Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.13.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07851	0.851
27DAP/17DAP	1.11997	0.902
39DAP/27DAP	0.89927	0.594
41DAP/39DAP	1.25449	0.423
42DAP/41DAP	1.08822	0.967
43DAP/42DAP	0.91863	0.863
47DAP/43DAP	1.02874	0.972
52DAP/47DAP	1.10697	0.832
57DAP/52DAP	1.12569	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97676	0.442
17DAP/reference	0.98757	0.737
27DAP/reference	0.97053	0.428
39DAP/reference	0.96205	0.276
41DAP/reference	0.98492	0.667
42DAP/reference	0.93881	0.025
43DAP/reference	0.98811	0.745
47DAP/reference	0.89896	0.002
52DAP/reference	0.94257	0.21
57DAP/reference	0.91091	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00786	0.99
27DAP/17DAP	0.99798	0.969
39DAP/27DAP	1.04342	0.514
41DAP/39DAP	0.99497	1
42DAP/41DAP	1.03704	0.514
43DAP/42DAP	0.96248	0.447
47DAP/43DAP	1.00681	0.969
52DAP/47DAP	1.01838	0.933
57DAP/52DAP	1.02386	0.911
57DAP/7DAP	1.09765	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93113	0.246
17DAP/reference	0.95143	0.049
27DAP/reference	0.93152	0.025
39DAP/reference	0.95761	0.083
41DAP/reference	0.9746	0.247
42DAP/reference	0.95895	0.211
43DAP/reference	0.96464	0.151
47DAP/reference	0.90824	0.101
52DAP/reference	0.92971	0.137
57DAP/reference	0.92567	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04906	0.304
17DAP/reference	1.00027	0.805
27DAP/reference	0.9405	0.257
39DAP/reference	0.91233	0.034
41DAP/reference	1.24754	0.241
42DAP/reference	1.07327	0.794
43DAP/reference	0.98555	0.692
47DAP/reference	0.88636	0.018
52DAP/reference	0.97913	0.38
57DAP/reference	1.00599	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99347	0.699
17DAP/reference	0.973	0.571
27DAP/reference	0.98361	0.624
39DAP/reference	0.97199	0.393
41DAP/reference	0.9527	0.148
42DAP/reference	0.92093	0.032
43DAP/reference	0.93003	0.131
47DAP/reference	0.9643	0.325
52DAP/reference	0.91697	0.211
57DAP/reference	0.77189	0.07

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94673	1
26DAP/20DAP	1.01659	1
34DAP/26DAP	0.85277	0.214
51DAP/34DAP	0.95133	0.618
52DAP/51DAP	0.99027	1
53DAP/52DAP	1.03323	0.882
55DAP/53DAP	1.07872	0.703
57DAP/55DAP	1.00144	0.97
62DAP/57DAP	1.19754	0.445
68DAP/62DAP	1.03764	0.991
68DAP/14DAP	1.0918	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87286	0.039

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89455	0.426
Mature Green Tomato/Ripe Tomato	0.90582	0.347
Immature Eggplant/Mature Eggplant	0.85632	0.117
Ripe Pepper/Ripe Tomato	1.59007	0.244
Mature Eggplant/Ripe Tomato	1.0632	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96855	0.944
1-1-2/M82	0.96718	1
12-2/M82	1.18945	0.2
12-4/M82	0.92764	1
1-3/M82	0.93206	0.501
2-1-1/M82	1.11062	0.764
2-1/M82	1.08734
2-6/M82	1.0183	1
3-2/M82	0.96964	1
4-1-1/M82	0.95398	1
4-1/M82	0.99597	1
4-3-2/M82	1.001	1
4-3/M82	0.99015	1
5-3/M82	1.02408	1
6-2/M82	1.01875	1
6-3/M82	0.99253	1
7-1/M82	0.9511	0.443
7-2/M82	1.01459	1
9-3-2/M82	0.82584	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.47272	0.243
IL2-6/WTpooled	1.10716	0.788
IL7-5/WTpooled	1.1724	0.792
IL7-3/WTpooled	0.53144	0.298
IL12-4/WTpooled	0.80298	0.581
IL1-4/WTpooled	0.86001	0.562
WT/WTpooled	0.94333	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	1.06288	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04851	0.921
DC3000/delta hrp 6h	0.89893	0.95
DC3000/delta hrp 12h	1.07942	1
DC3000/delta hrp 24h	1.06591	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07239	0.16
DC3000 delta B/DC3000 delta AB	1.06684	0.457

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.48137	1
Exp 60h	1.28276	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97432	1
Var 0h	1.10628	0.98
Var 12h I row2-row1	1.00045	1
Var 12h NI row2-row1	0.9009	0.713
Var 36h I row2-row1	0.98815	1
Var 36h NI row2-row1	0.8411	0.329
Var 60h I row2-row1	1.23059	0.562
Var 60h NI row2-row1	1.09095	1
Time course 0hI-0hNI	1.12153	0.799
Time course 12hI-12hNI	1.03649	0.798
Time course 36hI-36hNI	1.0389	0.355
Time course 60hI-60hNI	1.41999	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)	0.88159	0.301
transgenic ySAMdc/azygous control (breaker)	0.82337	0.15
transgenic ySAMdc/azygous control (red)	0.94061	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02128	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87703	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83987	1
Manapal/WT (break)	0.96851	1
Manapal/WT (red)	0.97559	0.728