Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82455	0.339
27DAP/17DAP	0.88273	0.7
39DAP/27DAP	1.52873	0.123
41DAP/39DAP	1.09738	0.822
42DAP/41DAP	1.00668	1
43DAP/42DAP	0.8708	0.773
47DAP/43DAP	1.06192	0.979
52DAP/47DAP	0.9188	0.75
57DAP/52DAP	0.96093	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8031	0.036
17DAP/reference	0.9046	0.158
27DAP/reference	1.00301	0.822
39DAP/reference	0.81375	0.044
41DAP/reference	0.86124	0.065
42DAP/reference	0.99117	0.484
43DAP/reference	0.98425	0.745
47DAP/reference	1.00932	0.674
52DAP/reference	1.26308	0.092
57DAP/reference	1.11429	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95099	0.509
27DAP/17DAP	0.92982	0.748
39DAP/27DAP	1.08243	0.654
41DAP/39DAP	1.02809	1
42DAP/41DAP	1.07509	0.719
43DAP/42DAP	1.08093	0.273
47DAP/43DAP	1.06879	0.817
52DAP/47DAP	0.97482	0.902
57DAP/52DAP	1.02637	0.997
57DAP/7DAP	0.80497	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.83762	0.036
17DAP/reference	1.70374	0.006
27DAP/reference	1.70511	0.006
39DAP/reference	1.54955	0.008
41DAP/reference	1.63362	0.026
42DAP/reference	2.04091	0.007
43DAP/reference	1.79124	0.006
47DAP/reference	1.37544	0.214
52DAP/reference	2.81477	0.007
57DAP/reference	2.33462	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.087	0.832
17DAP/reference	0.67504	0.063
27DAP/reference	0.79697	0.167
39DAP/reference	0.89176	0.189
41DAP/reference	0.8025	0.164
42DAP/reference	0.8422	0.089
43DAP/reference	0.8202	0.092
47DAP/reference	0.75524	0.053
52DAP/reference	0.70566	0.072
57DAP/reference	0.88163	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7117	0.023
17DAP/reference	1.21484	0.545
27DAP/reference	1.33544	0.04
39DAP/reference	1.76069	0.007
41DAP/reference	1.60196	0.008
42DAP/reference	1.69228	0.034
43DAP/reference	1.40567	0.209
47DAP/reference	0.93918	0.383
52DAP/reference	1.67214	0.1
57DAP/reference	1.04025	0.971

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85734	0.807
26DAP/20DAP	0.98497	1
34DAP/26DAP	1.34298	0.819
51DAP/34DAP	2.15304	0.029
52DAP/51DAP	0.87464	1
53DAP/52DAP	1.0528	0.845
55DAP/53DAP	0.88632	0.273
57DAP/55DAP	1.12533	0.34
62DAP/57DAP	1.1281	0.8
68DAP/62DAP	1.26515	0.582
68DAP/14DAP	1.51872	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.35051	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50718	0.126
Mature Green Tomato/Ripe Tomato	0.93069	0.611
Immature Eggplant/Mature Eggplant	1.5656
Ripe Pepper/Ripe Tomato	2.11594
Mature Eggplant/Ripe Tomato	1.35352	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80217
1-1-2/M82	1.04703	1
12-2/M82	N/A	N/A
12-4/M82	0.99461	1
1-3/M82	0.93541
2-1-1/M82	0.83775	0.92
2-1/M82	N/A	N/A
2-6/M82	1.14708	0.594
3-2/M82	1.06744
4-1-1/M82	N/A	N/A
4-1/M82	1.18397	1
4-3-2/M82	1.68415	0.262
4-3/M82	1.74363	1
5-3/M82	0.87562	0.642
6-2/M82	1.6114	1
6-3/M82	0.91672	1
7-1/M82	1.02134	1
7-2/M82	1.15581	0.385
9-3-2/M82	1.32414	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.85457	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19494	0.921
DC3000/delta hrp 6h	0.74422	0.95
DC3000/delta hrp 12h	0.90967	1
DC3000/delta hrp 24h	0.64602	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.69614	0.027
DC3000 delta B/DC3000 delta AB	0.7221	0.026

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	N/A	N/A

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	0.97327	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.21355	0.3
transgenic ySAMdc/azygous control (breaker)	0.81352	0.15
transgenic ySAMdc/azygous control (red)	1.05828	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98781	0.486

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07443	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1505	0.307
Manapal/WT (break)	1.17007	1
Manapal/WT (red)	0.86376	0.229