Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95814	0.728
27DAP/17DAP	1.04496	0.911
39DAP/27DAP	1.78001	0.041
41DAP/39DAP	0.93931	0.73
42DAP/41DAP	0.63727	0.397
43DAP/42DAP	0.97811	0.914
47DAP/43DAP	0.85178	0.54
52DAP/47DAP	1.31934	0.556
57DAP/52DAP	1.22431	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06662	0.9
17DAP/reference	0.74344	0.069
27DAP/reference	0.58909	0.012
39DAP/reference	0.82098	0.221
41DAP/reference	0.7199	0.026
42DAP/reference	1.09695	0.093
43DAP/reference	0.94847	0.538
47DAP/reference	0.7383	0.009
52DAP/reference	0.55169	0.019
57DAP/reference	0.83528	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92927	0.56
27DAP/17DAP	0.94471	0.537
39DAP/27DAP	1.24504	0.383
41DAP/39DAP	0.77852	0.137
42DAP/41DAP	1.19698	0.072
43DAP/42DAP	1.72454	0.014
47DAP/43DAP	1.08762	0.383
52DAP/47DAP	0.66092	0.041
57DAP/52DAP	1.17414	0.206
57DAP/7DAP	1.27751	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09198	0.399
17DAP/reference	0.84824	0.024
27DAP/reference	0.78679	0.016
39DAP/reference	0.78519	0.023
41DAP/reference	0.73096	0.021
42DAP/reference	0.67748	0.01
43DAP/reference	0.58683	0.011
47DAP/reference	1.09782	1
52DAP/reference	0.67495	0.012
57DAP/reference	0.58503	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82183	0.093
17DAP/reference	0.65047	0.006
27DAP/reference	1.04589	1
39DAP/reference	1.01176	0.769
41DAP/reference	1.09423	0.944
42DAP/reference	1.04281	0.899
43DAP/reference	0.5845	0.002
47DAP/reference	0.7822	0.015
52DAP/reference	0.58607	0.004
57DAP/reference	0.54745	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11092	0.691
17DAP/reference	1.20522	0.804
27DAP/reference	1.00637	0.763
39DAP/reference	0.96464	0.393
41DAP/reference	0.82869	0.028
42DAP/reference	0.83332	0.108
43DAP/reference	0.80783	0.106
47DAP/reference	0.46568	0.004
52DAP/reference	0.62915	0.064
57DAP/reference	0.82505	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06365	0.966
26DAP/20DAP	0.90846	1
34DAP/26DAP	1.03099	1
51DAP/34DAP	0.81596
52DAP/51DAP	1.04736	0.86
53DAP/52DAP	0.96628	0.835
55DAP/53DAP	1.30128	0.107
57DAP/55DAP	1.21532	0.448
62DAP/57DAP	0.80162	0.088
68DAP/62DAP	0.6733	0.177
68DAP/14DAP	0.8591	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.82494	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.51269	0.164
Mature Green Tomato/Ripe Tomato	0.82116	0.226
Immature Eggplant/Mature Eggplant	0.73549	0.072
Ripe Pepper/Ripe Tomato	0.70803	0.293
Mature Eggplant/Ripe Tomato	0.92352	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.59224	0.605
1-1-2/M82	1.1324	1
12-2/M82	0.82265	0.955
12-4/M82	0.84996	1
1-3/M82	2.75349	0.479
2-1-1/M82	0.36999
2-1/M82	N/A	N/A
2-6/M82	0.61038	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.46897	0.926
4-1/M82	0.79089
4-3-2/M82	0.52167
4-3/M82	0.38552	0.366
5-3/M82	2.33339	1
6-2/M82	2.12217	0.235
6-3/M82	1.03689	1
7-1/M82	N/A	N/A
7-2/M82	1.71276	0.291
9-3-2/M82	0.59379

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86838	0.247
IL2-6/WTpooled	1.16067	0.395
IL7-5/WTpooled	1.2448	0.792
IL7-3/WTpooled	1.04802	1
IL12-4/WTpooled	1.17173	0.595
IL1-4/WTpooled	0.88326	0.834
WT/WTpooled	0.99143	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	1.0774	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95592	1
DC3000/delta hrp 6h	0.9407	0.95
DC3000/delta hrp 12h	1.00147	1
DC3000/delta hrp 24h	1.17927	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19942	0.25
DC3000 delta B/DC3000 delta AB	1.10862	0.389

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24129	1
Exp 36h	1.04876	1
Exp 60h	1.27834	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0143	1
Var 0h	0.9606	1
Var 12h I row2-row1	1.03688	0.544
Var 12h NI row2-row1	0.97358	0.906
Var 36h I row2-row1	0.98811	1
Var 36h NI row2-row1	1.46627	0.482
Var 60h I row2-row1	0.83803	0.582
Var 60h NI row2-row1	1.07637	0.904
Time course 0hI-0hNI	1.20935	0.537
Time course 12hI-12hNI	0.99892	1
Time course 36hI-36hNI	1.10127	0.722
Time course 60hI-60hNI	1.11806	0.216

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)	1.32783	0.408
transgenic ySAMdc/azygous control (breaker)	0.43291	0.139
transgenic ySAMdc/azygous control (red)	0.67829	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07634	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85713	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98715	1
Manapal/WT (break)	0.83058	1
Manapal/WT (red)	0.78357	0.181