Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.15.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92936	0.627
27DAP/17DAP	1.03072	1
39DAP/27DAP	1.52792	0.603
41DAP/39DAP	1.09916	0.78
42DAP/41DAP	1.45947	0.722
43DAP/42DAP	0.87805	0.786
47DAP/43DAP	1.19024	0.926
52DAP/47DAP	0.98432	0.88
57DAP/52DAP	1.36864	0.904

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84883	0.118
17DAP/reference	1.10682	0.025
27DAP/reference	1.03988	0.66
39DAP/reference	0.90946	0.467
41DAP/reference	1.09957	0.338
42DAP/reference	0.80372	0.004
43DAP/reference	1.08086	0.217
47DAP/reference	0.97602	0.366
52DAP/reference	0.91832	0.267
57DAP/reference	0.82072	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95712	0.679
27DAP/17DAP	1.08899	0.724
39DAP/27DAP	1.38132	0.095
41DAP/39DAP	1.17527	0.565
42DAP/41DAP	1.00938	0.926
43DAP/42DAP	1.23447	0.446
47DAP/43DAP	1.12225	0.805
52DAP/47DAP	1.19872	0.492
57DAP/52DAP	1.28142	0.268
57DAP/7DAP	0.91074

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6908	0.066
17DAP/reference	1.00776	1
27DAP/reference	0.77017	0.045
39DAP/reference	0.79486	0.034
41DAP/reference	0.919	0.247
42DAP/reference	0.90429	0.211
43DAP/reference	0.97276	0.48
47DAP/reference	0.81069	0.168
52DAP/reference	0.76229	0.013
57DAP/reference	0.9603	0.411

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93384	0.286
17DAP/reference	0.97791	0.594
27DAP/reference	0.85653	0.134
39DAP/reference	0.9024	0.265
41DAP/reference	0.9102	0.231
42DAP/reference	0.80542	0.028
43DAP/reference	0.93954	0.344
47DAP/reference	0.95395	0.292
52DAP/reference	0.92557	0.051
57DAP/reference	1.05687	0.567

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01881	0.963
17DAP/reference	0.92509	0.389
27DAP/reference	1.01428	1
39DAP/reference	1.09778	0.211
41DAP/reference	0.91991	0.331
42DAP/reference	0.95138	0.552
43DAP/reference	0.91649	0.365
47DAP/reference	1.03728	0.68
52DAP/reference	0.88769	0.342
57DAP/reference	0.65798	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82239	0.246
26DAP/20DAP	1.81238	0.33
34DAP/26DAP	0.78164	0.197
51DAP/34DAP	0.90316	0.513
52DAP/51DAP	0.9747	1
53DAP/52DAP	1.24144	0.097
55DAP/53DAP	0.84096	0.082
57DAP/55DAP	0.90837	0.633
62DAP/57DAP	0.82343	0.681
68DAP/62DAP	0.90913	0.579
68DAP/14DAP	0.64201	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88161	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78426	0.236
Mature Green Tomato/Ripe Tomato	0.56587	0.017
Immature Eggplant/Mature Eggplant	2.13993	0.05
Ripe Pepper/Ripe Tomato	1.38513	1
Mature Eggplant/Ripe Tomato	0.78015	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99666
1-1-2/M82	0.96817	0.804
12-2/M82	N/A	N/A
12-4/M82	0.87059
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	0.6827
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	0.81187
5-3/M82	1.01329	1
6-2/M82	N/A	N/A
6-3/M82	1.14497	1
7-1/M82	N/A	N/A
7-2/M82	0.846	0.527
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86567	1
IL2-6/WTpooled	1.30577	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.92803	0.418
IL12-4/WTpooled	1.43148	0.538
IL1-4/WTpooled	0.87536	0.562
WT/WTpooled	1.01049	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	0.89484	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16622	0.914
DC3000/delta hrp 6h	1.16032	0.95
DC3000/delta hrp 12h	1.0814	1
DC3000/delta hrp 24h	0.96522	0.761

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17707
DC3000 delta B/DC3000 delta AB	1.25741

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99443	1
Exp 36h	1.36786	1
Exp 60h	1.31589	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98651	1
Var 0h	1.05057	1
Var 12h I row2-row1	1.12315	0.506
Var 12h NI row2-row1	1.24494	0.649
Var 36h I row2-row1	1.22555	0.339
Var 36h NI row2-row1	1.06466	1
Var 60h I row2-row1	0.77772	0.285
Var 60h NI row2-row1	0.99001	1
Time course 0hI-0hNI	0.96099	0.808
Time course 12hI-12hNI	1.18452	0.05
Time course 36hI-36hNI	1.37138	0.006
Time course 60hI-60hNI	1.78689	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)	1.10104	0.312
transgenic ySAMdc/azygous control (breaker)	0.85334	0.139
transgenic ySAMdc/azygous control (red)	0.92762	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98865	0.383

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7829	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11813	0.307
Manapal/WT (break)	0.86624	1
Manapal/WT (red)	0.72789	0.181