Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.2.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9314	0.617
27DAP/17DAP	0.71655	0.353
39DAP/27DAP	1.71633	0.056
41DAP/39DAP	0.79456	0.216
42DAP/41DAP	0.92966	1
43DAP/42DAP	0.98181	0.925
47DAP/43DAP	0.79124	0.386
52DAP/47DAP	1.47995	0.52
57DAP/52DAP	0.9582	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08537	0.928
17DAP/reference	0.77783	0.041
27DAP/reference	0.77523	0.085
39DAP/reference	0.78956	0.11
41DAP/reference	0.60367	0.016
42DAP/reference	1.70703	0.001
43DAP/reference	0.97695	0.708
47DAP/reference	1.05755	0.264
52DAP/reference	0.89086	0.115
57DAP/reference	0.87522	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93523	0.595
27DAP/17DAP	1.00323	1
39DAP/27DAP	1.05605	0.874
41DAP/39DAP	0.84754	0.31
42DAP/41DAP	0.91594	0.374
43DAP/42DAP	1.15222	0.382
47DAP/43DAP	1.05312	0.865
52DAP/47DAP	1.08355	0.8
57DAP/52DAP	0.93755	0.399
57DAP/7DAP	0.56353

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.9864	0.024
17DAP/reference	1.05896	0.574
27DAP/reference	1.69037	0.007
39DAP/reference	1.73379	0.007
41DAP/reference	1.70414	0.011
42DAP/reference	2.31841	0.016
43DAP/reference	3.04681	0.006
47DAP/reference	2.17753	0.014
52DAP/reference	2.63501	0.007
57DAP/reference	1.56818	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02962	1
17DAP/reference	0.88075	0.124
27DAP/reference	1.72019	0.013
39DAP/reference	1.43989	0.043
41DAP/reference	1.15909	0.096
42DAP/reference	1.56657	0.011
43DAP/reference	0.6697	0.028
47DAP/reference	1.06941	0.621
52DAP/reference	0.70581	0.007
57DAP/reference	0.61584	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51224	0.037
17DAP/reference	0.96635	0.571
27DAP/reference	1.52974	0.021
39DAP/reference	1.6637	0.015
41DAP/reference	1.2903	0.012
42DAP/reference	1.88818	0.009
43DAP/reference	2.02989	0.013
47DAP/reference	0.7185	0.013
52DAP/reference	1.15548	0.377
57DAP/reference	1.02359	0.991

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23805	0.362
26DAP/20DAP	1.60111	0.285
34DAP/26DAP	0.777	0.214
51DAP/34DAP	1.25672	0.458
52DAP/51DAP	1.03525	0.904
53DAP/52DAP	1.09676	0.961
55DAP/53DAP	0.69333	0.044
57DAP/55DAP	0.96152	0.831
62DAP/57DAP	1.00008	1
68DAP/62DAP	1.15701	0.897
68DAP/14DAP	2.01239	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37052	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.61484	0.136
Mature Green Tomato/Ripe Tomato	0.83557	0.347
Immature Eggplant/Mature Eggplant	0.98232	1
Ripe Pepper/Ripe Tomato	0.88087	0.293
Mature Eggplant/Ripe Tomato	0.9373	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11182
1-1-2/M82	1.11886	1
12-2/M82	N/A	N/A
12-4/M82	0.84374	0.319
1-3/M82	1.62716
2-1-1/M82	0.86659
2-1/M82	0.87827
2-6/M82	1.21878
3-2/M82	1.03467
4-1-1/M82	N/A	N/A
4-1/M82	0.94511
4-3-2/M82	1.20358
4-3/M82	0.88738	0.475
5-3/M82	1.15717	0.572
6-2/M82	1.5662
6-3/M82	1.00129	1
7-1/M82	N/A	N/A
7-2/M82	1.19442
9-3-2/M82	0.9218

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92851	1
IL2-6/WTpooled	0.84381	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03672	1
IL12-4/WTpooled	1.06649	0.673
IL1-4/WTpooled	0.90782	0.834
WT/WTpooled	1.00335	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	1.04732	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08994	0.921
DC3000/delta hrp 6h	0.77215	0.95
DC3000/delta hrp 12h	1.26163	1
DC3000/delta hrp 24h	1.02592	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22701	0.441
DC3000 delta B/DC3000 delta AB	1.07718

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20754	1
Exp 36h	1.22213	0.489
Exp 60h	1.28907	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98746	1
Var 0h	0.59672	0.933
Var 12h I row2-row1	1.5501	0.654
Var 12h NI row2-row1	1.10844	0.649
Var 36h I row2-row1	0.97012	1
Var 36h NI row2-row1	1.03442	1
Var 60h I row2-row1	1.60635	1
Var 60h NI row2-row1	0.89822	0.932
Time course 0hI-0hNI	0.90804	0.196
Time course 12hI-12hNI	0.99632	1
Time course 36hI-36hNI	1.14742	0.025
Time course 60hI-60hNI	1.16577	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)	1.03789	0.748
transgenic ySAMdc/azygous control (breaker)	0.86746	0.139
transgenic ySAMdc/azygous control (red)	1.11847	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25986	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52418	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86143	1
Manapal/WT (break)	0.75959	0.333
Manapal/WT (red)	0.83868	0.242