Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.9.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90568	0.543
27DAP/17DAP	0.46837	0.03
39DAP/27DAP	0.64553	0.335
41DAP/39DAP	0.55613	0.047
42DAP/41DAP	0.68753	0.774
43DAP/42DAP	1.17567	0.982
47DAP/43DAP	0.49226	0.055
52DAP/47DAP	1.27082	0.541
57DAP/52DAP	1.20004	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34248	0.028
17DAP/reference	0.79332	0.097
27DAP/reference	0.53021	0.012
39DAP/reference	0.52557	0.016
41DAP/reference	0.39635	0.008
42DAP/reference	0.85765	0.021
43DAP/reference	0.31323	0.013
47DAP/reference	0.5397	0.004
52DAP/reference	0.21951	0.012
57DAP/reference	1.04096	0.112

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01472	0.899
27DAP/17DAP	0.74607	0.218
39DAP/27DAP	0.3628	0.028
41DAP/39DAP	1.39247	0.018
42DAP/41DAP	0.81456	0.06
43DAP/42DAP	0.5044	0.022
47DAP/43DAP	0.93957	0.815
52DAP/47DAP	1.089	0.969
57DAP/52DAP	0.88469	0.359
57DAP/7DAP	0.88282

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.67589	0.036
17DAP/reference	0.95585	0.22
27DAP/reference	0.68855	0.01
39DAP/reference	0.5409	0.012
41DAP/reference	0.3977	0.009
42DAP/reference	0.38452	0.01
43DAP/reference	0.30018	0.011
47DAP/reference	0.23243	0.026
52DAP/reference	0.41435	0.01
57DAP/reference	0.46033	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91086	0.399
17DAP/reference	0.70398	0.034
27DAP/reference	0.61518	0.039
39DAP/reference	0.364	0.007
41DAP/reference	0.60455	0.023
42DAP/reference	0.42306	0.012
43DAP/reference	0.2418	0.002
47DAP/reference	0.37622	0.01
52DAP/reference	0.27925	0.003
57DAP/reference	0.20276	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.34462	0.015
17DAP/reference	2.23421	0.088
27DAP/reference	1.67471	0.02
39DAP/reference	1.22854	0.151
41DAP/reference	0.81237	0.086
42DAP/reference	0.55146	0.025
43DAP/reference	0.64896	0.035
47DAP/reference	0.33203	0.004
52DAP/reference	0.41122	0.06
57DAP/reference	0.71174	0.12

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0637	0.966
26DAP/20DAP	0.87996	1
34DAP/26DAP	1.01318	1
51DAP/34DAP	0.92418	0.598
52DAP/51DAP	1.00517	1
53DAP/52DAP	1.00497	0.783
55DAP/53DAP	0.96057	0.784
57DAP/55DAP	0.82603
62DAP/57DAP	0.97113	1
68DAP/62DAP	1.43441	0.597
68DAP/14DAP	0.64255	0.075

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83338	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.23595	0.058
Mature Green Tomato/Ripe Tomato	27.4317	0.149
Immature Eggplant/Mature Eggplant	0.39557	0.057
Ripe Pepper/Ripe Tomato	2.14735	1
Mature Eggplant/Ripe Tomato	74.0213	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04729	1
1-1-2/M82	1.09202	1
12-2/M82	0.64218
12-4/M82	1.01272	1
1-3/M82	N/A	N/A
2-1-1/M82	0.75653	0.92
2-1/M82	N/A	N/A
2-6/M82	1.56592	0.505
3-2/M82	1.0211
4-1-1/M82	N/A	N/A
4-1/M82	1.03284
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.48817	0.572
6-2/M82	N/A	N/A
6-3/M82	0.92039
7-1/M82	0.99066
7-2/M82	0.81685	0.599
9-3-2/M82	1.6581

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.35961	0.243
IL2-6/WTpooled	1.36818	0.531
IL7-5/WTpooled	0.91922	1
IL7-3/WTpooled	0.63489	0.294
IL12-4/WTpooled	0.75281	0.566
IL1-4/WTpooled	0.86066	0.562
WT/WTpooled	0.98659	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	0.99042	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95022	1
DC3000/delta hrp 6h	1.00382	1
DC3000/delta hrp 12h	0.92319	1
DC3000/delta hrp 24h	1.0553	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47882	0.023
DC3000 delta B/DC3000 delta AB	0.38458	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86651	1
Exp 36h	0.75929	0.449
Exp 60h	0.76873	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9799	1
Var 0h	1.22416	0.936
Var 12h I row2-row1	0.84035	0.338
Var 12h NI row2-row1	0.95885	0.82
Var 36h I row2-row1	0.81715	0.805
Var 36h NI row2-row1	0.94665	0.645
Var 60h I row2-row1	1.42936	0.543
Var 60h NI row2-row1	0.92892	0.932
Time course 0hI-0hNI	0.9624	0.725
Time course 12hI-12hNI	1.03808	0.687
Time course 36hI-36hNI	0.90926	0.102
Time course 60hI-60hNI	0.14789	0.006

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)	1.03314	0.798
transgenic ySAMdc/azygous control (breaker)	4.62824	0.162
transgenic ySAMdc/azygous control (red)	1.58747	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.58734	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.00016	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.5887	0.088
Manapal/WT (break)	15.6897	0.123
Manapal/WT (red)	4.76903	0.413