Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06697	0.912
27DAP/17DAP	1.1812	0.804
39DAP/27DAP	1.65048	0.04
41DAP/39DAP	1.17837	0.67
42DAP/41DAP	1.78138	0.251
43DAP/42DAP	2.3421	0.712
47DAP/43DAP	0.94094	0.716
52DAP/47DAP	0.74469	0.398
57DAP/52DAP	1.33837	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84138	0.074
17DAP/reference	1.08933	0.399
27DAP/reference	0.97739	0.61
39DAP/reference	0.92002	0.267
41DAP/reference	0.97675	0.667
42DAP/reference	0.87423	0.003
43DAP/reference	1.05518	0.705
47DAP/reference	0.969	0.3
52DAP/reference	0.99363	0.654
57DAP/reference	0.97254	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78275	0.158
27DAP/17DAP	0.95068	0.782
39DAP/27DAP	0.99569	0.964
41DAP/39DAP	0.85904	0.586
42DAP/41DAP	0.9876	0.85
43DAP/42DAP	0.98311	0.854
47DAP/43DAP	1.09122	0.708
52DAP/47DAP	1.08203	0.789
57DAP/52DAP	0.99227	0.813
57DAP/7DAP	1.06353	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79741	0.086
17DAP/reference	0.79569	0.019
27DAP/reference	0.86779	0.088
39DAP/reference	0.83458	0.027
41DAP/reference	0.79613	0.064
42DAP/reference	0.88437	0.144
43DAP/reference	0.96969	0.48
47DAP/reference	0.86914	0.222
52DAP/reference	0.76629	0.033
57DAP/reference	0.93433	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11249	0.319
17DAP/reference	1.03275	1
27DAP/reference	0.89636	0.24
39DAP/reference	1.21266	0.602
41DAP/reference	0.99606	0.615
42DAP/reference	0.78943	0.025
43DAP/reference	0.95165	0.494
47DAP/reference	0.80316	0.026
52DAP/reference	0.97195	0.469
57DAP/reference	1.06172	0.508

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01693	0.903
17DAP/reference	0.96116	0.55
27DAP/reference	0.95321	0.416
39DAP/reference	0.85102	0.058
41DAP/reference	0.8826	0.185
42DAP/reference	0.72897	0.036
43DAP/reference	0.8063	0.041
47DAP/reference	0.89934	0.114
52DAP/reference	0.88811	0.31
57DAP/reference	0.88191	0.18

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32878	1
26DAP/20DAP	1.12818	0.663
34DAP/26DAP	0.92143	0.874
51DAP/34DAP	1.30381	0.483
52DAP/51DAP	1.07137	1
53DAP/52DAP	1.06158	0.895
55DAP/53DAP	0.88448	0.313
57DAP/55DAP	0.86028	0.403
62DAP/57DAP	1.1566	1
68DAP/62DAP	0.92648	0.769
68DAP/14DAP	0.91076	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.59337	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.57391
Mature Green Tomato/Ripe Tomato	0.49455	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.1326	1
Mature Eggplant/Ripe Tomato	0.37635	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12497
1-1-2/M82	1.11298	1
12-2/M82	1.09807
12-4/M82	1.29458	1
1-3/M82	0.86732	0.501
2-1-1/M82	N/A	N/A
2-1/M82	1.58507
2-6/M82	1.03889	1
3-2/M82	0.74648
4-1-1/M82	N/A	N/A
4-1/M82	0.85047
4-3-2/M82	1.06588	1
4-3/M82	1.06072
5-3/M82	1.0889	1
6-2/M82	0.65445
6-3/M82	0.8037	1
7-1/M82	0.78334
7-2/M82	1.17848
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06789
IL2-6/WTpooled	1.19301	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.36582
IL12-4/WTpooled	1.51883	0.511
IL1-4/WTpooled	1.41476	1
WT/WTpooled	1.11796	0.999

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	1.10673	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08961	0.692
DC3000/delta hrp 6h	1.10699	1
DC3000/delta hrp 12h	1.0832	1
DC3000/delta hrp 24h	1.21627	0.049

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	1.1426	0.228
Exp 36h	1.01097	1
Exp 60h	1.09599	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.03	0.98
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.12194	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.41468
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.20246	0.023
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	1.09213	0.028
Time course 60hI-60hNI	2.35087	0.009

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)	0.97772	0.614
transgenic ySAMdc/azygous control (breaker)	1.08504	1
transgenic ySAMdc/azygous control (red)	0.96959	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98858	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87485	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96575	1
Manapal/WT (break)	1.10334	1
Manapal/WT (red)	0.84013	0.183