Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9016	0.532
27DAP/17DAP	0.6267	0.101
39DAP/27DAP	0.74657	0.449
41DAP/39DAP	0.81343	0.303
42DAP/41DAP	0.84597	1
43DAP/42DAP	1.15914	0.722
47DAP/43DAP	1.04003	0.95
52DAP/47DAP	0.79593	0.551
57DAP/52DAP	0.95082	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83625	0.205
17DAP/reference	0.54057	0.011
27DAP/reference	0.72184	0.134
39DAP/reference	0.61198	0.034
41DAP/reference	0.4921	0.021
42DAP/reference	0.58475	0.001
43DAP/reference	0.73846	0.18
47DAP/reference	0.65299	0.002
52DAP/reference	0.66367	0.091
57DAP/reference	0.86943	0.112

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25922	0.154
27DAP/17DAP	0.83334	0.446
39DAP/27DAP	0.53609	0.045
41DAP/39DAP	1.22869	0.061
42DAP/41DAP	0.80557	0.262
43DAP/42DAP	0.72863	0.031
47DAP/43DAP	1.13409	0.758
52DAP/47DAP	1.122	0.635
57DAP/52DAP	1.22891	0.366
57DAP/7DAP	0.82466	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88261	0.1
17DAP/reference	0.67594	0.012
27DAP/reference	0.57709	0.01
39DAP/reference	0.36397	0.011
41DAP/reference	0.30108	0.01
42DAP/reference	0.37406	0.01
43DAP/reference	0.38901	0.011
47DAP/reference	0.43188	0.035
52DAP/reference	0.43794	0.013
57DAP/reference	0.32089	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47443	0.006
17DAP/reference	0.46168	0.005
27DAP/reference	0.66572	0.056
39DAP/reference	0.65003	0.036
41DAP/reference	0.85556	0.059
42DAP/reference	0.69911	0.017
43DAP/reference	0.45848	0.004
47DAP/reference	0.64554	0.015
52DAP/reference	0.4855	0.005
57DAP/reference	0.37142	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29425	0.265
17DAP/reference	1.04358	0.918
27DAP/reference	0.81955	0.033
39DAP/reference	0.68192	0.009
41DAP/reference	0.50552	0.016
42DAP/reference	0.51733	0.016
43DAP/reference	0.57911	0.021
47DAP/reference	0.59283	0.008
52DAP/reference	0.54006	0.053
57DAP/reference	0.80735	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90416	0.841
26DAP/20DAP	0.98618	1
34DAP/26DAP	0.98187	0.972
51DAP/34DAP	0.54345	0.058
52DAP/51DAP	0.84493	1
53DAP/52DAP	0.79725	0.081
55DAP/53DAP	0.99267	0.838
57DAP/55DAP	0.92849	0.652
62DAP/57DAP	0.7934
68DAP/62DAP	1.33594	0.188
68DAP/14DAP	0.65086	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.32451	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.85538	0.058
Mature Green Tomato/Ripe Tomato	5.2346	0.015
Immature Eggplant/Mature Eggplant	0.47204	0.06
Ripe Pepper/Ripe Tomato	23.3066	0.258
Mature Eggplant/Ripe Tomato	41.8785	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3244
1-1-2/M82	1.9393	1
12-2/M82	N/A	N/A
12-4/M82	0.78229
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	1.10616	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.7831
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86218	0.321
IL2-6/WTpooled	1.44202	0.584
IL7-5/WTpooled	0.90945	1
IL7-3/WTpooled	0.74669	0.418
IL12-4/WTpooled	0.88408	1
IL1-4/WTpooled	0.92204	0.699
WT/WTpooled	1.06184	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	1.26482	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91166	0.512
DC3000/delta hrp 6h	1.05228	1
DC3000/delta hrp 12h	1.31579	1
DC3000/delta hrp 24h	0.83403	0.085

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62027	0.032
DC3000 delta B/DC3000 delta AB	0.45776	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96599	1
Exp 36h	0.80778	0.661
Exp 60h	0.79722	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0466	1
Var 0h	0.5602	0.782
Var 12h I row2-row1	0.88811	0.467
Var 12h NI row2-row1	0.94255	0.466
Var 36h I row2-row1	0.66483	0.805
Var 36h NI row2-row1	0.93568	0.478
Var 60h I row2-row1	1.46599	0.543
Var 60h NI row2-row1	1.03118	1
Time course 0hI-0hNI	1.04308	0.662
Time course 12hI-12hNI	1.03179	0.747
Time course 36hI-36hNI	0.96327	0.411
Time course 60hI-60hNI	0.27949	0.007

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)	0.91841	0.567
transgenic ySAMdc/azygous control (breaker)	1.68754	0.178
transgenic ySAMdc/azygous control (red)	1.50571	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.52654	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.12145	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	10.6674	0.083
Manapal/WT (break)	6.03708	0.126
Manapal/WT (red)	3.56749	0.413