Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.9.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77089	0.265
27DAP/17DAP	0.69074	0.185
39DAP/27DAP	1.23203	0.675
41DAP/39DAP	0.86111	0.469
42DAP/41DAP	3.33725	0.042
43DAP/42DAP	1.54942	0.772
47DAP/43DAP	1.13016	0.856
52DAP/47DAP	0.62433	0.18
57DAP/52DAP	1.60078	0.758

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01167	1
17DAP/reference	1.06441	0.717
27DAP/reference	1.01553	1
39DAP/reference	1.07448	0.174
41DAP/reference	1.19463	0.171
42DAP/reference	0.95081	0.169
43DAP/reference	0.98689	0.785
47DAP/reference	0.92959	0.191
52DAP/reference	0.8052	0.036
57DAP/reference	0.8501	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43427	0.033
27DAP/17DAP	1.21984	0.632
39DAP/27DAP	0.84105	0.382
41DAP/39DAP	0.48435	0.015
42DAP/41DAP	1.03478	0.734
43DAP/42DAP	2.06023	0.014
47DAP/43DAP	0.89435	0.428
52DAP/47DAP	0.9747	0.917
57DAP/52DAP	1.0745	0.699
57DAP/7DAP	0.28074	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84693	0.146
17DAP/reference	0.95443	0.253
27DAP/reference	1.00682	0.8
39DAP/reference	0.94505	0.23
41DAP/reference	0.97205	0.489
42DAP/reference	1.07557	0.405
43DAP/reference	0.81679	0.017
47DAP/reference	0.8691	0.168
52DAP/reference	0.8822	0.097
57DAP/reference	0.82941	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31909	0.051
17DAP/reference	1.30083	0.033
27DAP/reference	1.26707	0.704
39DAP/reference	1.01099	0.722
41DAP/reference	1.38255	0.129
42DAP/reference	0.96591	0.433
43DAP/reference	1.77061	0.033
47DAP/reference	0.90233	0.092
52DAP/reference	1.12362	0.181
57DAP/reference	1.23423	0.172

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86676	0.092
17DAP/reference	1.09135	0.65
27DAP/reference	0.94649	0.23
39DAP/reference	0.87969	0.083
41DAP/reference	0.91489	0.107
42DAP/reference	0.92775	0.445
43DAP/reference	0.79337	0.056
47DAP/reference	0.9699	0.509
52DAP/reference	0.84357	0.211
57DAP/reference	0.71435	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07141	0.966
26DAP/20DAP	0.98577	1
34DAP/26DAP	1.48565	0.819
51DAP/34DAP	0.60241	0.07
52DAP/51DAP	0.99595	1
53DAP/52DAP	0.67945
55DAP/53DAP	0.54739
57DAP/55DAP	1.17463	0.826
62DAP/57DAP	0.80421	0.681
68DAP/62DAP	1.0044	0.834
68DAP/14DAP	1.28562	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67101	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.76275	0.165
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.65773	1
Mature Eggplant/Ripe Tomato	0.21856	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03218	1
1-1-2/M82	0.94347	1
12-2/M82	1.06692	1
12-4/M82	1.75042	1
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	0.99242	1
3-2/M82	1.02922	0.84
4-1-1/M82	N/A	N/A
4-1/M82	1.26554
4-3-2/M82	0.99556	1
4-3/M82	1.17361	1
5-3/M82	0.94146	0.642
6-2/M82	0.79455
6-3/M82	1.16669
7-1/M82	0.73993
7-2/M82	0.92782	0.881
9-3-2/M82	0.72252	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15083	0.277
IL2-6/WTpooled	1.07766	0.419
IL7-5/WTpooled	1.3428	0.792
IL7-3/WTpooled	1.10782	1
IL12-4/WTpooled	0.97985	0.71
IL1-4/WTpooled	1.05121	1
WT/WTpooled	0.99558	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	1.04476	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0238	0.921
DC3000/delta hrp 6h	1.47413	1
DC3000/delta hrp 12h	0.59917
DC3000/delta hrp 24h	0.92966	0.503

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46793
DC3000 delta B/DC3000 delta AB	0.53283	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	0.59929	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00068	1
Var 0h	1.11319	0.98
Var 12h I row2-row1	0.89743	0.338
Var 12h NI row2-row1	0.9104	0.546
Var 36h I row2-row1	0.79895	1
Var 36h NI row2-row1	1.18462	1
Var 60h I row2-row1	0.87098	0.832
Var 60h NI row2-row1	1.04653	1
Time course 0hI-0hNI	1.09022	0.486
Time course 12hI-12hNI	0.94521	0.435
Time course 36hI-36hNI	0.88966	0.071
Time course 60hI-60hNI	0.34545	0.006

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)	1.36295	0.408
transgenic ySAMdc/azygous control (breaker)	1.02747	1
transgenic ySAMdc/azygous control (red)	0.96796	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99542	0.631

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11136	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28998	0.096
Manapal/WT (break)	1.48945	0.381
Manapal/WT (red)	1.16562	1