Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.9.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11371	0.932
27DAP/17DAP	1.02317	1
39DAP/27DAP	0.83331	0.507
41DAP/39DAP	1.38938	0.423
42DAP/41DAP	1.28418	0.999
43DAP/42DAP	0.86828	0.813
47DAP/43DAP	0.93625	0.671
52DAP/47DAP	2.02263	0.164
57DAP/52DAP	0.74371	0.613

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98275	0.616
17DAP/reference	1.01425	0.787
27DAP/reference	0.91571	0.201
39DAP/reference	0.93897	0.254
41DAP/reference	0.97446	0.542
42DAP/reference	1.02178	1
43DAP/reference	1.11989	0.05
47DAP/reference	0.96545	0.322
52DAP/reference	0.84227	0.053
57DAP/reference	0.85004	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04272	0.899
27DAP/17DAP	1.10021	0.694
39DAP/27DAP	1.21962	0.245
41DAP/39DAP	1.25069	0.719
42DAP/41DAP	0.94064	0.637
43DAP/42DAP	1.02907	0.746
47DAP/43DAP	1.11162	0.749
52DAP/47DAP	1.14693	0.609
57DAP/52DAP	1.19163	0.543
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84415	0.062
17DAP/reference	0.89708	0.025
27DAP/reference	0.92807	0.033
39DAP/reference	0.79046	0.011
41DAP/reference	0.72907	0.034
42DAP/reference	0.61569	0.01
43DAP/reference	0.78532	0.032
47DAP/reference	0.94603	0.504
52DAP/reference	0.76154	0.021
57DAP/reference	0.79808	0.028

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22726	0.141
17DAP/reference	1.1008	0.156
27DAP/reference	0.99404	0.686
39DAP/reference	1.00683	0.722
41DAP/reference	1.05055	0.614
42DAP/reference	0.83672	0.15
43DAP/reference	1.64771	0.041
47DAP/reference	0.87223	0.01
52DAP/reference	1.12085	0.181
57DAP/reference	1.45364	0.166

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84246	0.029
17DAP/reference	0.95295	0.519
27DAP/reference	0.93914	0.165
39DAP/reference	0.83245	0.013
41DAP/reference	0.95994	0.331
42DAP/reference	0.91446	0.172
43DAP/reference	0.84798	0.098
47DAP/reference	1.08558	0.501
52DAP/reference	1.01544	1
57DAP/reference	0.82348	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0467	0.966
26DAP/20DAP	0.98962	1
34DAP/26DAP	0.86608	0.61
51DAP/34DAP	1.06817	0.936
52DAP/51DAP	0.9782	1
53DAP/52DAP	0.7327
55DAP/53DAP	1.02085	0.976
57DAP/55DAP	1.20558	0.764
62DAP/57DAP	1.37078	0.003
68DAP/62DAP	0.90692	0.609
68DAP/14DAP	0.73428	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31589	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.3376	0.774
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.22583	0.224
Mature Eggplant/Ripe Tomato	0.58429	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99854	1
1-1-2/M82	0.88797	1
12-2/M82	1.08554	1
12-4/M82	0.98312	1
1-3/M82	0.79501	0.441
2-1-1/M82	1.19197	0.439
2-1/M82	N/A	N/A
2-6/M82	1.13214	0.695
3-2/M82	1.04596
4-1-1/M82	1.11576	1
4-1/M82	0.89746	1
4-3-2/M82	0.99446	1
4-3/M82	0.80836	0.72
5-3/M82	0.91838	0.642
6-2/M82	0.74848	1
6-3/M82	0.84763	1
7-1/M82	1.21128
7-2/M82	1.07461	1
9-3-2/M82	0.89304	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70324	0.243
IL2-6/WTpooled	0.88823	1
IL7-5/WTpooled	1.06874	1
IL7-3/WTpooled	0.93705	1
IL12-4/WTpooled	1.15353	0.737
IL1-4/WTpooled	1.08418	1
WT/WTpooled	1.05324	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	0.98967	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0019	1
DC3000/delta hrp 6h	1.49661	1
DC3000/delta hrp 12h	1.2789	1
DC3000/delta hrp 24h	1.05359	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14927
DC3000 delta B/DC3000 delta AB	1.2643	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9884	1
Exp 36h	N/A	N/A
Exp 60h	1.01151	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88661	1
Var 0h	0.66221	0.933
Var 12h I row2-row1	1.10528	0.544
Var 12h NI row2-row1	0.97974	0.906
Var 36h I row2-row1	0.9307	1
Var 36h NI row2-row1	0.91635	0.706
Var 60h I row2-row1	1.02869	0.562
Var 60h NI row2-row1	1.06979	1
Time course 0hI-0hNI	1.12896	0.63
Time course 12hI-12hNI	1.01927	0.836
Time course 36hI-36hNI	1.11449	0.401
Time course 60hI-60hNI	1.77643	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)	0.91115	0.324
transgenic ySAMdc/azygous control (breaker)	1.03457	1
transgenic ySAMdc/azygous control (red)	0.88521	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01428	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96042	0.59

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)	0.81065	0.333
Manapal/WT (red)	0.89605	0.315