Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.19.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17101	0.709
27DAP/17DAP	1.33612	0.89
39DAP/27DAP	1.20532	0.524
41DAP/39DAP	0.97556	0.935
42DAP/41DAP	0.94016	1
43DAP/42DAP	1.80901	0.823
47DAP/43DAP	0.93519	0.628
52DAP/47DAP	1.25742	0.906
57DAP/52DAP	0.9662	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82952	0.167
17DAP/reference	0.74884	0.012
27DAP/reference	0.85882	0.275
39DAP/reference	0.89034	0.068
41DAP/reference	0.83739	0.008
42DAP/reference	1.15573	0.13
43DAP/reference	1.24458
47DAP/reference	0.9932	0.674
52DAP/reference	1.17228	0.008
57DAP/reference	4.76228	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9859	0.75
27DAP/17DAP	0.82107	0.614
39DAP/27DAP	1.24743	0.418
41DAP/39DAP	1.07161	0.883
42DAP/41DAP	1.13337	0.334
43DAP/42DAP	1.27485	0.086
47DAP/43DAP	0.93522	0.743
52DAP/47DAP	1.28267	0.34
57DAP/52DAP	1.28705	0.224
57DAP/7DAP	1.27103	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81946	0.088
17DAP/reference	0.81482	0.011
27DAP/reference	0.73847	0.01
39DAP/reference	0.827	0.011
41DAP/reference	0.83711	0.022
42DAP/reference	0.76686	0.01
43DAP/reference	0.72271	0.014
47DAP/reference	1.079	0.885
52DAP/reference	0.74168	0.012
57DAP/reference	0.77978	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79205	0.029
17DAP/reference	0.79335	0.011
27DAP/reference	0.88576	0.111
39DAP/reference	0.89815	0.195
41DAP/reference	0.92351	0.237
42DAP/reference	0.966	0.261
43DAP/reference	0.86782	0.157
47DAP/reference	0.93032	0.068
52DAP/reference	0.9723	0.433
57DAP/reference	0.81636	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8413	0.034
17DAP/reference	0.92315	0.255
27DAP/reference	0.92262	0.097
39DAP/reference	0.79863	0.009
41DAP/reference	0.92781	0.148
42DAP/reference	1.15402	0.848
43DAP/reference	1.15283	0.531
47DAP/reference	1.03982	0.792
52DAP/reference	0.69766	0.047
57DAP/reference	1.33253	0.05

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.64068	0.966
26DAP/20DAP	1.13677	0.683
34DAP/26DAP	1.06489	1
51DAP/34DAP	0.97542	0.883
52DAP/51DAP	1.10347	0.792
53DAP/52DAP	0.87004	0.572
55DAP/53DAP	1.23758	0.444
57DAP/55DAP	0.9899	0.867
62DAP/57DAP	1.0633	1
68DAP/62DAP	1.54756	0.331
68DAP/14DAP	1.86441	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31572	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.52185
Ripe Pepper/Ripe Tomato	0.09891	0.224
Mature Eggplant/Ripe Tomato	0.25049	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9067	0.605
1-1-2/M82	1.14684	1
12-2/M82	1.16309	1
12-4/M82	0.9701	1
1-3/M82	0.65281	0.378
2-1-1/M82	0.69777	0.465
2-1/M82	0.91195
2-6/M82	0.85057	0.501
3-2/M82	0.9568
4-1-1/M82	0.91711	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.45632	0.551
5-3/M82	0.9099	1
6-2/M82	1.08273
6-3/M82	1.12769	1
7-1/M82	0.72599	1
7-2/M82	0.85765	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90012	0.243
IL2-6/WTpooled	0.81532	0.383
IL7-5/WTpooled	0.80486	1
IL7-3/WTpooled	0.83024	0.418
IL12-4/WTpooled	1.09448	0.695
IL1-4/WTpooled	0.93366	0.834
WT/WTpooled	1.07005	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	0.96576	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9908	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.18163	1
DC3000/delta hrp 24h	0.89723	0.395

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.8444	0.359

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90325	1
Exp 36h	N/A	N/A
Exp 60h	1.16494	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00571	1
Var 0h	1.01252	1
Var 12h I row2-row1	0.87175	0.327
Var 12h NI row2-row1	0.89947	0.713
Var 36h I row2-row1	1.48882	0.489
Var 36h NI row2-row1	0.98864	0.791
Var 60h I row2-row1	0.91916	0.285
Var 60h NI row2-row1	0.77639	0.904
Time course 0hI-0hNI	0.9648	0.799
Time course 12hI-12hNI	0.94347	0.719
Time course 36hI-36hNI	1.04075	0.513
Time course 60hI-60hNI	0.78483	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)	1.28528	0.218
transgenic ySAMdc/azygous control (breaker)	1.19359	1
transgenic ySAMdc/azygous control (red)	0.91399	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02508	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07508	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.35024	0.181