Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90407	0.486
27DAP/17DAP	1.35991	0.881
39DAP/27DAP	0.81672	0.573
41DAP/39DAP	1.22977	0.553
42DAP/41DAP	0.97715	1
43DAP/42DAP	0.91213	0.867
47DAP/43DAP	2.11217	0.241
52DAP/47DAP	1.46747
57DAP/52DAP	0.90741	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86216	0.029
17DAP/reference	1.02657	0.696
27DAP/reference	1.02538	0.981
39DAP/reference	0.99763	0.957
41DAP/reference	1.01671	1
42DAP/reference	0.99264	0.484
43DAP/reference	0.90691	0.302
47DAP/reference	0.86565	0.009
52DAP/reference	0.84719	0.131
57DAP/reference	0.88191	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88234	0.496
27DAP/17DAP	1.27524	0.653
39DAP/27DAP	0.96307	0.673
41DAP/39DAP	0.97117	0.885
42DAP/41DAP	0.85702	0.584
43DAP/42DAP	0.94419	0.665
47DAP/43DAP	0.97372	0.911
52DAP/47DAP	0.98368	0.907
57DAP/52DAP	1.03279	0.697
57DAP/7DAP	1.50843	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.77371	0.024
17DAP/reference	4.87293	0.006
27DAP/reference	4.04759	0.006
39DAP/reference	5.29804	0.005
41DAP/reference	6.17713	0.01
42DAP/reference	6.61483	0.006
43DAP/reference	6.89846	0.006
47DAP/reference	3.61159	0.195
52DAP/reference	5.45394	0.007
57DAP/reference	4.58063	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05339	0.679
17DAP/reference	0.98778	0.711
27DAP/reference	0.92326	0.257
39DAP/reference	1.00211	0.603
41DAP/reference	1.01666	1
42DAP/reference	0.93512	0.355
43DAP/reference	0.80871	0.32
47DAP/reference	0.99575	0.695
52DAP/reference	0.98572	0.576
57DAP/reference	1.14486	0.057

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19454	0.041
17DAP/reference	2.08992	0.412
27DAP/reference	4.78583	0.02
39DAP/reference	4.36385	0.014
41DAP/reference	4.58184	0.006
42DAP/reference	3.44933	0.021
43DAP/reference	3.73255	0.084
47DAP/reference	0.85966	0.325
52DAP/reference	6.65581	0.042
57DAP/reference	0.88688	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.37343	0.878
26DAP/20DAP	0.55828	0.512
34DAP/26DAP	0.72533	0.311
51DAP/34DAP	0.70055	0.555
52DAP/51DAP	1.38358
53DAP/52DAP	1.28254	0.753
55DAP/53DAP	0.9941	0.925
57DAP/55DAP	1.02235	0.872
62DAP/57DAP	0.87529	0.681
68DAP/62DAP	1.36443	0.866
68DAP/14DAP	0.48138	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98119	0.665

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	N/A	N/A
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	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.08287
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	0.59762
7-1/M82	N/A	N/A
7-2/M82	1.42625
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95506	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94541	1
IL12-4/WTpooled	0.96226	1
IL1-4/WTpooled	1.16087	1
WT/WTpooled	0.98895	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	0.99942	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89312	1
DC3000/delta hrp 6h	1.77441	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.26647	0.604

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	N/A	N/A
Exp 36h	1.59945	1
Exp 60h	1.16463	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07961
Var 0h	1.08335	0.936
Var 12h I row2-row1	1.08996	0.473
Var 12h NI row2-row1	1.61494	0.649
Var 36h I row2-row1	0.90438	0.805
Var 36h NI row2-row1	0.65581	1
Var 60h I row2-row1	0.76157	0.439
Var 60h NI row2-row1	0.95191	1
Time course 0hI-0hNI	0.7791	0.489
Time course 12hI-12hNI	1.30976	0.009
Time course 36hI-36hNI	1.39433	0.006
Time course 60hI-60hNI	1.83205	0.011

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)	1.0368	0.798
transgenic ySAMdc/azygous control (breaker)	0.57012	0.137
transgenic ySAMdc/azygous control (red)	1.11088	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99613	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96607	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9009	1
Manapal/WT (break)	0.98203	1
Manapal/WT (red)	0.65262	0.181