Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.2.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61963	0.018
27DAP/17DAP	0.76945	0.287
39DAP/27DAP	0.82656	0.397
41DAP/39DAP	1.20524	0.642
42DAP/41DAP	1.04122	1
43DAP/42DAP	1.16233	0.772
47DAP/43DAP	1.23764	0.733
52DAP/47DAP	1.0662	0.953
57DAP/52DAP	0.95481	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69591	0.036
17DAP/reference	0.58669	0.008
27DAP/reference	0.67918	0.022
39DAP/reference	0.60345	0.012
41DAP/reference	0.51398	0.01
42DAP/reference	0.63329	0.001
43DAP/reference	0.63734	0.025
47DAP/reference	0.67396	0.005
52DAP/reference	0.71507	0.105
57DAP/reference	0.82333	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87897	0.336
27DAP/17DAP	1.01973	0.973
39DAP/27DAP	0.86071	0.26
41DAP/39DAP	0.91388	0.68
42DAP/41DAP	1.03352	0.961
43DAP/42DAP	1.47969	0.014
47DAP/43DAP	1.00632	0.99
52DAP/47DAP	0.90882	0.899
57DAP/52DAP	1.12406	0.963
57DAP/7DAP	0.78765	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11944	0.427
17DAP/reference	1.14241	0.627
27DAP/reference	0.88265	0.088
39DAP/reference	1.20089	0.141
41DAP/reference	0.92578	0.341
42DAP/reference	0.89592	0.222
43DAP/reference	0.80041	0.017
47DAP/reference	0.61478	0.057
52DAP/reference	0.91011	0.066
57DAP/reference	0.98278	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53627	0.009
17DAP/reference	0.56251	0.012
27DAP/reference	0.59866	0.015
39DAP/reference	0.48568	0.008
41DAP/reference	0.5438	0.007
42DAP/reference	0.53086	0.01
43DAP/reference	0.53297	0.01
47DAP/reference	0.49292	0.007
52DAP/reference	0.42331	0.003
57DAP/reference	0.34453	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21723	0.207
17DAP/reference	1.15088	0.182
27DAP/reference	1.00031	0.805
39DAP/reference	1.01092	0.693
41DAP/reference	1.17277	0.714
42DAP/reference	0.93709	0.552
43DAP/reference	0.80419	0.165
47DAP/reference	0.46975	0.004
52DAP/reference	0.87303	0.405
57DAP/reference	1.02615	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0181	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.16014
51DAP/34DAP	1.05999	0.978
52DAP/51DAP	0.97285	1
53DAP/52DAP	0.8485	0.365
55DAP/53DAP	0.82031	0.404
57DAP/55DAP	1.01856	0.947
62DAP/57DAP	4.7805	0.767
68DAP/62DAP	1.07671	0.939
68DAP/14DAP	0.98567	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27447	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.85906	0.058
Mature Green Tomato/Ripe Tomato	1.22785	0.044
Immature Eggplant/Mature Eggplant	0.36818	0.057
Ripe Pepper/Ripe Tomato	8.4977	0.236
Mature Eggplant/Ripe Tomato	16.5197	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26422	0.5
1-1-2/M82	1.11711	1
12-2/M82	N/A	N/A
12-4/M82	0.823
1-3/M82	0.77296
2-1-1/M82	1.30336
2-1/M82	N/A	N/A
2-6/M82	1.21059	0.505
3-2/M82	1.14363
4-1-1/M82	1.10898
4-1/M82	1.23762
4-3-2/M82	N/A	N/A
4-3/M82	0.89539
5-3/M82	0.90639	1
6-2/M82	1.18418
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.07676	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06526	1
IL2-6/WTpooled	1.13895	0.584
IL7-5/WTpooled	1.15183	1
IL7-3/WTpooled	1.02942	1
IL12-4/WTpooled	0.94688	1
IL1-4/WTpooled	0.98049	1
WT/WTpooled	0.95872	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	0.91979	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03785	0.921
DC3000/delta hrp 6h	1.03742	1
DC3000/delta hrp 12h	1.04045	1
DC3000/delta hrp 24h	0.45952	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46144	0.038
DC3000 delta B/DC3000 delta AB	0.61832	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90914	1
Exp 36h	0.7914	0.406
Exp 60h	0.63477	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99562	1
Var 0h	2.45745	0.594
Var 12h I row2-row1	0.67085	0.467
Var 12h NI row2-row1	0.94468	0.713
Var 36h I row2-row1	0.8233	0.805
Var 36h NI row2-row1	1.06728	1
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.11231	0.904
Time course 0hI-0hNI	0.96947	0.839
Time course 12hI-12hNI	0.91797	0.309
Time course 36hI-36hNI	0.66603	0.023
Time course 60hI-60hNI	0.16987	0.005

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)	1.09469	0.748
transgenic ySAMdc/azygous control (breaker)	2.06818	0.172
transgenic ySAMdc/azygous control (red)	1.08165	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.58565	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.05289	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	9.82549	0.083
Manapal/WT (break)	7.28973	0.123
Manapal/WT (red)	0.99288	0.863