Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13584	0.964
27DAP/17DAP	1.05345	0.922
39DAP/27DAP	0.85787	0.458
41DAP/39DAP	1.32931	0.303
42DAP/41DAP	0.9941	1
43DAP/42DAP	1.25842	1
47DAP/43DAP	1.04096	0.943
52DAP/47DAP	0.96449	0.758
57DAP/52DAP	0.74037	0.602

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86758	0.254
17DAP/reference	0.81828	0.079
27DAP/reference	0.92798	0.17
39DAP/reference	0.96219	0.6
41DAP/reference	0.95426	0.542
42DAP/reference	0.76688	0.003
43DAP/reference	0.9504	0.538
47DAP/reference	0.95804	0.322
52DAP/reference	0.92105	0.172
57DAP/reference	1.15239	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98532	0.75
27DAP/17DAP	1.06863	0.912
39DAP/27DAP	0.78185	0.113
41DAP/39DAP	0.91683	0.793
42DAP/41DAP	1.00671	0.936
43DAP/42DAP	0.92928	0.522
47DAP/43DAP	0.91581	0.734
52DAP/47DAP	0.93231	0.801
57DAP/52DAP	1.03665	0.971
57DAP/7DAP	1.63715	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83652	0.077
17DAP/reference	0.86417	0.028
27DAP/reference	0.90635	0.033
39DAP/reference	0.97047	0.474
41DAP/reference	1.10408	0.314
42DAP/reference	0.91394	0.338
43DAP/reference	0.98007	0.459
47DAP/reference	0.95099	0.671
52DAP/reference	0.70485	0.027
57DAP/reference	0.97739	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04662	0.704
17DAP/reference	0.92446	0.297
27DAP/reference	0.88921	0.16
39DAP/reference	0.83026	0.105
41DAP/reference	0.69286	0.018
42DAP/reference	1.0937	0.759
43DAP/reference	1.23922	0.259
47DAP/reference	0.92283	0.292
52DAP/reference	0.90256	0.22
57DAP/reference	0.89403	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02466	1
17DAP/reference	1.07208	0.522
27DAP/reference	0.98083	0.566
39DAP/reference	1.01504	1
41DAP/reference	1.15473	0.129
42DAP/reference	0.91876	0.361
43DAP/reference	0.83587	0.088
47DAP/reference	0.97328	0.525
52DAP/reference	0.79866	0.089
57DAP/reference	0.94609	0.43

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.43539	0.966
26DAP/20DAP	0.88073	0.512
34DAP/26DAP	1.1538	0.819
51DAP/34DAP	0.79473	0.104
52DAP/51DAP	1.16321	0.873
53DAP/52DAP	0.88197	0.426
55DAP/53DAP	1.01854	0.964
57DAP/55DAP	1.06427	0.969
62DAP/57DAP	1.01768	1
68DAP/62DAP	0.99012	0.914
68DAP/14DAP	0.83406	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73021	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.30759	0.079
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.08949
Mature Eggplant/Ripe Tomato	0.41582

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	0.87089	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	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	1.23669	0.365
IL2-6/WTpooled	1.01397	1
IL7-5/WTpooled	1.36651	0.792
IL7-3/WTpooled	1.17409	1
IL12-4/WTpooled	0.9997	1
IL1-4/WTpooled	1.0146	1
WT/WTpooled	0.97639	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	1.10386	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00588	1
DC3000/delta hrp 6h	1.31004	0.978
DC3000/delta hrp 12h	0.92868	1
DC3000/delta hrp 24h	1.20255	0.254

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.72236	0.105
DC3000 delta B/DC3000 delta AB	0.44871	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08522	1
Exp 36h	0.92451	0.749
Exp 60h	0.79199	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9955	1
Var 0h	0.92025	1
Var 12h I row2-row1	0.79197	0.467
Var 12h NI row2-row1	1.02928	1
Var 36h I row2-row1	0.95543	1
Var 36h NI row2-row1	1.19811	0.253
Var 60h I row2-row1	1.44175	0.562
Var 60h NI row2-row1	1.05754	1
Time course 0hI-0hNI	0.98174	0.947
Time course 12hI-12hNI	1.0228	0.868
Time course 36hI-36hNI	0.86227	0.144
Time course 60hI-60hNI	0.18252	0.005

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)	0.88331	0.286
transgenic ySAMdc/azygous control (breaker)	0.87444	0.251
transgenic ySAMdc/azygous control (red)	0.87369	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98204	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.45216	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.21311	0.096
Manapal/WT (break)	1.01731	1
Manapal/WT (red)	0.94682	0.607