/reference	0.83217	0.048
41DAP/reference	0.91684	0.041
42DAP/reference	0.76546	0.017
43DAP/reference	0.79366	0.087
47DAP/reference	0.89372	0.032
52DAP/reference	0.87531	0.027
57DAP/reference	1.01259	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92901	0.29
17DAP/reference	0.79335	0.132
27DAP/reference	0.80662	0.049
39DAP/reference	0.90962	0.101
41DAP/reference	0.8142	0.04
42DAP/reference	0.73421	0.025
43DAP/reference	0.73694	0.028
47DAP/reference	0.8034	0.009
52DAP/reference	1.05365	0.674
57DAP/reference	0.85652	0.149

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13468	0.916
26DAP/20DAP	0.68293
34DAP/26DAP	1.44661	1
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.45213	0.404
53DAP/52DAP	1.03606	1
55DAP/53DAP	1.14871	0.737
57DAP/55DAP	0.97784	0.855
62DAP/57DAP	0.94109	0.871
68DAP/62DAP	1.06503	1
68DAP/14DAP	0.98918	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.6597	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	9.9547	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	26.552

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	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	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	1.67294	0.277
IL2-6/WTpooled	0.71886	0.473
IL7-5/WTpooled	0.41265	0.559
IL7-3/WTpooled	1.23151	0.362
IL12-4/WTpooled	1.1335	0.52
IL1-4/WTpooled	1.05852
WT/WTpooled	1.05615	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	0.96035	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96521	1
DC3000/delta hrp 6h	1.06094	1
DC3000/delta hrp 12h	0.63036	1
DC3000/delta hrp 24h	9.57987	0.018

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.66361	0.042
DC3000 delta B/DC3000 delta AB	1.45499	0.09

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.71275	0.265
Exp 36h	1.23326	1
Exp 60h	0.78761	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.49384	1
Var 0h	0.97931	1
Var 12h I row2-row1	1.41891	0.692
Var 12h NI row2-row1	3.30272	0.649
Var 36h I row2-row1	1.27182	0.908
Var 36h NI row2-row1	0.14361	0.45
Var 60h I row2-row1	0.87511	0.952
Var 60h NI row2-row1	0.79579	0.904
Time course 0hI-0hNI	0.64206	0.145
Time course 12hI-12hNI	1.41924	0.409
Time course 36hI-36hNI	1.45369	0.45
Time course 60hI-60hNI	0.65171	0.161

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)	2.31368	0.511
transgenic ySAMdc/azygous control (breaker)	5.90541	1
transgenic ySAMdc/azygous control (red)	1.31739	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8945	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92138	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95771	1
Manapal/WT (break)	0.82412	0.299
Manapal/WT (red)	N/A	N/A